Deprecated API
Contents
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Deprecated InterfacesInterfaceDescriptionas Person is deprecated
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Deprecated ClassesClassDescriptionrenaming probes is not a good idea in generaluse
DifferentialExpressionAnalysisWriterCliinstead.this will be removed as soon as all the old-style characteristics are migratedshould not be part of Gemma main codethis should not be necessary and the regular batch population tool can be used instead.This has been replaced with Spring-based configurationSettingsConfigand usage ofValueto inject configurations. You can use@Value("${property}")as replacement.This has been replaced with Spring-based configurationSettingsConfigand usage ofValueto inject configurations. You can use@Value("${property}")as replacement.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.not neededaim towards using theFactorValueBasicValueObject. This one is confusing. Once usage of this type has been completely phased out, revise the BioMaterialValueObject and relevant DAOs and Services.as Person is deprecated
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Deprecated FieldsFieldDescriptionuse
Values.SINGLE_CELL_RNA_SEQUENCING_ASSAYinsteaduseValues.SINGLE_CELL_RNA_SEQUENCING_ASSAYinsteadUseFilterArgLexer.VOCABULARYinstead.UseFilterArgParser.VOCABULARYinstead.
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Deprecated MethodsMethodDescriptionbecause this is too ad hoc and messythis method does not support producing Gemma Web contexts, please migrate existing code to use
SpringContextUtils.getApplicationContext(String[], String...)instead.modifying the matrix directly is not recommended, make a copy instead.useExpressionDataMatrix.getDesignElementForRow(int)insteaduseExpressionDataMatrix.getDesignElements()insteaduseSearchSource.searchBioSequence(SearchSettings, SearchContext)(SearchSettings)} insteadThis was renamed for clarity.you should never use this property, rely instead on the actual type viaObject.getClass().useArrayDesignValueObject.getTaxonObject()insteadUseCellTypeAssignment.getCellTypes()instead.UseCellTypeAssignment.getCellTypeIndices()instead.UseCellTypeAssignment.getNumberOfCellTypes()instead.Do not use, there's never been an accession field in the data model.Do not use, there's never been an accession field in the data model.useExpressionExperimentValueObject.getTaxonObject()insteaduseFactorValue.getMeasurement()orFactorValue.getCharacteristics()to retrieve the value.use eitherAbstractFactorValueValueObject.getCharacteristics()orinvalid reference
#getMeasurement()use eitherAbstractFactorValueValueObject.getCharacteristics()orinvalid reference
#getMeasurement()useStatement.getSubject()insteaduseStatement.getSubjectUri()insteaduseStatement.setSubject(String)insteaduseStatement.setSubjectUri(String)insteadUseTypedResultTransformer.transformListTyped(List)instead.avoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate sessionavoid using this if possible and ensure that all operations are properly enclosed by a single Hibernate sessionUseBulkExpressionDataVectorService.findAndThaw(QuantitationType),BulkExpressionDataVectorService.findAndThaw(Collection)orBulkExpressionDataVectorService.findAndThaw(BioAssayDimension)instead, it's much more efficient.do not use this, it is only a workaround to make FV migration fasterbecauseFactorValue.getValue()is deprecateddo not use, this is only for migrating old-style characteristics to statements and will be removeddo not use this, it is only meant for the purpose of migrating old-style characteristics to statementsdo not use this, it is meant for FactorValue migration onlyuseUserValueObject.getGroups()insteaduseUserValueObject.getGroups()instead
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Deprecated Enum ConstantsEnum ConstantDescriptionubic.gemma.persistence.service.expression.experiment.ExpressionExperimentMetaFileType.MULTIQC_REPORTkept for backward-compatibility since we expose this for
addMetadataFile --file-type.