Serialized Form

Package ubic.gemma.core.analysis.expression.diff

Exception Class ubic.gemma.core.analysis.expression.diff.AllAnalysesFailedException

class AllAnalysesFailedException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AllSubSetAnalysesFailedException

class AllSubSetAnalysesFailedException extends AllAnalysesFailedException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.AnalysisException

class AnalysisException extends RuntimeException implements Serializable

Serialized Fields

config

DifferentialExpressionAnalysisConfig config

Class ubic.gemma.core.analysis.expression.diff.DifferentialExpressionMetaAnalysisValueObject

class DifferentialExpressionMetaAnalysisValueObject extends Object implements Serializable

Serialized Fields

activeExperiments

Collection<BioAssaySet> activeExperiments

fisherPValue

Double fisherPValue

gene

GeneValueObject gene

numExperimentsInScope

int numExperimentsInScope

numMetThreshold

int numMetThreshold

numSearchedExperiments

int numSearchedExperiments

probeResults

Collection<DifferentialExpressionValueObject> probeResults

sortKey

String sortKey

Class ubic.gemma.core.analysis.expression.diff.DiffExpressionSelectedFactorCommand

class DiffExpressionSelectedFactorCommand extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

eeId

Long eeId

efId

Long efId

Exception Class ubic.gemma.core.analysis.expression.diff.EbayesFailureException

class EbayesFailureException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.FilteringRelatedAnalysisException

class FilteringRelatedAnalysisException extends AnalysisException implements Serializable

Serialized Fields

result

DifferentialExpressionAnalysisFilterResult result

Exception Class ubic.gemma.core.analysis.expression.diff.InvalidQuantitationTypeConversionException

class InvalidQuantitationTypeConversionException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.MeanVarianceFailureException

class MeanVarianceFailureException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.MultipleBaselinesRequireSubsetException

class MultipleBaselinesRequireSubsetException extends AnalysisException implements Serializable

Exception Class ubic.gemma.core.analysis.expression.diff.NoFactorLeftForAnalysisException

class NoFactorLeftForAnalysisException extends AnalysisException implements Serializable

Package ubic.gemma.core.analysis.preprocess

Exception Class ubic.gemma.core.analysis.preprocess.FilteringRelatedPreprocessingException

class FilteringRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

FilteringException cause

Class ubic.gemma.core.analysis.preprocess.OutlierDetails

class OutlierDetails extends Object implements Serializable

Serialized Fields

bioAssayId

Long bioAssayId

firstQuartile

double firstQuartile

medianCorrelation

double medianCorrelation

thirdQuartile

double thirdQuartile

Exception Class ubic.gemma.core.analysis.preprocess.PreprocessingException

class PreprocessingException extends RuntimeException implements Serializable

serialVersionUID:

-8463478950898408838L

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeConversionRelatedPreprocessingException

class QuantitationTypeConversionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeConversionException cause

Exception Class ubic.gemma.core.analysis.preprocess.QuantitationTypeDetectionRelatedPreprocessingException

class QuantitationTypeDetectionRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

QuantitationTypeDetectionException cause

Exception Class ubic.gemma.core.analysis.preprocess.SampleCoexpressionRelatedPreprocessingException

class SampleCoexpressionRelatedPreprocessingException extends PreprocessingException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.SVDRelatedPreprocessingException

class SVDRelatedPreprocessingException extends PreprocessingException implements Serializable

Serialized Fields

cause

SVDException cause

Package ubic.gemma.core.analysis.preprocess.batcheffects

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoMissingException

class BatchInfoMissingException extends BatchInfoPopulationException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.BatchInfoPopulationException

class BatchInfoPopulationException extends PreprocessingException implements Serializable

serialVersionUID:

-1770591991479420212L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.FASTQHeadersPresentButNotUsableException

class FASTQHeadersPresentButNotUsableException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1917074433646650950L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.SingletonBatchesException

class SingletonBatchesException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

9088141067684148902L

Exception Class ubic.gemma.core.analysis.preprocess.batcheffects.UnsupportedRawdataFileFormatException

class UnsupportedRawdataFileFormatException extends BatchInfoPopulationException implements Serializable

serialVersionUID:

1L

Package ubic.gemma.core.analysis.preprocess.convert

Exception Class ubic.gemma.core.analysis.preprocess.convert.QuantitationTypeConversionException

class QuantitationTypeConversionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationRepresentationConversionException

class UnsupportedQuantitationRepresentationConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationScaleConversionException

class UnsupportedQuantitationScaleConversionException extends UnsupportedQuantitationTypeConversionException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.convert.UnsupportedQuantitationTypeConversionException

class UnsupportedQuantitationTypeConversionException extends QuantitationTypeConversionException implements Serializable

Package ubic.gemma.core.analysis.preprocess.detect

Exception Class ubic.gemma.core.analysis.preprocess.detect.InferredQuantitationMismatchException

class InferredQuantitationMismatchException extends QuantitationMismatchException implements Serializable

Serialized Fields

inferredQuantitationType

QuantitationType inferredQuantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationMismatchException

class QuantitationMismatchException extends QuantitationTypeDetectionException implements Serializable

Serialized Fields

quantitationType

QuantitationType quantitationType

Exception Class ubic.gemma.core.analysis.preprocess.detect.QuantitationTypeDetectionException

class QuantitationTypeDetectionException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.detect.SuspiciousValuesForQuantitationException

class SuspiciousValuesForQuantitationException extends QuantitationMismatchException implements Serializable

Serialized Fields

suspiciousValues

List<SuspiciousValuesForQuantitationException.SuspiciousValueResult> suspiciousValues

Package ubic.gemma.core.analysis.preprocess.filter

Class ubic.gemma.core.analysis.preprocess.filter.ExpressionExperimentFilterConfig

class ExpressionExperimentFilterConfig extends Object implements Serializable

Serialized Fields

highExpressionCut

double highExpressionCut

High cut for expression.

Design elements expressed above the cut will be filtered out.

This threshold applies on the rank of gene expression. A value of 0.9 will drop the top 10% of the data.

Set this to 1.0 to disable.

ignoreMinimumDesignElementsThreshold

boolean ignoreMinimumDesignElementsThreshold

If true, the ExpressionExperimentFilter.MINIMUM_DESIGN_ELEMENTS is ignored.

ignoreMinimumSamplesThreshold

boolean ignoreMinimumSamplesThreshold

If true, ExpressionExperimentFilter.MINIMUM_SAMPLES is ignored.

lowDistinctValueCut

double lowDistinctValueCut

Minimum fraction of distinct values for a design element to be retained.

lowExpressionCut

double lowExpressionCut

Low cut for expression.

Design elements expressed below the cut will be filtered out.

This threshold applies on the rank. A value of 0.9 will drop the top 10% of the data.

Set this to one to disable.

lowVarianceCut

double lowVarianceCut

This threshold applies on the variance of the row.

The threshold applies to data on a log2-scale, so a value of 0.01 will retain values with a standard deviation of 0.1.

Set this to zero disable.

See Also:

• LowVarianceFilter

maskOutliers

boolean maskOutliers

Mask outliers in the data by replacing the affected columns with Double.NaN.

This filter is sensitive to multi-assay matrices and will only mask design elements that belong to the affected assays.

The default is to mask outliers which is sensible for most applications.

See Also:

• OutliersFilter

minPresentCount

int minPresentCount

Minimum number of samples for keeping rows when min-present filtering. Rows with more missing values than this are always removed. This can be increased by the use of the min fraction present filter which sets a fraction.

See Also:

• RowMissingValueFilter

minPresentFraction

double minPresentFraction

Minimum fraction of samples that must have a value (or a present call if a present/absent boolean matrix is provided) for the design element to be retained.

See Also:

• RowMissingValueFilter

requireSequences

boolean requireSequences

Set to true if design elements lacking associated BioSequences for the element should be removed.

Note that this filter is ignored if ALL design elements lack sequences.

See Also:

• RowsWithSequencesFilter

Exception Class ubic.gemma.core.analysis.preprocess.filter.FilteringException

class FilteringException extends Exception implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDataException

class InsufficientDataException extends FilteringException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientDesignElementsException

class InsufficientDesignElementsException extends InsufficientDataException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.InsufficientSamplesException

class InsufficientSamplesException extends InsufficientDataException implements Serializable

serialVersionUID:

1L

Exception Class ubic.gemma.core.analysis.preprocess.filter.NoDesignElementsException

class NoDesignElementsException extends InsufficientDesignElementsException implements Serializable

Exception Class ubic.gemma.core.analysis.preprocess.filter.NoSamplesException

class NoSamplesException extends InsufficientSamplesException implements Serializable

Package ubic.gemma.core.analysis.preprocess.svd

Exception Class ubic.gemma.core.analysis.preprocess.svd.SVDException

class SVDException extends Exception implements Serializable

Package ubic.gemma.core.analysis.sequence

Class ubic.gemma.core.analysis.sequence.CompositeSequenceMapValueObject

class CompositeSequenceMapValueObject extends Object implements Serializable

Serialized Fields

arrayDesignId

Long arrayDesignId

arrayDesignName

String arrayDesignName

arrayDesignShortName

String arrayDesignShortName

bioSequenceId

String bioSequenceId

bioSequenceName

String bioSequenceName

bioSequenceNcbiId

String bioSequenceNcbiId

compositeSequenceDescription

String compositeSequenceDescription

compositeSequenceId

String compositeSequenceId

compositeSequenceName

String compositeSequenceName

geneProducts

Map<Long, GeneProductValueObject> geneProducts

genes

Map<Long, GeneValueObject> genes

numBlatHits

Integer numBlatHits

Package ubic.gemma.core.analysis.singleCell.aggregate

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.SingleCellAggregationException

class SingleCellAggregationException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.analysis.singleCell.aggregate.UnsupportedScaleTypeForSingleCellAggregationException

class UnsupportedScaleTypeForSingleCellAggregationException extends SingleCellAggregationException implements Serializable

Package ubic.gemma.core.job

Class ubic.gemma.core.job.TaskCommand

class TaskCommand extends Object implements Serializable

Serialized Fields

emailAlert

boolean emailAlert

Should an email be sent to the user when the job is done?

maxQueueMillis

long maxQueueMillis

How long we will allow this task to be queued before giving up, or -1 for no limit.

maxRuntimeMillis

long maxRuntimeMillis

How long we will allow this task to run before giving up, or -1 for no limit.

persistJobDetails

Boolean persistJobDetails

If true, the jobDetails associated with this task will be persisted in the database. Consider setting to false for test jobs or other super-frequent maintenance tasks.

securityContext

org.springframework.security.core.context.SecurityContext securityContext

Used to propagate security to grid workers.

submitter

String submitter

Task submitted, if known.

Class ubic.gemma.core.job.TaskResult

class TaskResult extends Object implements Serializable

Serialized Fields

answer

Serializable answer

The actual result object

Package ubic.gemma.core.job.progress

Class ubic.gemma.core.job.progress.ProgressData

class ProgressData extends Object implements Serializable

serialVersionUID:

-4303625064082352461L

Serialized Fields

description

String description

done

boolean done

failed

boolean failed

forwardingURL

String forwardingURL

percent

int percent

taskId

String taskId

Package ubic.gemma.core.loader.entrez

Exception Class ubic.gemma.core.loader.entrez.EntrezException

class EntrezException extends RuntimeException implements Serializable

Serialized Fields

errors

List<String> errors

Package ubic.gemma.core.loader.expression.arrayDesign

Class ubic.gemma.core.loader.expression.arrayDesign.Reporter

class Reporter extends AbstractDescribable implements Serializable

serialVersionUID:

3703827938981026012L

Serialized Fields

col

Integer col

row

Integer row

startInBioChar

Long startInBioChar

strand

String strand

Package ubic.gemma.core.loader.expression.geo

Class ubic.gemma.core.loader.expression.geo.GeoSampleCorrespondence

class GeoSampleCorrespondence extends Object implements Serializable

serialVersionUID:

-5285504953530483114L

Serialized Fields

accToDataset

Map<String,String> accToDataset

accToTitle

Map<String,String> accToTitle

sets

Collection<Set<String>> sets

Package ubic.gemma.core.loader.expression.geo.model

Class ubic.gemma.core.loader.expression.geo.model.GeoContact

class GeoContact extends Object implements Serializable

serialVersionUID:

-2042747972349661568L

Serialized Fields

address

String address

city

String city

country

String country

department

String department

email

String email

fax

String fax

institute

String institute

laboratory

String laboratory

name

String name

phone

String phone

postCode

String postCode

state

String state

webLink

String webLink

Class ubic.gemma.core.loader.expression.geo.model.GeoData

class GeoData extends Object implements Serializable

Serialized Fields

columnDescriptions

List<String> columnDescriptions

columnNames

List<String> columnNames

The column names mean different things in different subclasses. For samples, the column names are the "quantitation types". For platforms, they are descriptor names.

contact

GeoContact contact

geoAccession

String geoAccession

relations

Map<String, Collection<String>> relations

title

String title

Class ubic.gemma.core.loader.expression.geo.model.GeoDataset

class GeoDataset extends GeoData implements Serializable

Serialized Fields

completeness

String completeness

datasetType

String datasetType

description

String description

experimentType

GeoDataset.ExperimentType experimentType

featureCount

String featureCount

numChannels

int numChannels

numProbes

int numProbes

numSamples

int numSamples

order

String order

organism

String organism

platform

GeoPlatform platform

platformType

GeoDataset.PlatformType platformType

pubmedId

String pubmedId

sampleType

GeoDataset.SampleType sampleType

series

Collection<GeoSeries> series

subsets

Collection<GeoSubset> subsets

updateDate

String updateDate

valueType

GeoDataset.ValueType valueType

Class ubic.gemma.core.loader.expression.geo.model.GeoPlatform

class GeoPlatform extends GeoData implements Serializable

serialVersionUID:

1L

Serialized Fields

catalogNumbers

Collection<String> catalogNumbers

coating

String coating

contributer

Collection<String> contributer

description

String description

designElements

Collection<String> designElements

distribution

String distribution

id

String id

lastUpdateDate

String lastUpdateDate

manufactureProtocol

String manufactureProtocol

manufacturer

String manufacturer

organisms

Collection<String> organisms

platformData

List<List<String>> platformData

platformInformation

Map<String, List<String>> platformInformation

Store information on the platform here. Map of designElements to other information. This has to be lists so the values "line up".

probeNamesInGemma

Map<String,String> probeNamesInGemma

Map of original probe names provided by GEO to the names in Gemma (if this platform is already there). This is needed because probe names are sometimes changed after import. This map must be populated prior to import of the data.

pubMedIds

Collection<Integer> pubMedIds

sample

String sample

status

String status

submissionDate

String submissionDate

supplementaryFile

String supplementaryFile

support

String support

technology

GeoDataset.PlatformType technology

useDataFromGEO

boolean useDataFromGEO

Will be set to false during parsing if data are missing.

webLink

String webLink

webLinks

Collection<String> webLinks

Class ubic.gemma.core.loader.expression.geo.model.GeoRecord

class GeoRecord extends GeoData implements Serializable

Serialized Fields

contactName

String contactName

correspondingExperiments

Collection<Long> correspondingExperiments

detailsIncomplete

boolean detailsIncomplete

True when the detailed MINiML fetch for this record failed and was tolerated (GeoRetrieveConfig.isIgnoreErrors()), so the record is returned with whatever the eutils summary gave and without sample details.

Exists so a caller can say WHICH records it is reporting on incomplete information. GEO serves invalid MINiML for withdrawn / restricted / transiently-broken series, and the condition is usually temporary — a later pass over the same accession often succeeds.

librarySource

String librarySource

libraryStrategy

String libraryStrategy

meshHeadings

Collection<String> meshHeadings

MeSh headings, collected from PubMed.

numSamples

int numSamples

organisms

Collection<String> organisms

overallDesign

String overallDesign

platform

String platform

previousClicks

int previousClicks

How many times a curator has already looked at the details. this helps us track data sets we've already examined for usefulness.

pubMedIds

List<String> pubMedIds

releaseDate

Date releaseDate

sampleDataProcessing

String sampleDataProcessing

sampleDescriptions

String sampleDescriptions

sampleDetails

String sampleDetails

sampleExtractProtocols

String sampleExtractProtocols

sampleGEOAccessions

Collection<String> sampleGEOAccessions

sampleLabelProtocols

String sampleLabelProtocols

sampleLabels

String sampleLabels

sampleMolecules

String sampleMolecules

seriesType

String seriesType

subSeries

boolean subSeries

subSeriesOf

String subSeriesOf

summary

String summary

superSeries

boolean superSeries

usable

boolean usable

Curator judgement about whether this is loadable. False indicates a problem.

Class ubic.gemma.core.loader.expression.geo.model.GeoSample

class GeoSample extends GeoData implements Serializable

Serialized Fields

anchor

String anchor

channels

List<GeoChannel> channels

dataProcessing

String dataProcessing

description

String description

hybProtocol

String hybProtocol

id

String id

instrumentModel

String instrumentModel

Verbatim !Sample_instrument_model, e.g. Illumina HiSeq 2000. Raw string for the same reason as GeoSample.librarySelection. Empty when GEO did not state one.

isGenePix

boolean isGenePix

lastUpdateDate

String lastUpdateDate

librarySelection

String librarySelection

Verbatim !Sample_library_selection, e.g. cDNA, PCR, other.

Kept as the submitter's raw string rather than an enum, unlike GeoSample.libSource and GeoSample.libStrategy: this feeds the verbatim upstream-metadata payload (Investigation.sourceMetadata), where normalizing to a closed set would both lose the original spelling and silently drop values the enum does not know. Empty when GEO did not state one.

libSource

GeoLibrarySource libSource

libStrategy

GeoLibraryStrategy libStrategy

mightNotHaveDataInFile

boolean mightNotHaveDataInFile

Indicate if the data might be separate, as for some RNA-seq studies.

platforms

Collection<GeoPlatform> platforms

replicates

Collection<GeoReplication> replicates

scanProtocol

String scanProtocol

seriesAppearsIn

Collection<String> seriesAppearsIn

status

String status

submissionDate

String submissionDate

supplementaryFiles

Collection<String> supplementaryFiles

tagCount

int tagCount

tagLength

int tagLength

titleInDataset

String titleInDataset

This is used to store the title for the sample as found in the GDS file, if it differs from the one in the GSE file

type

GeoSampleType type

The sample type (ie. DNA, RNA, etc.)

variables

Collection<GeoVariable> variables

warnedAboutGenePix

boolean warnedAboutGenePix

Class ubic.gemma.core.loader.expression.geo.model.GeoSeries

class GeoSeries extends GeoData implements Serializable

Serialized Fields

contributors

Collection<GeoContact> contributors

dataSets

Collection<GeoDataset> dataSets

isSubSeries

boolean isSubSeries

isSuperSeries

boolean isSuperSeries

keyWords

Collection<String> keyWords

lastUpdateDate

String lastUpdateDate

overallDesign

String overallDesign

platformId

String platformId

pubmedIds

Collection<String> pubmedIds

replicates

Map<Integer, GeoReplication> replicates

sampleCorrespondence

GeoSampleCorrespondence sampleCorrespondence

samples

Collection<GeoSample> samples

seriesId

String seriesId

seriesTypes

Collection<GeoSeriesType> seriesTypes

status

String status

submissionDate

String submissionDate

subSeries

Collection<String> subSeries

summaries

List<String> summaries

supplementaryFiles

Collection<String> supplementaryFiles

values

GeoValues values

variables

Map<Integer, GeoVariable> variables

webLinks

Collection<String> webLinks

Class ubic.gemma.core.loader.expression.geo.model.GeoSubset

class GeoSubset extends GeoData implements Serializable

Serialized Fields

dataSet

String dataSet

description

String description

owningDataset

GeoDataset owningDataset

samples

Collection<GeoSample> samples

type

GeoVariable.VariableType type

Class ubic.gemma.core.loader.expression.geo.model.GeoValues

class GeoValues extends Object implements Serializable

serialVersionUID:

3748363645735281578L

Serialized Fields

data

Map<GeoPlatform, Map<Integer, Map<String, List<String>>>> data

quantitationTypeIndexMap

Map<GeoPlatform, Map<Integer, Collection<String>>> quantitationTypeIndexMap

quantitationTypeNameMap

Map<GeoPlatform, Map<String,Integer>> quantitationTypeNameMap

sampleDimensions

Map<GeoPlatform, Map<Integer, LinkedHashSet<GeoSample>>> sampleDimensions

Package ubic.gemma.core.loader.expression.geo.singleCell

Exception Class ubic.gemma.core.loader.expression.geo.singleCell.NoSingleCellDataFoundException

class NoSingleCellDataFoundException extends Exception implements Serializable

Package ubic.gemma.core.loader.expression.simple.model

Class ubic.gemma.core.loader.expression.simple.model.SimpleCharacteristic

class SimpleCharacteristic extends Object implements Serializable

Serialized Fields

category

String category

categoryUri

String categoryUri

value

String value

valueUri

String valueUri

Class ubic.gemma.core.loader.expression.simple.model.SimpleContactMetadata

class SimpleContactMetadata extends Object implements Serializable

Class ubic.gemma.core.loader.expression.simple.model.SimpleDatabaseEntry

class SimpleDatabaseEntry extends Object implements Serializable

Serialized Fields

accession

String accession

externalDatabaseId

Long externalDatabaseId

externalDatabaseName

String externalDatabaseName

Class ubic.gemma.core.loader.expression.simple.model.SimpleExpressionExperimentMetadata

class SimpleExpressionExperimentMetadata extends Object implements Serializable

Serialized Fields

accession

SimpleDatabaseEntry accession

arrayDesigns

Collection<SimplePlatformMetadata> arrayDesigns

Platforms associated to the experiments.

Once declared here, they may be referred to in SimpleExpressionExperimentMetadata.samples.

description

String description

experimentalDesignDescription

String experimentalDesignDescription

experimentalDesignName

String experimentalDesignName

name

String name

probeIdsAreImageClones

boolean probeIdsAreImageClones

If true, biological characteristics imaging the probes will be created.

pubMedId

String pubMedId

PubMed identifier.

quantitationType

SimpleQuantitationTypeMetadata quantitationType

Required if data is provided.

samples

Collection<SimpleSampleMetadata> samples

Samples to be associated with this experiment.

If left unset, the assays will be inferred from the data file.

shortName

String shortName

source

String source

taxon

SimpleTaxonMetadata taxon

Class ubic.gemma.core.loader.expression.simple.model.SimplePlatformMetadata

class SimplePlatformMetadata extends Object implements Serializable

Serialized Fields

description

String description

id

Long id

name

String name

shortName

String shortName

technologyType

TechnologyType technologyType

Class ubic.gemma.core.loader.expression.simple.model.SimpleQuantitationTypeMetadata

class SimpleQuantitationTypeMetadata extends Object implements Serializable

Serialized Fields

description

String description

generalType

GeneralType generalType

isBatchCorrected

Boolean isBatchCorrected

isPreferred

Boolean isPreferred

isRatio

Boolean isRatio

name

String name

representation

PrimitiveType representation

scale

ScaleType scale

type

StandardQuantitationType type

Class ubic.gemma.core.loader.expression.simple.model.SimpleSampleMetadata

class SimpleSampleMetadata extends Object implements Serializable

Serialized Fields

accession

SimpleDatabaseEntry accession

characteristics

Collection<SimpleCharacteristic> characteristics

description

String description

name

String name

platformUsed

SimplePlatformMetadata platformUsed

Class ubic.gemma.core.loader.expression.simple.model.SimpleTaxonMetadata

class SimpleTaxonMetadata extends Object implements Serializable

Serialized Fields

id

Long id

name

String name

Taxon name, either common or scientific.

ncbiId

Integer ncbiId

Package ubic.gemma.core.loader.expression.singleCell

Exception Class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellLevelCharacteristicsByNameException

class NonUniqueCellLevelCharacteristicsByNameException extends NonUniqueDescribableByNameException implements Serializable

Exception Class ubic.gemma.core.loader.expression.singleCell.NonUniqueCellTypeAssignmentByNameException

class NonUniqueCellTypeAssignmentByNameException extends NonUniqueDescribableByNameException implements Serializable

Package ubic.gemma.core.loader.util

Exception Class ubic.gemma.core.loader.util.AlreadyExistsInSystemException

class AlreadyExistsInSystemException extends RuntimeException implements Serializable

serialVersionUID:

5677999264920938691L

Serialized Fields

data

Object data

Package ubic.gemma.core.loader.util.anndata

Exception Class ubic.gemma.core.loader.util.anndata.AnnDataException

class AnnDataException extends RuntimeException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.InvalidEncodingAttributeException

class InvalidEncodingAttributeException extends AnnDataException implements Serializable

Exception Class ubic.gemma.core.loader.util.anndata.MissingEncodingAttributeException

class MissingEncodingAttributeException extends AnnDataException implements Serializable

Package ubic.gemma.core.loader.util.biomart

Class ubic.gemma.core.loader.util.biomart.Ensembl2NcbiValueObject

class Ensembl2NcbiValueObject extends Object implements Serializable

serialVersionUID:

-859220901359582113L

Serialized Fields

enemblTranscriptId

String enemblTranscriptId

ensembleGeneId

String ensembleGeneId

ensemblPeptideId

String ensemblPeptideId

hgcnId

String hgcnId

ncbiGenes

Collection<String> ncbiGenes

ncbiTaxonId

Integer ncbiTaxonId

Package ubic.gemma.core.loader.util.hdf5

Exception Class ubic.gemma.core.loader.util.hdf5.H5Exception

class H5Exception extends RuntimeException implements Serializable

Serialized Fields

cause

hdf.hdf5lib.exceptions.HDF5Exception cause

Exception Class ubic.gemma.core.loader.util.hdf5.TruncatedH5FileException

class TruncatedH5FileException extends IOException implements Serializable

Package ubic.gemma.core.loader.util.parser

Exception Class ubic.gemma.core.loader.util.parser.FileFormatException

class FileFormatException extends RuntimeException implements Serializable

serialVersionUID:

-1984918923089214361L

Package ubic.gemma.core.ontology

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult

class ObsoleteTermCorrectionResult extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

characteristicsRewritten

int characteristicsRewritten

dryRun

boolean dryRun

experimentsAffected

int experimentsAffected

resync

ObsoleteTermCorrectionResult.Resync resync

skippedDeferred

List<String> skippedDeferred

skippedNotCorrectable

List<String> skippedNotCorrectable

terms

List<ObsoleteTermCorrectionResult.TermCorrection> terms

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.Resync

class Resync extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

annotationRelationRowsWritten

int annotationRelationRowsWritten

ee2cRowsWritten

int ee2cRowsWritten

experimentsResynced

int experimentsResynced

resyncFailures

List<String> resyncFailures

Class ubic.gemma.core.ontology.ObsoleteTermCorrectionResult.TermCorrection

class TermCorrection extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

characteristicsRewritten

int characteristicsRewritten

experimentsAffected

int experimentsAffected

fromLabel

String fromLabel

fromUri

String fromUri

inCategory

int inCategory

inObject

int inObject

inPredicate

int inPredicate

inValue

int inValue

resolvedVia

String resolvedVia

toLabel

String toLabel

toUri

String toUri

Class ubic.gemma.core.ontology.ObsoleteTermUsage

class ObsoleteTermUsage extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

autoCorrectable

boolean autoCorrectable

blockedReason

String blockedReason

considerUris

List<String> considerUris

experimentCount

long experimentCount

label

String label

replacedByLabel

String replacedByLabel

replacedByUri

String replacedByUri

replacementHops

int replacementHops

resolvedVia

String resolvedVia

Which mechanical rule produced ObsoleteTermUsage.replacedByUri. This is what gets written into the corrected characteristic's supportingEvidence as assertedBy, so a later reader can tell a derived correction from a curator's decision, and tell which derivation was used.

storedValue

String storedValue

uri

String uri

usedAsCategory

boolean usedAsCategory

Whether the term is used as a CATEGORY. This is a different repair from a stale value and worth knowing before acting: EFO_0000408 is the "disease" category on a large share of the corpus, so correcting it rewrites the shape of the annotation rather than one of its terms.

usedAsTerm

boolean usedAsTerm

Package ubic.gemma.core.ontology.chembl

Class ubic.gemma.core.ontology.chembl.ChemblCompound

class ChemblCompound extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

chemblId

String chemblId

code

String code

matchedSynonym

String matchedSynonym

preferredName

String preferredName

release

String release

Package ubic.gemma.core.ontology.lexical

Class ubic.gemma.core.ontology.lexical.LexicalAnnotationProperty

class LexicalAnnotationProperty extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

contents

String contents

Class ubic.gemma.core.ontology.lexical.LexicalOntologyTerm

class LexicalOntologyTerm extends OntologyTermSimple implements Serializable

Serialized Fields

metadata

LexicalTermMetadata metadata

Package ubic.gemma.core.ontology.ols

Class ubic.gemma.core.ontology.ols.OlsTerm

class OlsTerm extends Object implements Serializable

Serialized Fields

found

boolean found

iri

String iri

label

String label

Exception Class ubic.gemma.core.ontology.ols.OlsUnavailableException

class OlsUnavailableException extends Exception implements Serializable

Package ubic.gemma.core.ontology.search

Exception Class ubic.gemma.core.ontology.search.OntologySearchException

class OntologySearchException extends Exception implements Serializable

Serialized Fields

query

String query

Package ubic.gemma.core.ontology.simple

Class ubic.gemma.core.ontology.simple.AbstractOntologyResourceSimple

class AbstractOntologyResourceSimple extends Object implements Serializable

Serialized Fields

label

String label

localName

String localName

uri

String uri

Class ubic.gemma.core.ontology.simple.OntologyIndividualSimple

class OntologyIndividualSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

instanceOf

OntologyTermSimple instanceOf

Class ubic.gemma.core.ontology.simple.OntologyPropertySimple

class OntologyPropertySimple extends AbstractOntologyResourceSimple implements Serializable

Class ubic.gemma.core.ontology.simple.OntologyTermSimple

class OntologyTermSimple extends AbstractOntologyResourceSimple implements Serializable

Serialized Fields

comment

String comment

obsolete

boolean obsolete

Package ubic.gemma.core.pipeline

Exception Class ubic.gemma.core.pipeline.PipelineSchedulerException

class PipelineSchedulerException extends Exception implements Serializable

Package ubic.gemma.core.search

Exception Class ubic.gemma.core.search.BaseCodeOntologySearchException

class BaseCodeOntologySearchException extends SearchException implements Serializable

Serialized Fields

cause

OntologySearchException cause

Exception Class ubic.gemma.core.search.ParseSearchException

class ParseSearchException extends SearchException implements Serializable

Serialized Fields

originalParseException

ParseSearchException originalParseException

query

String query

Exception Class ubic.gemma.core.search.SearchException

class SearchException extends Exception implements Serializable

Exception Class ubic.gemma.core.search.SearchTimeoutException

class SearchTimeoutException extends SearchException implements Serializable

Serialized Fields

cause

TimeoutException cause

Package ubic.gemma.core.search.lucene

Exception Class ubic.gemma.core.search.lucene.LuceneParseSearchException

class LuceneParseSearchException extends ParseSearchException implements Serializable

Package ubic.gemma.core.search.source

Exception Class ubic.gemma.core.search.source.HibernateSearchException

class HibernateSearchException extends SearchException implements Serializable

Serialized Fields

cause

org.hibernate.search.util.common.SearchException cause

Package ubic.gemma.core.security.acl.domain

Class ubic.gemma.core.security.acl.domain.AclEntry

class AclEntry extends Object implements Serializable

serialVersionUID:

-4697361841061166973L

Serialized Fields

aceOrder

int aceOrder

acl

org.springframework.security.acls.model.Acl acl

granting

boolean granting

id

Long id

mask

int mask

sid

AclSid sid

Class ubic.gemma.core.security.acl.domain.AclGrantedAuthoritySid

class AclGrantedAuthoritySid extends AclSid implements Serializable

serialVersionUID:

7755206462003052441L

Serialized Fields

grantedAuthority

String grantedAuthority

Class ubic.gemma.core.security.acl.domain.AclImpl

class AclImpl extends Object implements Serializable

serialVersionUID:

-953242274878593548L

Serialized Fields

entries

List<AclEntry> entries

objectIdentity

AclObjectIdentity objectIdentity

parentAcl

org.springframework.security.acls.model.Acl parentAcl

Class ubic.gemma.core.security.acl.domain.AclObjectIdentity

class AclObjectIdentity extends Object implements Serializable

serialVersionUID:

-6715898560226971244L

Serialized Fields

entries

Set<AclEntry> entries

entriesInheriting

boolean entriesInheriting

id

Long id

identifier

Long identifier

objectIdClass

Long objectIdClass

Spring Security canonical acl_object_identity.object_id_class FK to acl_class.id. The AclObjectIdentity.type field is the human-readable class name derived from this FK via a Hibernate formula at load time (see AclObjectIdentity.hbm.xml). Application code reads AclObjectIdentity.getType(); this field exists so Hibernate's hbm2ddl generates the canonical column for Spring Security's stock JdbcMutableAclService to read/write through JDBC.

ownerSid

AclSid ownerSid

parentObject

AclObjectIdentity parentObject

type

String type

Class ubic.gemma.core.security.acl.domain.AclPrincipalSid

class AclPrincipalSid extends AclSid implements Serializable

serialVersionUID:

-4679911678447417301L

Serialized Fields

principal

String principal

Class ubic.gemma.core.security.acl.domain.AclSid

class AclSid extends Object implements Serializable

serialVersionUID:

-3256613712125656321L

Serialized Fields

id

Long id

Package ubic.gemma.core.security.audit

Class ubic.gemma.core.security.audit.AuditedEvent

class AuditedEvent extends org.springframework.context.ApplicationEvent implements Serializable

Serialized Fields

auditEvent

AuditEvent auditEvent

eventType

AuditEventType eventType

payload

AuditEventPayload payload

target

Auditable target

Package ubic.gemma.core.security.authentication

Class ubic.gemma.core.security.authentication.UserDetailsImpl

class UserDetailsImpl extends Object implements Serializable

serialVersionUID:

1650537135541038216L

Serialized Fields

email

String email

enabled

boolean enabled

grantedAuthorities

Collection<org.springframework.security.core.GrantedAuthority> grantedAuthorities

password

String password

signupToken

String signupToken

signupTokenDatestamp

Date signupTokenDatestamp

userName

String userName

Exception Class ubic.gemma.core.security.authentication.UserExistsException

class UserExistsException extends Exception implements Serializable

serialVersionUID:

-6191531408977402526L

Package ubic.gemma.core.security.model

Package ubic.gemma.core.tasks

Class ubic.gemma.core.tasks.EntityTaskCommand

class EntityTaskCommand extends TaskCommand implements Serializable

Serialized Fields

entityClass

Class<T extends Identifiable> entityClass

entityId

Long entityId

Package ubic.gemma.core.tasks.analysis.diffex

Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisRemoveTaskCommand

class DifferentialExpressionAnalysisRemoveTaskCommand extends DifferentialExpressionAnalysisTaskCommand implements Serializable

serialVersionUID:

-6881129987842634598L

Serialized Fields

toRemove

DifferentialExpressionAnalysis toRemove

Class ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand

class DifferentialExpressionAnalysisTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

analysisType

AnalysisType analysisType

Proposed analysis type. If null the system tries to figure it out.

expressionExperiment

ExpressionExperiment expressionExperiment

factors

Collection<ExperimentalFactor> factors

The factors to actually use in the analysis. If null the system tries to figure it out.

forceAnalysis

boolean forceAnalysis

includeInteractions

boolean includeInteractions

Whether interactions among the factors should be included. The implementation may limit this to two-way interactions for only up to two factors, so this may not have the effect desired.

moderateStatistics

boolean moderateStatistics

Whether to moderate test statistics via empirical Bayes

subsetFactor

ExperimentalFactor subsetFactor

toRedo

DifferentialExpressionAnalysis toRedo

useWeights

boolean useWeights

Whether to use weighted regression based on mean-variance relationships (voom)

Class ubic.gemma.core.tasks.analysis.diffex.DiffExMetaAnalyzerTaskCommand

class DiffExMetaAnalyzerTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

analysisResultSetIds

Collection<Long> analysisResultSetIds

description

String description

name

String name

persist

boolean persist

Package ubic.gemma.core.tasks.analysis.expression

Class ubic.gemma.core.tasks.analysis.expression.BatchInfoFetchTaskCommand

class BatchInfoFetchTaskCommand extends ExpressionExperimentReportTaskCommand implements Serializable

serialVersionUID:

-1901958943061377082L

Class ubic.gemma.core.tasks.analysis.expression.BioAssayOutlierProcessingTaskCommand

class BioAssayOutlierProcessingTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

3083077516188614790L

Serialized Fields

bioAssayIds

Collection<Long> bioAssayIds

revert

boolean revert

Class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentLoadTaskCommand

class ExpressionExperimentLoadTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

accession

String accession

aggressiveQtRemoval

boolean aggressiveQtRemoval

Set to true to attempt to remove all unneeded quantitation types during parsing.

allowArrayExpressDesign

boolean allowArrayExpressDesign

allowSubSeriesLoad

boolean allowSubSeriesLoad

allowSuperSeriesLoad

boolean allowSuperSeriesLoad

arrayDesignName

String arrayDesignName

isArrayExpress

boolean isArrayExpress

isSplitByPlatform

boolean isSplitByPlatform

loadPlatformOnly

boolean loadPlatformOnly

suppressMatching

boolean suppressMatching

Used to turn off 'bioassay to biomaterial' matching.

suppressPostProcessing

boolean suppressPostProcessing

Set to true to skip post-processing (processed-vector creation and downstream diagnostics) after loading. Mirrors the CLI -nopost flag; the usual case for RNA-seq loads whose data is reanalyzed from raw sequence later.

Class ubic.gemma.core.tasks.analysis.expression.ExpressionExperimentPlatformSwitchTaskCommand

class ExpressionExperimentPlatformSwitchTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

expressionExperiment

ExpressionExperiment expressionExperiment

targetArrayDesign

ArrayDesign targetArrayDesign

Class ubic.gemma.core.tasks.analysis.expression.GeeqTaskCommand

class GeeqTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

expressionExperiment

ExpressionExperiment expressionExperiment

mode

GeeqService.ScoreMode mode

Class ubic.gemma.core.tasks.analysis.expression.PreprocessTaskCommand

class PreprocessTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

diagnosticsOnly

boolean diagnosticsOnly

expressionExperiment

ExpressionExperiment expressionExperiment

Class ubic.gemma.core.tasks.analysis.expression.SvdTaskCommand

class SvdTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

expressionExperiment

ExpressionExperiment expressionExperiment

postProcessOnly

boolean postProcessOnly

Class ubic.gemma.core.tasks.analysis.expression.TwoChannelMissingValueTaskCommand

class TwoChannelMissingValueTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

expressionExperiment

ExpressionExperiment expressionExperiment

extraMissingValueIndicators

Collection<Double> extraMissingValueIndicators

s2n

double s2n

Class ubic.gemma.core.tasks.analysis.expression.UpdateEEDetailsCommand

class UpdateEEDetailsCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

description

String description

entityId

Long entityId

name

String name

pubMedId

String pubMedId

removePrimaryPublication

boolean removePrimaryPublication

shortName

String shortName

Class ubic.gemma.core.tasks.analysis.expression.UpdatePubMedCommand

class UpdatePubMedCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

entityId

Long entityId

pubmedId

String pubmedId

Package ubic.gemma.core.tasks.analysis.sequence

Class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignProbeMapTaskCommand

class ArrayDesignProbeMapTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesign

ArrayDesign arrayDesign

forceAnalysis

boolean forceAnalysis

Class ubic.gemma.core.tasks.analysis.sequence.ArrayDesignRepeatScanTaskCommand

class ArrayDesignRepeatScanTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

arrayDesign

ArrayDesign arrayDesign

Package ubic.gemma.core.tasks.maintenance

Class ubic.gemma.core.tasks.maintenance.ArrayDesignReportTaskCommand

class ArrayDesignReportTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

all

boolean all

arrayDesign

ArrayDesign arrayDesign

Class ubic.gemma.core.tasks.maintenance.CharacteristicUpdateCommand

class CharacteristicUpdateCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

annotationValueObjects

Collection<AnnotationValueObject> annotationValueObjects

remove

boolean remove

If set to true, the annotations passed in will be deleted.

Class ubic.gemma.core.tasks.maintenance.ExpressionExperimentReportTaskCommand

class ExpressionExperimentReportTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

all

boolean all

expressionExperiment

ExpressionExperiment expressionExperiment

Class ubic.gemma.core.tasks.maintenance.GeoScrapeTaskCommand

class GeoScrapeTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

criteria

Collection<String> criteria

Deprecated.

dryRun

boolean dryRun

Deprecated.

maxRecords

Integer maxRecords

Deprecated.

since

Date since

Deprecated.

skip

Integer skip

Deprecated.

Records to skip at the start of the resolved window; see ScrapeRequest.skip.

startAt

String startAt

Deprecated.

GEO accession to resume from; see ScrapeRequest.startAt.

until

Date until

Deprecated.

Class ubic.gemma.core.tasks.maintenance.IndexerTaskCommand

class IndexerTaskCommand extends TaskCommand implements Serializable

Serialized Fields

indexBioSequences

boolean indexBioSequences

indexDatasetGroups

boolean indexDatasetGroups

indexDatasets

boolean indexDatasets

indexDesignElements

boolean indexDesignElements

indexGeneGroups

boolean indexGeneGroups

indexGenes

boolean indexGenes

indexPlatforms

boolean indexPlatforms

indexPublications

boolean indexPublications

Class ubic.gemma.core.tasks.maintenance.MultifunctionalityTaskCommand

class MultifunctionalityTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

taxon

Taxon taxon

Class ubic.gemma.core.tasks.maintenance.ObsoleteTermCorrectionTaskCommand

class ObsoleteTermCorrectionTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

1L

Serialized Fields

dryRun

boolean dryRun

timeoutSeconds

int timeoutSeconds

uris

Collection<String> uris

Package ubic.gemma.core.tasks.visualization

Class ubic.gemma.core.tasks.visualization.DifferentialExpressionAnalysisResultSetVisualizationValueObject

class DifferentialExpressionAnalysisResultSetVisualizationValueObject extends Object implements Serializable

Serialized Fields

analysisId

Long analysisId

analysisNotRun

boolean analysisNotRun

baselineFactorValue

String baselineFactorValue

baselineFactorValueId

Long baselineFactorValueId

contrastsFactorValueIds

List<Long> contrastsFactorValueIds

contrastsFactorValues

Map<Long,String> contrastsFactorValues

datasetId

Long datasetId

datasetLink

String datasetLink

datasetName

String datasetName

datasetShortName

String datasetShortName

factorCategory

String factorCategory

factorDescription

String factorDescription

factorId

Long factorId

factorName

String factorName

numberOfProbes

List<List<Integer>> numberOfProbes

numberOfProbesDiffExpressed

int numberOfProbesDiffExpressed

numberOfProbesDownRegulated

int numberOfProbesDownRegulated

numberOfProbesTotal

int numberOfProbesTotal

numberOfProbesUpRegulated

int numberOfProbesUpRegulated

qValues

List<List<Double>> qValues

resultSetId

Long resultSetId

visualizationValues

List<List<Double>> visualizationValues

Class ubic.gemma.core.tasks.visualization.DifferentialExpressionGenesConditionsValueObject

class DifferentialExpressionGenesConditionsValueObject extends Object implements Serializable

Class ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskCommand

class DifferentialExpressionSearchTaskCommand extends TaskCommand implements Serializable

serialVersionUID:

-8510536003059837349L

Serialized Fields

experimentGroup

Collection<ExpressionExperimentDetailsValueObject> experimentGroup

experimentGroupName

String experimentGroupName

geneGroup

Collection<GeneValueObject> geneGroup

geneGroupName

String geneGroupName

Package ubic.gemma.core.util

Exception Class ubic.gemma.core.util.GemmaRestApiClientException

class GemmaRestApiClientException extends RuntimeException implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestAnnotatedVo

class TestAnnotatedVo extends Object implements Serializable

Class ubic.gemma.core.util.StrictBeanDefinitionValidatorTest.TestImplicitValueObject

class TestImplicitValueObject extends Object implements Serializable

Package ubic.gemma.core.util.graphics

Class ubic.gemma.core.util.graphics.MatrixDisplay

class MatrixDisplay extends JPanel implements Serializable

serialVersionUID:

-8078532270193813539L

Serialized Fields

colorMatrix

ColorMatrix<R,C> colorMatrix

m_cellSize

Dimension m_cellSize

m_columnLabelHeight

int m_columnLabelHeight

m_defaultResolution

int m_defaultResolution

m_fontGutter

int m_fontGutter

m_fontSize

int m_fontSize

m_isShowingStandardizedMatrix

boolean m_isShowingStandardizedMatrix

m_isShowLabels

boolean m_isShowLabels

m_isShowScale

boolean m_isShowScale

m_labelFont

Font m_labelFont

m_labelGutter

int m_labelGutter

m_maxColumnLength

int m_maxColumnLength

m_maxFontSize

int m_maxFontSize

m_ratioWidth

int m_ratioWidth

m_resolution

int m_resolution

m_rowLabelWidth

int m_rowLabelWidth

m_standardizedMatrix

ColorMatrix<R,C> m_standardizedMatrix

m_textSize

int m_textSize

m_unstandardizedMatrix

ColorMatrix<R,C> m_unstandardizedMatrix

SCALE_BAR_ROOM

int SCALE_BAR_ROOM

Package ubic.gemma.core.util.math.linearmodels

Class ubic.gemma.core.util.math.linearmodels.AnovaEffect

class AnovaEffect extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

dof

double dof

effectName

String effectName

fStat

double fStat

isInteraction

boolean isInteraction

isResiduals

boolean isResiduals

meanSq

double meanSq

pValue

double pValue

ssQ

double ssQ

Package ubic.gemma.core.util.matrix

Class ubic.gemma.core.util.matrix.AbstractMatrix

class AbstractMatrix extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

colMap

Map<C,Integer> colMap

colNames

List<C> colNames

lastColumnIndex

int lastColumnIndex

lastRowIndex

int lastRowIndex

rowMap

Map<R,Integer> rowMap

rowNames

List<R> rowNames

Class ubic.gemma.core.util.matrix.CompressedSparseDoubleMatrix

class CompressedSparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

5771918031750038719L

Class ubic.gemma.core.util.matrix.DenseDoubleMatrix

class DenseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-239226762166912931L

Serialized Fields

matrix

DoubleMatrix2D matrix

Class ubic.gemma.core.util.matrix.DenseDoubleMatrix1D

class DenseDoubleMatrix1D extends DenseDoubleMatrix1D implements Serializable

serialVersionUID:

-5196826500179433512L

Class ubic.gemma.core.util.matrix.DoubleMatrix

class DoubleMatrix extends AbstractMatrix<R,C,Double> implements Serializable

serialVersionUID:

1L

Class ubic.gemma.core.util.matrix.FastRowAccessDoubleMatrix

class FastRowAccessDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-5458302072944941517L

Serialized Fields

data

DoubleArrayList[] data

Class ubic.gemma.core.util.matrix.IntegerMatrix

class IntegerMatrix extends AbstractMatrix<R,C,Integer> implements Serializable

serialVersionUID:

-8413796057024940237L

Serialized Fields

matrix

ObjectMatrixImpl<R,C,Integer> matrix

Class ubic.gemma.core.util.matrix.ObjectMatrixImpl

class ObjectMatrixImpl extends AbstractMatrix<R,C,V> implements Serializable

serialVersionUID:

-902358802107186038L

Serialized Fields

matrix

DenseObjectMatrix2D matrix

Class ubic.gemma.core.util.matrix.SparseDoubleMatrix

class SparseDoubleMatrix extends DoubleMatrix<R,C> implements Serializable

serialVersionUID:

-1651885517252689369L

Serialized Fields

matrix

SparseDoubleMatrix2D matrix

Class ubic.gemma.core.util.matrix.StringMatrix

class StringMatrix extends AbstractMatrix<R,C,String> implements Serializable

serialVersionUID:

-7369003979104984162L

Serialized Fields

matrix

DenseObjectMatrix2D matrix

Package ubic.gemma.core.visualization

Class ubic.gemma.core.visualization.ExpressionDataHeatmap

class ExpressionDataHeatmap extends Object implements Serializable

Serialized Fields

assayIndex

int[] assayIndex

assays

List<BioAssay> assays

bioAssaySet

BioAssaySet bioAssaySet

cellLevelCharacteristics

CellLevelCharacteristics cellLevelCharacteristics

cellSize

int cellSize

designElements

Slice<CompositeSequence> designElements

dimension

BioAssayDimension dimension

focusedCellLevelCharacteristic

Characteristic focusedCellLevelCharacteristic

genes

List<Gene> genes

List of genes to use for display purposes.

singleCellQuantitationType

QuantitationType singleCellQuantitationType

Quantitation type of the single-cell data this heatmap was generated from, if applicable.

transpose

boolean transpose

vectors

Slice<? extends BulkExpressionDataVector> vectors

Class ubic.gemma.core.visualization.SingleCellSparsityHeatmap

class SingleCellSparsityHeatmap extends Object implements Serializable

Serialized Fields

cellSize

int cellSize

designElementsPerSample

Map<BioAssay,Long> designElementsPerSample

dimension

BioAssayDimension dimension

expressionExperiment

ExpressionExperiment expressionExperiment

samples

List<BioAssay> samples

singleCellDimension

SingleCellDimension singleCellDimension

subSets

List<ExpressionExperimentSubSet> subSets

transpose

boolean transpose

type

SingleCellSparsityHeatmap.SingleCellHeatmapType type

Package ubic.gemma.model.analysis

Class ubic.gemma.model.analysis.AnalysisResultSetValueObject

class AnalysisResultSetValueObject extends IdentifiableValueObject<R extends AnalysisResultSet<K>> implements Serializable

Class ubic.gemma.model.analysis.AnalysisResultValueObject

class AnalysisResultValueObject extends IdentifiableValueObject<A extends AnalysisResult> implements Serializable

Class ubic.gemma.model.analysis.AnalysisValueObject

class AnalysisValueObject extends IdentifiableValueObject<T extends Analysis> implements Serializable

Serialized Fields

name

String name

protocol

ProtocolValueObject protocol

Class ubic.gemma.model.analysis.CellTypeAssignmentValueObject

class CellTypeAssignmentValueObject extends AnalysisValueObject<CellTypeAssignment> implements Serializable

Serialized Fields

cellTypeIds

List<Long> cellTypeIds

A list of IDs, one-per-cell, that refers to one of the cell type labels in CellTypeAssignmentValueObject.cellTypes.

null is used to indicate an unknown cell type.

cellTypes

Set<CharacteristicValueObject> cellTypes

A set of cell types that are assigned to individual cells.

isPreferred

boolean isPreferred

Indicate if this assignment is the preferred one.

numberOfAssignedCells

Integer numberOfAssignedCells

Indicate how many cells have an assigned cell type, or null if this information is not available.

numberOfAssignedCellsByCellType

Map<Long,Integer> numberOfAssignedCellsByCellType

How many cells carry each cell type, keyed by the id of the entry in CellTypeAssignmentValueObject.cellTypes. null when the indices are unavailable.

The tally comes off the same cellTypeIndices array CellTypeAssignmentValueObject.cellTypeIds is built from, so it costs one extra pass and no extra query. It exists because the per-cell array was the only way to answer "how many astrocytes" — 89,700 entries and 809 KB on one dataset to recover ten numbers (uib, 2026-09-03) — and a client that only needs the tally can now exclude the array outright.

Class ubic.gemma.model.analysis.ProtocolValueObject

class ProtocolValueObject extends IdentifiableValueObject<Protocol> implements Serializable

Serialized Fields

description

String description

name

String name

Package ubic.gemma.model.analysis.expression.diff

Class ubic.gemma.model.analysis.expression.diff.ContrastResultValueObject

class ContrastResultValueObject extends IdentifiableValueObject<ContrastResult> implements Serializable

Serialized Fields

coefficient

Double coefficient

factorValue

FactorValueBasicValueObject factorValue

factorValueId

Long factorValueId

logFoldChange

Double logFoldChange

pvalue

Double pvalue

The four contrast statistics are rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out; see DifferentialExpressionAnalysisResultValueObject for why significant digits and why at serialization time rather than in the constructor.

secondFactorValue

FactorValueBasicValueObject secondFactorValue

secondFactorValueId

Long secondFactorValueId

tStat

Double tStat

Class ubic.gemma.model.analysis.expression.diff.ContrastsValueObject

class ContrastsValueObject extends Object implements Serializable

Serialized Fields

contrasts

List<ContrastVO> contrasts

resultId

Long resultId

Class ubic.gemma.model.analysis.expression.diff.ContrastVO

class ContrastVO extends Object implements Serializable

Serialized Fields

factorValueId

Long factorValueId

id

Long id

logFoldChange

Double logFoldChange

pvalue

Double pvalue

secondFactorValueId

Long secondFactorValueId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultSetValueObject

class DifferentialExpressionAnalysisResultSetValueObject extends AnalysisResultSetValueObject<DifferentialExpressionAnalysisResult, ExpressionAnalysisResultSet> implements Serializable

Serialized Fields

analysis

DifferentialExpressionAnalysisValueObject analysis

baselineGroup

FactorValueBasicValueObject baselineGroup

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

results

Collection<DifferentialExpressionAnalysisResultValueObject> results

Related analysis results.

Note that this field is excluded from the JSON serialization if left unset.

secondBaselineGroup

FactorValueBasicValueObject secondBaselineGroup

taxa

Set<TaxonValueObject> taxa

When genes are included, this field is populated.

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisResultValueObject

class DifferentialExpressionAnalysisResultValueObject extends AnalysisResultValueObject<DifferentialExpressionAnalysisResult> implements Serializable

Serialized Fields

contrasts

List<ContrastResultValueObject> contrasts

correctedPvalue

Double correctedPvalue

Rounded on the way out, as pValue is.

genes

List<GeneValueObject> genes

probeId

Long probeId

probeName

String probeName

pValue

Double pValue

Rounded to RoundingUtils.JSON_SIGNIFICANT_DIGITS significant digits on the way out. Significant digits rather than decimal places because a p-value of 1e-300 has to survive.

Rounding happens at serialization, not in the constructor: getDatasetsDifferentialExpression ranks rows by corrected p-value, and rounding before that sort can reorder near-ties.

rank

Double rank

resultSetId

Long resultSetId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysisValueObject

class DifferentialExpressionAnalysisValueObject extends AnalysisValueObject<DifferentialExpressionAnalysis> implements Serializable

serialVersionUID:

622877438067070041L

Serialized Fields

arrayDesignsUsed

Collection<Long> arrayDesignsUsed

bioAssaysAnalyzed

Collection<BioAssayValueObject> bioAssaysAnalyzed

The BioAssays analyzed in this differential expression analysis.

This is filled in very narrow cases since it can be quite large. Use DifferentialExpressionAnalysisValueObject.experimentAnalyzedId for a more reliable way of retrieving the analyzed experiment and then its assays.

experimentAnalyzedId

Long experimentAnalyzedId

factorValuesUsed

Map<Long, Collection<FactorValueValueObject>> factorValuesUsed

resultSets

Collection<DiffExResultSetSummaryValueObject> resultSets

sourceExperimentId

Long sourceExperimentId

subsetFactor

ExperimentalFactorValueObject subsetFactor

subsetFactorId

Long subsetFactorId

subsetFactorValue

FactorValueValueObject subsetFactorValue

subsetFactorValueId

Long subsetFactorValueId

Class ubic.gemma.model.analysis.expression.diff.DifferentialExpressionValueObject

class DifferentialExpressionValueObject extends Object implements Serializable

Serialized Fields

contrasts

ContrastsValueObject contrasts

corrP

Double corrP

direction

Direction direction

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

expressionExperiment

BioAssaySetValueObject expressionExperiment

fisherContribution

Boolean fisherContribution

gene

GeneValueObject gene

id

Long id

metThreshold

Boolean metThreshold

p

Double p

probe

String probe

probeId

Long probeId

resultSetId

Long resultSetId

sortKey

String sortKey

Class ubic.gemma.model.analysis.expression.diff.DiffExprGeneSearchResult

class DiffExprGeneSearchResult extends Object implements Serializable

serialVersionUID:

-6199218806972657112L

Serialized Fields

analysisResultId

Long analysisResultId

correctedPvalue

Double correctedPvalue

geneId

Long geneId

numberOfProbes

int numberOfProbes

numberOfProbesDiffExpressed

int numberOfProbesDiffExpressed

pvalue

Double pvalue

resultSetId

Long resultSetId

score

Double score

Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject

class DiffExResultSetSummaryValueObject extends Object implements Serializable

serialVersionUID:

2063274043081170625L

Serialized Fields

analysisId

Long analysisId

arrayDesignsUsed

Collection<Long> arrayDesignsUsed

baselineGroup

FactorValueValueObject baselineGroup

bioAssaysAnalyzed

Collection<BioAssayValueObject> bioAssaysAnalyzed

List of BioAssays analyzed

bioAssaySetAnalyzedId

Long bioAssaySetAnalyzedId

Analyzed BioAssaySet ID.

This is redundant because of DifferentialExpressionAnalysisValueObject.getExperimentAnalyzedId(), and always displayed in that context in the RESTful API.

downregulatedCount

Integer downregulatedCount

Number of diffex probes in the Direction.DOWN hit list if available.

experimentalFactors

Collection<ExperimentalFactorValueObject> experimentalFactors

factorIds

Collection<Long> factorIds

id

Long id

numberOfDiffExpressedProbes

Integer numberOfDiffExpressedProbes

Number of diffex probes in the Direction.EITHER hit list if available.

numberOfGenesAnalyzed

Integer numberOfGenesAnalyzed

numberOfProbesAnalyzed

Integer numberOfProbesAnalyzed

threshold

Double threshold

Threshold applied to the hitlist.

upregulatedCount

Integer upregulatedCount

Number of diffex probes in the Direction.UP hit list if available.

Class ubic.gemma.model.analysis.expression.diff.DiffExResultSetSummaryValueObject.Prefetch

class Prefetch extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

baselineGroup

FactorValue baselineGroup

experimentalFactors

Set<ExperimentalFactor> experimentalFactors

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisDetailValueObject

class GeneDifferentialExpressionMetaAnalysisDetailValueObject extends Object implements Serializable

serialVersionUID:

3868004995989355452L

Serialized Fields

includedResultSetsInfo

Collection<IncludedResultSetInfoValueObject> includedResultSetsInfo

numGenesAnalyzed

Integer numGenesAnalyzed

results

Collection<GeneDifferentialExpressionMetaAnalysisResultValueObject> results

Class ubic.gemma.model.analysis.expression.diff.GeneDifferentialExpressionMetaAnalysisResultValueObject

class GeneDifferentialExpressionMetaAnalysisResultValueObject extends Object implements Serializable

serialVersionUID:

6099286095885830140L

Serialized Fields

geneName

String geneName

geneSymbol

String geneSymbol

metaPvalue

Double metaPvalue

metaQvalue

Double metaQvalue

upperTail

Boolean upperTail

Class ubic.gemma.model.analysis.expression.diff.IncludedResultSetInfoValueObject

class IncludedResultSetInfoValueObject extends Object implements Serializable

serialVersionUID:

-4660741839991839187L

Serialized Fields

analysisId

Long analysisId

experimentId

Long experimentId

resultSetId

Long resultSetId

Class ubic.gemma.model.analysis.expression.diff.ResultSetCountsValueObject

class ResultSetCountsValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

downregulatedCount

Integer downregulatedCount

numberOfDiffExpressedProbes

Integer numberOfDiffExpressedProbes

numberOfGenesAnalyzed

Integer numberOfGenesAnalyzed

numberOfProbesAnalyzed

Integer numberOfProbesAnalyzed

threshold

Double threshold

upregulatedCount

Integer upregulatedCount

Package ubic.gemma.model.analysis.sequence

Class ubic.gemma.model.analysis.sequence.GeneMappingSummary

class GeneMappingSummary extends Object implements Serializable

serialVersionUID:

8899320580201273360L

Serialized Fields

blatResult

BlatResultValueObject blatResult

blatResultId

String blatResultId

compositeSequence

CompositeSequenceValueObject compositeSequence

geneProductIdGeneMap

Map<String, GeneValueObject> geneProductIdGeneMap

geneProductIdMap

Map<String, GeneProductValueObject> geneProductIdMap

geneProductMap

Map<GeneProductValueObject, GeneValueObject> geneProductMap

identity

double identity

score

double score

Class ubic.gemma.model.analysis.sequence.GeneMappingSummaryValueObject

class GeneMappingSummaryValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

blatResult

BlatResultValueObject blatResult

The alignment this mapping rests on, carrying the scores (identity, score), the genomic coordinates, and the probe's biological sequence under querySequence.

Null only for mappings that come from an annotation association rather than a real alignment.

genes

List<GeneReferenceValueObject> genes

Genes this alignment supports, deduplicated — a gene reached through several of its gene products appears once. Empty for an alignment that maps to no gene, which is a real and reportable outcome rather than a missing value.

Package ubic.gemma.model.blacklist

Class ubic.gemma.model.blacklist.BlacklistedValueObject

class BlacklistedValueObject extends IdentifiableValueObject<BlacklistedEntity> implements Serializable

serialVersionUID:

-4817418347388923905L

Serialized Fields

accession

String accession

externalDatabase

ExternalDatabaseValueObject externalDatabase

name

String name

reason

String reason

shortName

String shortName

type

String type

Package ubic.gemma.model.common

Class ubic.gemma.model.common.BaseValueObject

class BaseValueObject extends Object implements Serializable

serialVersionUID:

-5290562301261202171L

Serialized Fields

accessDenied

boolean accessDenied

errorFound

boolean errorFound

objectAlreadyRemoved

boolean objectAlreadyRemoved

userNotLoggedIn

boolean userNotLoggedIn

valueObject

Serializable valueObject

Class ubic.gemma.model.common.IdentifiableValueObject

class IdentifiableValueObject extends Object implements Serializable

Serialized Fields

id

Long id

Exception Class ubic.gemma.model.common.NonUniqueDescribableByNameException

class NonUniqueDescribableByNameException extends IllegalArgumentException implements Serializable

Package ubic.gemma.model.common.auditAndSecurity

Class ubic.gemma.model.common.auditAndSecurity.AuditEventValueObject

class AuditEventValueObject extends IdentifiableValueObject<AuditEvent> implements Serializable

serialVersionUID:

1L

Serialized Fields

action

String action

date

Date date

detail

String detail

eventType

Class<? extends AuditEventType> eventType

note

String note

onBehalfOf

String onBehalfOf

The curator an agent acted for, when the credential that authenticated the write is not the person who asked for it.

AuditEventValueObject.performer is the authenticated principal, so an agent commit is stamped with the agent's own account whoever requested it. This names the requester beside it. Null on any event written directly by the account that performed it, which is every event before 2026-09-05.

performer

String performer

Class ubic.gemma.model.common.auditAndSecurity.GroupAuthority

class GroupAuthority extends AbstractIdentifiable implements Serializable

Serialized Fields

authority

String authority

Package ubic.gemma.model.common.auditAndSecurity.curation

Class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

class AbstractCuratableValueObject extends IdentifiableValueObject<C extends Curatable> implements Serializable

Serialized Fields

curationNote

String curationNote

lastNeedsAttentionEvent

AuditEventValueObject lastNeedsAttentionEvent

lastNoteUpdateEvent

AuditEventValueObject lastNoteUpdateEvent

lastTroubledEvent

AuditEventValueObject lastTroubledEvent

lastUpdated

Date lastUpdated

needsAttention

boolean needsAttention

troubled

boolean troubled

Class ubic.gemma.model.common.auditAndSecurity.curation.AnnotationSetSummaryValueObject

class AnnotationSetSummaryValueObject extends IdentifiableValueObject<AnnotationSet> implements Serializable

serialVersionUID:

1L

Serialized Fields

agentName

String agentName

agentVersion

String agentVersion

createdAt

Date createdAt

createdBy

String createdBy

datasetShortName

String datasetShortName

The dataset's short name (GSE6966), so a list row can name its experiment.

The inbox groups rows by experiment and labels each group; carrying only investigationId cost a fetch per row to print the label (uib, 2026-09-04). Null when the investigation is not an ExpressionExperiment -- the join that supplies it is a LEFT join for exactly that reason, so a set on some other Investigation subtype still appears in the list rather than vanishing from it.

factorCount

Integer factorCount

Derived hint; null means unknown, never zero. See AnnotationSetPayloadCounts.

finalizedAt

Date finalizedAt

finalizedBy

String finalizedBy

investigationId

Long investigationId

kind

AgentCurationKind kind

model

String model

parentId

Long parentId

payloadSize

Long payloadSize

Size of the omitted payloadJson in characters. UI uses this to gate a fetch-full vs skip decision. Null when the database could not compute it (e.g. CLOB length unsupported in some projection paths).

ranAt

Date ranAt

role

AnnotationSetRole role

runId

String runId

runSha

String runSha

source

AnnotationSetSource source

status

String status

Where a proposal stands with its reviewer. A free string, not an enum -- see AnnotationSet.getStatus(). Null on roles that are not reviewed.

tagCount

Integer tagCount

Derived hint; null means unknown, never zero. See AnnotationSetPayloadCounts.

updatedAt

Date updatedAt

Class ubic.gemma.model.common.auditAndSecurity.curation.CurationDetailsValueObject

class CurationDetailsValueObject extends IdentifiableValueObject<CurationDetails> implements Serializable

Serialized Fields

curationNote

String curationNote

curationPending

Boolean curationPending

Whether curation of the dataset is under way right now.

Administrators only, like curationNote beside it. Derived from the curation lock: true exactly while an unexpired claim exists. It names nobody, and it lapses with the lease rather than waiting on a sign-off, so a curator who only relabels does not leave it stuck on.

lastNeedsAttentionEvent

AuditEventValueObject lastNeedsAttentionEvent

lastNoteUpdateEvent

AuditEventValueObject lastNoteUpdateEvent

lastTroubledEvent

AuditEventValueObject lastTroubledEvent

lastUpdated

Date lastUpdated

needsAttention

boolean needsAttention

troubled

boolean troubled

Class ubic.gemma.model.common.auditAndSecurity.curation.CurationLock

class CurationLock extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

agentName

String agentName

Which agent, when the holder is one. Null for a person. Matches ANNOTATION_SET.AGENT_NAME.

expiresAt

Date expiresAt

When the claim lapses. Refreshed by curator activity (each draft autosave), so working holds the lease and walking away releases it — one signal rather than an explicit unlock nobody remembers.

investigation

Investigation investigation

investigationId

Long investigationId

The primary key, derived from CurationLock.investigation by @MapsId rather than declared on the association itself.

With @Id on the @OneToOne, Hibernate treats the identifier type as the entity and warns HHH000038/HHH000039 that the composite-id class overrides neither equals() nor hashCode() — on every startup. Supplying those on the entity is the wrong answer here: an id that flips from null to a value on persist is the hashCode footgun this codebase has been bitten by. A derived Long identifier removes the composite id altogether, and makes session.get( CurationLock.class, ee.getId() ) correct by construction rather than by coincidence — that call already passed a Long against an identifier declared as an Investigation.

The table is unchanged: INVESTIGATION_FK remains the single primary-key column, so no migration goes with this.

lockedAt

Date lockedAt

lockedBy

String lockedBy

Whatever identity the holder authenticated as. VARCHAR(255) rather than an FK to CONTACT, matching AnnotationSet.getCreatedBy() — an FK would make the lock un-writable for any identity without a Gemma Contact row.

runId

String runId

What is holding this, when the holder is a job rather than a person.

A blocked curator has to choose between waiting and stealing, and CurationLock.lockedBy alone cannot tell them: an agent acting via ?onBehalfOf= records the CURATOR there, which is right, and leaves nothing naming the run. Written at acquire time because a batch takes its locks BEFORE doing the work, so joining to the holder's draft would answer only once the answer stopped being needed.

Null for a person. Matches ANNOTATION_SET.RUN_ID, so the same run is the same string in both places -- adhoc-decision-ticket, category-policy-rebuild-2026-08-09.

stolenAt

Date stolenAt

stolenFrom

String stolenFrom

Previous holder, when this row was taken by a steal.

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketEventValueObject

class TicketEventValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

actorId

Long actorId

actorName

String actorName

id

Long id

occurredAt

Date occurredAt

payload

String payload

type

TicketEventType type

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketSearchHitValueObject

class TicketSearchHitValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

priority

TicketPriority priority

The ticket's priority. Never null: Ticket defaults it to TicketPriority.NORMAL.

state

TicketState state

targetCount

long targetCount

How many TicketTargets the ticket holds. A count, never the targets themselves.

title

String title

type

TicketType type

updatedAt

Date updatedAt

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketSummaryForTargetValueObject

class TicketSummaryForTargetValueObject extends TicketSearchHitValueObject implements Serializable

serialVersionUID:

1L

Serialized Fields

targetStatus

TicketTargetStatus targetStatus

This target's status on this ticket. Never null: TicketTarget defaults it to TicketTargetStatus.NOT_DONE.

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketTargetValueObject

class TicketTargetValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

displayLabel

String displayLabel

Short display label for the target (e.g. an EE's shortName like GSE12345). null when no cheap join is available.

displayName

String displayName

Human-readable name for the target (e.g. an EE's full name). null when no cheap join is available.

id

Long id

screeningResult

ScreeningResult screeningResult

screeningResultReason

String screeningResultReason

status

TicketTargetStatus status

targetId

Long targetId

targetType

TicketTargetType targetType

Class ubic.gemma.model.common.auditAndSecurity.curation.TicketValueObject

class TicketValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

acceptsTargets

boolean acceptsTargets

Whether experiments may be added to this ticket after it was opened. False unless a curator has opened the ticket up — a scratchpad. Note a RESOLVED ticket refuses additions even when this is true, so this alone does not tell a client the add will succeed.

assigneeId

Long assigneeId

assigneeName

String assigneeName

body

String body

Curator-facing instructions text. May be empty for tickets filed by scripts that didn't set a body. Empty string (not null) on serialization to match the UI contract — see TicketValueObject TypeScript interface in gemma-curation-ui.

createdAt

Date createdAt

dueDate

Date dueDate

events

List<TicketEventValueObject> events

externalIssueSyncState

ExternalIssueSyncState externalIssueSyncState

externalIssueUrl

String externalIssueUrl

id

Long id

mode

TicketMode mode

How the ticket advances between actions. MANUAL (default) requires explicit curator action for each step; AUTO auto-schedules the next defined action when the current one finishes with all targets DONE.

payload

String payload

What the screen that produced this ticket asked, verbatim and opaque.

See Also:

• Ticket.getPayload()

payloadSchemaVersion

Integer payloadSchemaVersion

Which schema TicketValueObject.payload follows; null when the writer declared none.

On the wire beside the payload on purpose — a version a client cannot read is a version that does not exist for it.

priority

TicketPriority priority

reporterId

Long reporterId

reporterName

String reporterName

state

TicketState state

targets

List<TicketTargetValueObject> targets

title

String title

type

TicketType type

updatedAt

Date updatedAt

Package ubic.gemma.model.common.description

Class ubic.gemma.model.common.description.AnnotationValueObject

class AnnotationValueObject extends IdentifiableValueObject<Characteristic> implements Serializable

Serialized Fields

category

String category

Category label. Same field as Characteristic.getCategory(), under the same name.

categoryUri

String categoryUri

Category URI. Same field as Characteristic.getCategoryUri(), under the same name.

description

String description

evidenceCode

String evidenceCode

object

String object

objectClass

String objectClass

objectUri

String objectUri

parentDescription

String parentDescription

parentLink

String parentLink

parentName

String parentName

parentOfParentDescription

String parentOfParentDescription

parentOfParentLink

String parentOfParentLink

parentOfParentName

String parentOfParentName

predicate

String predicate

Predicate label for Statement-backed annotations (e.g. "has_dose"). Null when the underlying row is a plain Characteristic. The predicate* / object* pair, together with the optional secondPredicate* / secondObject* pair, exposes the Statement relational shape to read-side consumers without breaking the Characteristic wire shape — AnnotationValueObject.valueUri and AnnotationValueObject.value carry the statement's subject URI and label (Statement aliases subject → value internally).

predicateUri

String predicateUri

secondObject

String secondObject

secondObjectUri

String secondObjectUri

secondPredicate

String secondPredicate

secondPredicateUri

String secondPredicateUri

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

Verbatim provenance backing a curated tag — a JSON array of {quote, source, location, ...} items the curation agents emitted (the agents-side FindingEvidence shape). Gemma stores and serves it opaquely, so the agents repo owns the schema. Null when the tag has no recorded evidence (plain/legacy tags, and ontology-term hits that were never accepted from a proposal).

value

String value

Label of the annotated term — the value as curated. On a Statement row this is the subject's label, and the predicate / object labels stay in their own fields: this field never carries a composed sentence. FactorValueUtils.getSummaryString(FactorValue) is the separate sentence-builder for display.

valueUri

String valueUri

URI of the annotated term. On a Statement row this is the subject's URI.

Class ubic.gemma.model.common.description.BibliographicReferenceValueObject

class BibliographicReferenceValueObject extends IdentifiableValueObject<BibliographicReference> implements Serializable

Serialized Fields

abstractText

String abstractText

authorList

String authorList

chemicalsTerms

Collection<String> chemicalsTerms

citation

CitationValueObject citation

experiments

Collection<ExpressionExperimentValueObject> experiments

issue

String issue

meshTerms

Collection<String> meshTerms

pages

String pages

pubAccession

String pubAccession

publication

String publication

publicationDate

Date publicationDate

publisher

String publisher

retracted

boolean retracted

title

String title

volume

String volume

Class ubic.gemma.model.common.description.CharacteristicValueObject

class CharacteristicValueObject extends IdentifiableValueObject<Characteristic> implements Serializable

Serialized Fields

alreadyPresentInDatabase

boolean alreadyPresentInDatabase

alreadyPresentOnGene

boolean alreadyPresentOnGene

category

String category

categoryUri

String categoryUri

child

boolean child

child term from a root

numTimesUsed

int numTimesUsed

ontologyUsed

String ontologyUsed

what Ontology uses this term

originalValue

String originalValue

The submitter's own wording, as it arrived — before curation replaced CharacteristicValueObject.value with an ontology label, and before a compound field was split.

Once value has been grounded the original is not recoverable from anything else on the wire: organism part: "hypothalamus" does not say the submitter wrote tissue: "Hypothalamus". That makes two questions unanswerable without it — "is this the right resolution of what they actually wrote?" and "what literal should a curator revisit when no term covers it?" (a mouse cohort aged "2-3 months" straddles two stages; the span is real and only the literal carries it). Curators were preserving such strings by hand in free-text tags because nothing surfaced this field.

Null means "not recorded", NEVER "same as value". It is populated at GEO import and backfilled from the pre-edit value when a curator grounds a tag, so it is absent for rows written through the curation API and for anything that never had a distinct original. A consumer that reads null as "unchanged" turns an unknown into a confirmed no-op.

Serialized only when present. Was withheld from REST under the old @GemmaWebOnly marker until the field's only consumer, Gemma Web, was retired.

privateGeneCount

long privateGeneCount

publicGeneCount

long publicGeneCount

number of occurrences in all genes

root

boolean root

root of a query

supplementary

boolean supplementary

True when this candidate came from a flat lexical catalogue (MGI names, Cellosaurus) rather than a conventional ontology.

These sources exist to back-fill names the ontologies lack, and their index applies a large exact-name boost whose scores are not comparable with a Jena index's — which is why OntologyServiceImpl.findTermsInexact ranks them below every conventional hit rather than merging them. Carrying the flag onto the value object lets the ranking layers keep that distinction instead of re-deriving it from URI namespaces one pair at a time.

Provenance rather than identity, so it is excluded from equals/hashCode: the same term reached through two sources is the same term.

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

Verbatim provenance backing a curated characteristic — a JSON array of {quote, source, location, …} items the curation agents emitted. Gemma stores and serves it opaquely; the agents repo owns the schema.

This is the field that answers "where did this come from" for an ExperimentalFactor's category, which is a Characteristic like any other and therefore already has the storage. Null means "nothing recorded", which is the expected reading for most rows — it is not an error and must not be rendered as one.

Provenance rather than identity, so it is excluded from equals/hashCode for the same reason CharacteristicValueObject.supplementary is: the same term reached with and without recorded evidence is the same term, and including it here would break the de-duplication the search paths rely on.

taxon

String taxon

urlId

String urlId

id used by url on the client side

value

String value

valueDefinition

String valueDefinition

The definition of the value, if it is an ontology term, as supplied by the ontology. If the value is free text, this will be empty

valueId

String valueId

A unique ontology identifier (i.e. IRI) for this characteristic.

valueUri

String valueUri

Class ubic.gemma.model.common.description.CitationValueObject

class CitationValueObject extends Object implements Serializable

Serialized Fields

citation

String citation

id

Long id

The ID of the BibliographicReference being represented.

pubmedAccession

String pubmedAccession

pubmedURL

String pubmedURL

retracted

boolean retracted

Class ubic.gemma.model.common.description.DatabaseEntryValueObject

class DatabaseEntryValueObject extends IdentifiableValueObject<DatabaseEntry> implements Serializable

serialVersionUID:

-527323410580090L

Serialized Fields

accession

String accession

externalDatabase

ExternalDatabaseValueObject externalDatabase

label

String label

A label for display purposes.

This is usually the DatabaseEntryValueObject.accession, but for some databases, it may be a bit cryptic for the end-user, so another string is used.

uri

String uri

Class ubic.gemma.model.common.description.DatasetPublicationValueObject

class DatasetPublicationValueObject extends BibliographicReferenceValueObject implements Serializable

Serialized Fields

association

PublicationAssociationValueObject association

Class ubic.gemma.model.common.description.ExternalDatabaseValueObject

class ExternalDatabaseValueObject extends IdentifiableValueObject<ExternalDatabase> implements Serializable

serialVersionUID:

-1714429166594162374L

Serialized Fields

checked

boolean checked

description

String description

externalDatabases

Set<ExternalDatabaseValueObject> externalDatabases

lastUpdated

Date lastUpdated

name

String name

releaseUrl

URL releaseUrl

releaseVersion

String releaseVersion

uri

String uri

Package ubic.gemma.model.common.measurement

Class ubic.gemma.model.common.measurement.MeasurementValueObject

class MeasurementValueObject extends IdentifiableValueObject<Measurement> implements Serializable

Serialized Fields

representation

String representation

type

String type

unit

String unit

unitId

Long unitId

value

String value

Package ubic.gemma.model.common.quantitationtype

Class ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject

class QuantitationTypeValueObject extends IdentifiableValueObject<QuantitationType> implements Serializable

serialVersionUID:

7537853492100102404L

Serialized Fields

description

String description

expressionExperimentId

Long expressionExperimentId

Associated expression experiment ID.

This is unnecessary in the context of the RESTful API because vector types are always retrieved when the associated ExpressionExperiment is known.

generalType

String generalType

isBackground

boolean isBackground

isBackgroundSubtracted

boolean isBackgroundSubtracted

isBatchCorrected

boolean isBatchCorrected

isMaskedPreferred

boolean isMaskedPreferred

Deprecated.

isNormalized

boolean isNormalized

isPreferred

boolean isPreferred

True when this quantitation type is preferred in ANY of the three senses Gemma records: the preferred processed data, the preferred single-cell data, or the preferred masked data.

🛑 It is an OR, so it does not identify one quantitation type per experiment. A single-cell dataset normally has three that answer true — the single-cell counts, the aggregate, and the masked aggregate — and after a re-aggregation the superseded cut keeps its masked-preferred flag, so two subset groups can each hold one. A client picking "the live cut" by this field alone resolved the wrong group on 2 of 92 single-cell datasets (uib, 2026-09-03). QuantitationTypeValueObject.isMaskedPreferred and QuantitationTypeValueObject.isSingleCellPreferred say which flag fired; isPreferred && !isMaskedPreferred && !isSingleCellPreferred is the processed-data sense on its own.

isRatio

boolean isRatio

isRecomputedFromRawData

boolean isRecomputedFromRawData

isSingleCellPreferred

boolean isSingleCellPreferred

True when this is the preferred single-cell quantitation type.

One of the three flags QuantitationTypeValueObject.isPreferred ORs together. Exposed because it was the only one of them a client could not see, which left isPreferred true with no way to tell why.

name

String name

representation

String representation

scale

String scale

type

String type

vectorType

String vectorType

Vector type this QT is associated to.

This only makes sense in the context of an associated EE.

Package ubic.gemma.model.common.search

Class ubic.gemma.model.common.search.SearchSettingsValueObject

class SearchSettingsValueObject extends Object implements Serializable

serialVersionUID:

-934534534L

Serialized Fields

datasetConstraint

String datasetConstraint

maxResults

Integer maxResults

platformConstraint

String platformConstraint

query

String query

searchBibrefs

boolean searchBibrefs

searchBioSequences

boolean searchBioSequences

searchExperiments

boolean searchExperiments

searchExperimentSets

boolean searchExperimentSets

searchGenes

boolean searchGenes

searchGeneSets

boolean searchGeneSets

searchPlatforms

boolean searchPlatforms

searchProbes

boolean searchProbes

taxonConstraint

String taxonConstraint

termUri

String termUri

useCharacteristics

boolean useCharacteristics

useDatabase

boolean useDatabase

useGo

boolean useGo

useIndices

boolean useIndices

Package ubic.gemma.model.expression.arrayDesign

Class ubic.gemma.model.expression.arrayDesign.ArrayDesignReferenceValueObject

class ArrayDesignReferenceValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

Gemma-internal platform id, suitable for GET /platforms/{id}.

name

String name

Full name, e.g. Affymetrix GeneChip Human Genome U133A 2.0 Array.

The short name is an accession and the full name is the only part a curator reads as a description of the hardware, so a reference that carries only the accession cannot in fact name the platform it points at.

shortName

String shortName

Short name, e.g. GPL96. This is what a page displays.

technologyType

String technologyType

What kind of platform it is — ONECOLOR, TWOCOLOR, SEQUENCING, GENELIST, OTHER. Rendered as the enum's name.

Here because a client that has to say whether a dataset is a microarray or a sequencing run was otherwise reduced to matching the platform's NAME against a pattern — which reads correctly for Affymetrix GeneChip … by luck and returns nothing for a sequencing platform that does not say so in its name (uib, 2026-08-28).

Class ubic.gemma.model.expression.arrayDesign.ArrayDesignValueObject

class ArrayDesignValueObject extends AbstractCuratableValueObject<ArrayDesign> implements Serializable

serialVersionUID:

-8259245319391937522L

Serialized Fields

blackListed

Boolean blackListed

color

String color

Deprecated.

createDate

Date createDate

dateCached

String dateCached

description

String description

designElementCount

Integer designElementCount

expressionExperimentCount

Long expressionExperimentCount

externalReferences

Set<DatabaseEntryValueObject> externalReferences

Main external reference.

geneCountsLastUpdated

String geneCountsLastUpdated

When the report backing ArrayDesignValueObject.numberOfGenes / ArrayDesignValueObject.numberOfMappedElements was written, as yyyy.MM.dd HH:mm.

Null when the counts were derived live rather than read from a report (gene-list platforms, where the element count answers both), or when no counts were populated at all. Exposed because a count read from a monthly report is not the same claim as a fresh one, and a client showing the number should be able to say how old it is.

hasBlatAssociations

Boolean hasBlatAssociations

hasGeneAssociations

Boolean hasGeneAssociations

hasSequenceAssociations

Boolean hasSequenceAssociations

isAffymetrixAltCdf

Boolean isAffymetrixAltCdf

isMerged

Boolean isMerged

Indicates this array design is the merger of other array designs.

isMergee

Boolean isMergee

Indicates that this array design has been merged into another.

isSubsumed

Boolean isSubsumed

Indicate if this array design is subsumed by some other array design.

isSubsumer

Boolean isSubsumer

Indicates if this array design subsumes some other array design(s)

lastGeneMapping

Date lastGeneMapping

lastRepeatMask

Date lastRepeatMask

lastSequenceAnalysis

Date lastSequenceAnalysis

lastSequenceUpdate

Date lastSequenceUpdate

mergedInto

ArrayDesignReferenceValueObject mergedInto

The platform this one was merged into, or null when it was not merged.

The companion to ArrayDesignValueObject.isMergee, which says only THAT a merge happened. Batch-hydrated in ArrayDesignDaoImpl.populateMergeRelations; the association is LAZY on the entity, so reading shortName off the proxy inside the constructor would fire one extra query per row of a listing.

mergees

List<ArrayDesignReferenceValueObject> mergees

The platforms merged INTO this one — the inverse of ArrayDesignValueObject.mergedInto, empty when there are none. Companion to ArrayDesignValueObject.isMerged.

name

String name

numberOfGenes

Long numberOfGenes

Distinct genes the platform's elements map to, or null when the caller did not ask.

Opt-in via ?withGeneCounts=true; see ArrayDesignDao.getGeneCounts(Collection) for why it is not computed by default.

numberOfMappedElements

Long numberOfMappedElements

Elements on the platform that map to at least one gene, or null when the caller did not ask. Pairs with ArrayDesignValueObject.numberOfGenes and comes from the same query — the difference between the two is what tells a reader whether a platform is densely or sparsely annotated.

numGenes

String numGenes

The number of unique genes that this array design maps to.

Report-era field: a String, written by ArrayDesignReportService into a disk-serialized report and never populated on the REST path. Left as-is because those report files are Java-serialized on production and retyping the field would break reading them. The live, typed counterpart on the wire is ArrayDesignValueObject.numberOfGenes.

numProbeAlignments

String numProbeAlignments

The number of probes that have BLAT alignments.

numProbeSequences

String numProbeSequences

The number of probes that map to bioSequences.

numProbesToGenes

String numProbesToGenes

The number of probes that map to genes. This count includes probe-aligned regions, predicted genes, and known genes.

releaseUrl

URL releaseUrl

releaseVersion

String releaseVersion

shortName

String shortName

switchedExpressionExperimentCount

Long switchedExpressionExperimentCount

taxonObject

TaxonValueObject taxonObject

technologyType

String technologyType

Package ubic.gemma.model.expression.bioAssay

Class ubic.gemma.model.expression.bioAssay.BioAssayValueObject

class BioAssayValueObject extends IdentifiableValueObject<BioAssay> implements Serializable

serialVersionUID:

9164284536309673585L

Serialized Fields

accession

DatabaseEntryValueObject accession

arrayDesign

ArrayDesignValueObject arrayDesign

The platform this assay was run on, serialized as ArrayDesignReferenceValueObject — id, shortName, name, technologyType.

The full platform VO is byte-identical across every assay of a dataset and was serialized once per assay: on GET /datasets/3937/samples (278 assays) the two platform fields were 706,120 of 5,265,852 bytes, 13.4% of the response, most of it 278 copies of one platform's 1.4 kB description. GET /datasets/{id}/platforms?original=true serves the full object once for callers that want the rest of it.

The Java type stays ArrayDesignValueObject because three in-JVM readers consume it — BioAssayDimensionValueObject, DoubleVectorValueObject and DoubleVectorValueObjectUtils#toArrayDesign, the last of which reads getTaxonObject(), absent from the reference shape. So this is a serialization projection, not a type change.

description

String description

extractedMolecule

ExtractedMolecule extractedMolecule

What was extracted from the sample and assayed — GEO's molecule. Null when the source did not say, and on everything imported before this field existed.

🛑 The only thing that separates single-NUCLEUS from single-CELL RNA-seq: isSingleCell is true for both, and before this the distinction lived solely as one molecular entity characteristic among a sample's several, with no typed way to ask.

librarySelection

String librarySelection

How the library was selected — GEO's library_selection (polyA, cDNA, RANDOM, …), verbatim.

⚠️ Read beside BioAssayValueObject.extractedMolecule, not instead of it: totalRNA with a polyA selection is common and the two together are the real answer.

libraryStrategy

String libraryStrategy

What kind of library — GEO's library_strategy (RNA-Seq, scRNA-seq, Ribo-Seq, ATAC-seq, …). A string rather than an enum so a strategy nobody anticipated arrives intact instead of needing a schema change.

metadata

String metadata

name

String name

numberOfCells

Integer numberOfCells

numberOfCellsByDesignElements

Integer numberOfCellsByDesignElements

numberOfDesignElements

Integer numberOfDesignElements

originalPlatform

ArrayDesignValueObject originalPlatform

The platform this assay was originally run on before a platform switch, or null if it was never switched. Projected to ArrayDesignReferenceValueObject for the same reason as BioAssayValueObject.arrayDesign.

outlier

boolean outlier

predictedOutlier

Boolean predictedOutlier

Whether the median-correlation algorithm flags this assay as a possible outlier.

Null when it was not computed, which is the default: the calculation loads the dataset's whole sample-correlation matrix, so the sample-listing routes only do it when asked (?includePredictedOutliers=true). Absent therefore means "not computed" and is deliberately distinguishable from false, which means the algorithm ran and did not flag this assay. The curated BioAssayValueObject.outlier flag is always populated either way.

processingDate

Date processingDate

sample

BioMaterialValueObject sample

sequencePairedReads

Boolean sequencePairedReads

sequenceReadCount

Long sequenceReadCount

sequenceReadLength

Integer sequenceReadLength

shortName

String shortName

sourceBioAssayId

Long sourceBioAssayId

If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.

This is context-dependent because the parent depends on which BioAssaySet is under consideration. For example, an experiment could have two sets of EE subsets with distinct parents.

userFlaggedOutlier

boolean userFlaggedOutlier

Package ubic.gemma.model.expression.bioAssayData

Class ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject

class BioAssayDimensionValueObject extends IdentifiableValueObject<BioAssayDimension> implements Serializable

serialVersionUID:

-8686807689616396835L

Serialized Fields

bioAssays

List<BioAssayValueObject> bioAssays

description

String description

Deprecated.

isReordered

boolean isReordered

Only mutated via BioAssayDimensionValueObject.reorder(List).

isSubset

boolean isSubset

Boolean property with legacy getIsSubset()/setIsSubset() naming.

name

String name

Deprecated.

sourceBioAssayDimension

BioAssayDimensionValueObject sourceBioAssayDimension

If this is a subset, or a padded, BioAssayDimensionValueObject, the sourceBioAssayDimension is the original.

Class ubic.gemma.model.expression.bioAssayData.BooleanVectorValueObject

class BooleanVectorValueObject extends DataVectorValueObject implements Serializable

Serialized Fields

data

boolean[] data

Class ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristicsValueObject

class CellLevelCharacteristicsValueObject extends IdentifiableValueObject<CellLevelCharacteristics> implements Serializable

Serialized Fields

characteristicIds

List<Long> characteristicIds

characteristics

Set<CharacteristicValueObject> characteristics

numberOfAssignedCells

Integer numberOfAssignedCells

Indicate how many cells have an assigned characteristic, or null if this information is not available.

Class ubic.gemma.model.expression.bioAssayData.DataVectorValueObject

class DataVectorValueObject extends IdentifiableValueObject<DataVector> implements Serializable

Serialized Fields

bioAssayDimension

BioAssayDimensionValueObject bioAssayDimension

Represents the order of the bioassays for this. It might not be a real (persistent) BioAssayDimension: it might be a subset, or a "padded" one.

designElement

CompositeSequenceValueObject designElement

expressionExperiment

BioAssaySetValueObject expressionExperiment

genes

Collection<Long> genes

quantitationType

QuantitationTypeValueObject quantitationType

Class ubic.gemma.model.expression.bioAssayData.DoubleVectorValueObject

class DoubleVectorValueObject extends DataVectorValueObject implements Serializable

Serialized Fields

data

double[] data

The data of this vector.

masked

boolean masked

Indicate if this vector is "masked", i.e. it is processed.

numberOfCells

int[] numberOfCells

pvalue

Double pvalue

If this vector is associated to a statistical test (i.e. from a DE analysis), this is the P-value.

rank

Double rank

rankByMax

Double rankByMax

rankByMean

Double rankByMean

reorganized

boolean reorganized

True if the data has been rearranged relative to the bioassay dimension (as a matter of practice the bioassay dimension should be set to null if it is not valid; this boolean is an additional check)

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject

class ExperimentExpressionLevelsValueObject extends Object implements Serializable

Serialized Fields

datasetId

long datasetId

geneExpressionLevels

LinkedList<ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject> geneExpressionLevels

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject

class GeneElementExpressionsValueObject extends Object implements Serializable

Serialized Fields

correctedPvalue

Double correctedPvalue

FDR-corrected p-value for the contrast represented by the result-set used to populate this VO. Only set for the /datasets/{id}/expressions/differential endpoint; null otherwise.

elements

List<ExperimentExpressionLevelsValueObject.VectorElementValueObject> elements

Exposed via ExperimentExpressionLevelsValueObject.GeneElementExpressionsValueObject.getVectors() (legacy getter name).

geneEnsemblId

String geneEnsemblId

geneNcbiId

Integer geneNcbiId

geneOfficialName

String geneOfficialName

geneOfficialSymbol

String geneOfficialSymbol

log2FoldChange

Double log2FoldChange

Log2 fold change for the primary contrast of the represented result-set. For multi-contrast result sets the producer picks the contrast on the gene's most-significant row (smallest corrected p-value). Only set for the /datasets/{id}/expressions/differential endpoint; null otherwise.

pvalue

Double pvalue

Uncorrected p-value for the contrast represented by the result-set used to populate this VO. Only set for the /datasets/{id}/expressions/differential endpoint; null otherwise.

Class ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject.VectorElementValueObject

class VectorElementValueObject extends Object implements Serializable

Serialized Fields

bioAssayExpressionLevels

Map<String,Double> bioAssayExpressionLevels

designElementName

String designElementName

Class ubic.gemma.model.expression.bioAssayData.SingleCellDimensionValueObject

class SingleCellDimensionValueObject extends IdentifiableValueObject<SingleCellDimension> implements Serializable

Serialized Fields

bioAssayIds

List<Long> bioAssayIds

A list of BioAssay IDs that are applicable to the cells.

cellIds

List<String> cellIds

Cell identifiers.

This may be null if cell IDs are explicitly omitted (i.e. ExpressionExperimentDao.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment)), in which case it will not be serialized in JSON.

cellLevelCharacteristics

Set<CellLevelCharacteristicsValueObject> cellLevelCharacteristics

All the other cell-level characteristics.

cellTypeAssignments

Set<CellTypeAssignmentValueObject> cellTypeAssignments

All the cell type assignments.

numberOfCellIds

int numberOfCellIds

Number of cells.

This is always equal to the length of SingleCellDimensionValueObject.cellIds.

Class ubic.gemma.model.expression.bioAssayData.SlicedDoubleVectorValueObject

class SlicedDoubleVectorValueObject extends DoubleVectorValueObject implements Serializable

Serialized Fields

sourceVectorId

Long sourceVectorId

Obtain the ID of the vector from which this slice is derived from.

Package ubic.gemma.model.expression.biomaterial

Class ubic.gemma.model.expression.biomaterial.BioMaterialValueObject

class BioMaterialValueObject extends IdentifiableValueObject<BioMaterial> implements Serializable

serialVersionUID:

-145137827948521045L

Serialized Fields

assayDescription

String assayDescription

assayName

String assayName

assayProcessingDate

Date assayProcessingDate

basicFVs

boolean basicFVs

Indicate if this is using the BioMaterialValueObject.fVBasicVOs or BioMaterialValueObject.factorValueObjects for representing factor values.

bioAssayIds

Collection<Long> bioAssayIds

Related BioAssay IDs.

characteristicOriginalValues

Map<String,String> characteristicOriginalValues

Map of categories to original text values (for this biomaterial). This is only used for display and will only be populated if the original value is different from the value.

characteristics

Collection<CharacteristicValueObject> characteristics

characteristicValues

Map<String,String> characteristicValues

description

String description

factorIdToFactorValueId

Map<String,String> factorIdToFactorValueId

Map of factor ids (factor232) to factor value (id or the actual value) for this biomaterial.

factorValueObjects

Collection<FactorValueValueObject> factorValueObjects

factorValues

Map<String,String> factorValues

Map of ids (fv133) to a representation of the value (for this biomaterial.)

fastqHeaders

String fastqHeaders

fVBasicVOs

Collection<FactorValueBasicValueObject> fVBasicVOs

🛑 This field's JsonIgnore does not hide it: the payload carries an fvbasicVOs key regardless.

Lombok generates the getter as getFVBasicVOs(), and a generated getter does not inherit the field's annotations. Jackson then derives an implicit property name from each accessor independently — fVBasicVOs from the field, fvbasicVOs from the getter (the bean de-capitalization rule lowercases the whole leading run of capitals in FVBasicVOs). Those two names are not equal, so Jackson never pairs the getter with the field, the @JsonIgnore applies only to the unpaired field, and the getter serializes as a property in its own right. The same shape on BioMaterialValueObject.factorValueObjects is harmless because its getter is getFactorValueObjects(), whose implicit name does match its field.

Repeating @JsonIgnore on BioMaterialValueObject.getFVBasicVOs() closes it, and is deliberately NOT done here: fvbasicVOs has live readers in the curation-agents repos, which are being moved off it separately. Do not delete the getter either — BioAssayDimensionValueObject calls BioMaterialValueObject.getFactorValueObjects() from Java, and Java-live is not the same as wire-live.

name

String name

sourceBioMaterialId

Long sourceBioMaterialId

The BioMaterial this one was derived from, or null if this is a sample in its own right.

This is always null on GET /datasets/{dataset}/samples, for every dataset including single-cell ones, and that is the correct answer rather than missing data: that route returns the dataset's own assays, whose samples are the biological samples themselves and so derive from nothing. Derived samples are created only by single-cell aggregation, which files each {sample, cell type} population as a BioMaterial pointing back at the sample it came from, and hangs it off an ExpressionExperimentSubSet rather than the parent dataset. So the populated values are reached through GET /datasets/{dataset}/subSets/{subSet}/samples, where each value is the id of a sample the parent route returned.

Do not read this field to decide whether a dataset is single-cell: it is null on single-cell datasets too, so the test silently answers "no" everywhere. Use the pre-added assay ExperimentTag (OBI_0002631 / OBI_0003109), or GET /datasets/{dataset}/singleCellDimension, which 404s for datasets that have no single-cell data.

statements

Collection<StatementValueObject> statements

The same annotations as BioMaterialValueObject.characteristics, as statements — carrying the predicate and object when a curator wrote one.

🛑 A sample annotation can be predicated: DatasetsWebService.tagToCharacteristic builds a Statement whenever the write carries a statement field, and it is the same method that writes experiment tags. CharacteristicValueObject has no predicate or object, so before this the sample payload flattened such an annotation to its subject on every read — a curator could write a predicated sample characteristic and never see it again.

Null, and so absent from the payload, when the caller opted out with GET /datasets/{dataset}/samples?exclude=sample.statements. It is 21.5% of that response and every row in it also appears under BioMaterialValueObject.characteristics minus the predicate and object, so a client that renders only subjects can decline it. It stays on by default: an opt-out that defaults to off would put predicated sample characteristics back out of sight, which is the thing this collection was added to end.

Package ubic.gemma.model.expression.designElement

Class ubic.gemma.model.expression.designElement.CompositeSequenceValueObject

class CompositeSequenceValueObject extends IdentifiableValueObject<CompositeSequence> implements Serializable

serialVersionUID:

4915680501039784666L

Serialized Fields

arrayDesign

ArrayDesignValueObject arrayDesign

description

String description

geneMappingSummaries

List<GeneMappingSummaryValueObject> geneMappingSummaries

Per-alignment gene mappings for this element, or null when the caller did not ask for them (only GET /platforms/{platform}/elements/{probe}/mappingSummary populates this).

An EMPTY list means the probe has no gene mappings — a real answer, distinct from the field being absent. Until 2026-08-22 this field was @JsonIgnored while the endpoint computed it, so the mappingSummary response silently omitted the key altogether and a client could not tell a missing feature from a probe with no alignments.

genes

List<GeneReferenceValueObject> genes

Compact identities of the genes this element maps to, via the denormalized GENE2CS table.

Populated only when the caller opts in via ?withGenes=true on the platform-elements endpoints (otherwise null and elided from the wire by @JsonInclude(NON_NULL)). Off by default for the same reason as CompositeSequenceValueObject.sequence: the mapping is a second query per page, and most callers paging a 22k-element platform listing never render the column.

An empty list means "this element maps to no gene" — distinct from null, which means "not requested". A probe with no gene mapping still gets [] when withGenes=true, so a client can tell a real negative from an unpopulated field.

name

String name

sequence

String sequence

Raw probe sequence from the associated BioSequence.sequence. Populated only when the caller opts in via ?withSequence=true on the platform-elements endpoint (otherwise null and elided from the wire by @JsonInclude(NON_NULL)). Kept out of the default response because sequences are 25-300bp per probe and would inflate a 22k-element platform listing by ~1 MB.

sequenceLength

Long sequenceLength

Pre-computed length from BioSequence.length, exposed alongside sequence. Independent so a caller can request length without paying the full-string cost (future-proofing; for now both come together with ?withSequence=true).

Package ubic.gemma.model.expression.experiment

Class ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject

class AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue> implements Serializable

Serialized Fields

baseline

Boolean baseline

Whether this factor value is a "forced" baseline condition. Mirrors FactorValue.getIsBaseline(); null when unset. Ignored for continuous factors. Exposed on the wire as isBaseline so the design read/write round-trip (e.g. the composite curation commit) can carry the baseline flag.

characteristics

List<CharacteristicValueObject> characteristics

The characteristics associated with this factor value.

experimentalFactorCategory

CharacteristicValueObject experimentalFactorCategory

The experiment factor category.

experimentalFactorId

Long experimentalFactorId

The ID of the experimental factor this factor value belongs to.

experimentalFactorType

String experimentalFactorType

The experimental factor type.

measurementObject

MeasurementValueObject measurementObject

The measurement associated with this factor value.

This is named as such to avoid conflict with AbstractFactorValueValueObject.isMeasurement().

ontologyId

String ontologyId

A unique ontology identifier (i.e. IRI) for this factor value.

statements

List<StatementValueObject> statements

The statements associated with this factor value.

summary

String summary

Human-readable summary of the factor value.

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

Verbatim provenance backing this factor VALUE — a JSON array of {quote, source, location, …} items the curation agents emitted. Gemma stores and serves it opaquely; the agents repo owns the schema.

🛑 Not a roll-up of the evidence on statements, and not a fallback for it. A statement's evidence backs its triple; this backs the value — its label, its baseline flag, its measurement, the samples it covers — and a value carrying no statements at all still has a curator behind those choices. Reading one for the other conflates two levels that a composed factor value keeps apart.

Null means nothing was recorded, which is the expected reading for most rows.

Class ubic.gemma.model.expression.experiment.DesignApplyOutcome

class DesignApplyOutcome extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

applied

boolean applied

design

ExperimentalDesignValueObject design

preflightAtApply

DesignPreflightReport preflightAtApply

Class ubic.gemma.model.expression.experiment.DesignPreflightReport

class DesignPreflightReport extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

blockers

List<DesignPreflightReport.Blocker> blockers

Hard validation errors. A non-empty list means the PUT would be rejected; fix the payload and re-run.

differentialExpressionAnalysesToDelete

List<DesignPreflightReport.AnalysisRef> differentialExpressionAnalysesToDelete

factorsToDelete

List<DesignPreflightReport.EntityRef> factorsToDelete

factorsToUpdate

List<DesignPreflightReport.EntityRef> factorsToUpdate

Kept factors whose name, description or category the proposal rewrites.

Nothing is created or deleted by such an edit, so every counter above it stays at zero and the report used to describe a real change as unchanged. The apply path has always performed these — see isNoOpDesignApply, which consults the same comparison — so the gap was in what the report could say, not in what a PUT would do.

factorValuesToDelete

List<DesignPreflightReport.EntityRef> factorValuesToDelete

factorValuesToUpdate

List<DesignPreflightReport.EntityRef> factorValuesToUpdate

Kept factor values the proposal edits in place: a statement re-termed, evidence attached, the baseline flag flipped, a measurement retimed, the deprecated free-text value rewritten.

cab hit the gap on GSE49354.1 (2026-08-27): re-terming one factor value's subject URI preflighted as {created: 0, updated: 0, deleted: 0, unchanged: 1}, which reads as "nothing to do" for an edit that a PUT would in fact apply.

subsetsWithStaleAnchor

List<DesignPreflightReport.SubsetRef> subsetsWithStaleAnchor

Subsets whose definitional factor-value anchors would be deleted. These are not blockers (subsets carry no FK to FactorValue), but their semantics drift after the change, so they require the same explicit consent as the analysis cascade — see DesignPreflightReport.requiresForce().

summary

DesignPreflightReport.Summary summary

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.AnalysisRef

class AnalysisRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

name

String name

subsetFactorValueId

Long subsetFactorValueId

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.Blocker

class Blocker extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

bioMaterialId

Long bioMaterialId

factorId

Long factorId

factorValueId

Long factorValueId

message

String message

statementId

Long statementId

type

String type

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.EntityRef

class EntityRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

name

String name

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.SubsetRef

class SubsetRef extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

lostFactorValueIds

List<Long> lostFactorValueIds

name

String name

Class ubic.gemma.model.expression.experiment.DesignPreflightReport.Summary

class Summary extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

biomaterialsWithChangedAssignments

int biomaterialsWithChangedAssignments

differentialExpressionAnalysesToDelete

int differentialExpressionAnalysesToDelete

factorsToCreate

int factorsToCreate

factorsToDelete

int factorsToDelete

factorsToUpdate

int factorsToUpdate

See Also:

• DesignPreflightReport.getFactorsToUpdate()

factorValuesToCreate

int factorValuesToCreate

factorValuesToDelete

int factorValuesToDelete

factorValuesToUpdate

int factorValuesToUpdate

See Also:

• DesignPreflightReport.getFactorValuesToUpdate()

subsetsWithStaleAnchor

int subsetsWithStaleAnchor

Class ubic.gemma.model.expression.experiment.ExperimentalDesignValueObject

class ExperimentalDesignValueObject extends IdentifiableValueObject<ExperimentalDesign> implements Serializable

serialVersionUID:

1L

Serialized Fields

bioMaterialAssignments

List<ExperimentalDesignValueObject.BioMaterialFactorValueAssignment> bioMaterialAssignments

Many-to-many assignment of BioMaterials to FactorValues, materialized as a flat list.

description

String description

experimentalFactors

List<ExperimentalDesignValueObject.ExperimentalFactorEntry> experimentalFactors

name

String name

normalizationDescription

String normalizationDescription

qualityControlDescription

String qualityControlDescription

replicateDescription

String replicateDescription

Class ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject

class ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor> implements Serializable

serialVersionUID:

-2615804031123874251L

Serialized Fields

baselineRelevance

String baselineRelevance

Curator/agent hint about baseline relevance. Mirrors the curation-ui Factor.baseline_relevance field. "required", "not_applicable" and "uncertain" are the values in use; null when the curation pipeline has not set it.

The list is documented and not enforced. It used to be a closed allowableValues set, which a generated client turns into an enum that fails to deserialize the first response carrying a word the vocabulary has since gained — and this one has moved once already. The write side (DatasetsWebService.FactorCommit.baselineRelevance) accepts an unfamiliar value rather than 400ing it, so advertising a closed set here would promise a constraint the server does not keep.

baselineRelevanceReason

String baselineRelevanceReason

Free-text rationale paired with ExperimentalFactorValueObject.baselineRelevance. null when unset.

category

String category

categoryUri

String categoryUri

description

String description

factorValues

String factorValues

Deprecated.

name

String name

type

String type

values

Collection<FactorValueValueObject> values

Class ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject

class ExpressionExperimentDetailsValueObject extends ExpressionExperimentValueObject implements Serializable

serialVersionUID:

-1219449523930648392L

Serialized Fields

arrayDesigns

Collection<ArrayDesignValueObject> arrayDesigns

batchFetchEventType

String batchFetchEventType

cellBrowserDatasetName

String cellBrowserDatasetName

cellBrowserUrl

String cellBrowserUrl

URL for the Cell Browser, if available.

dateArrayDesignLastUpdated

Date dateArrayDesignLastUpdated

The date the platform associated with the experiment was last updated.

If there are multiple platforms this should be the date of the most recent modification of them. This is used to help flag experiments that need re-analysis due to changes in the underlying array design(s).

dateBatchFetch

Date dateBatchFetch

dateCached

Date dateCached

The date this object was generated.

dateDifferentialAnalysis

Date dateDifferentialAnalysis

dateLinkAnalysis

Date dateLinkAnalysis

dateMissingValueAnalysis

Date dateMissingValueAnalysis

datePcaAnalysis

Date datePcaAnalysis

dateProcessedDataVectorComputation

Date dateProcessedDataVectorComputation

differentialAnalysisEventType

String differentialAnalysisEventType

differentialExpressionAnalyses

Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses

expressionExperimentSets

Collection<ExpressionExperimentSetValueObject> expressionExperimentSets

EE sets this experiment is part of.

font

String font

Font to use when rendering diagnostic plots, etc.

hasBatchInformation

boolean hasBatchInformation

FIXME: rename this to hasUsableBatchInformation

hasBothIntensities

boolean hasBothIntensities

hasCellBrowser

boolean hasCellBrowser

Indicate if this experiment has a Cell Browser associated with it.

hasCoexpressionAnalysis

boolean hasCoexpressionAnalysis

hasDifferentialExpressionAnalysis

boolean hasDifferentialExpressionAnalysis

hasEitherIntensity

boolean hasEitherIntensity

Indicate if the experiment has any intensity information available. Relevant for two-channel studies.

hasMultiplePreferredQuantitationTypes

boolean hasMultiplePreferredQuantitationTypes

hasMultipleTechnologyTypes

boolean hasMultipleTechnologyTypes

isReprocessedFromRawData

boolean isReprocessedFromRawData

isRNASeq

boolean isRNASeq

lastArrayDesignUpdateDate

String lastArrayDesignUpdateDate

linkAnalysisEventType

String linkAnalysisEventType

missingValueAnalysisEventType

String missingValueAnalysisEventType

numAnnotations

Long numAnnotations

The number of terms (Characteristics) the experiment has to describe it.

numPopulatedFactors

Long numPopulatedFactors

The number of experimental factors the experiment has (counting those that are populated with biomaterials).

pcaAnalysisEventType

String pcaAnalysisEventType

primaryCitation

CitationValueObject primaryCitation

processedDataVectorComputationEventType

String processedDataVectorComputationEventType

QChtml

String QChtml

sampleRemovedFlags

Collection<AuditEventValueObject> sampleRemovedFlags

Details of samples that were removed (or marked as outliers). This can happen multiple times in the life of data set, so this is a collection of AuditEvents.

secondaryAccession

String secondaryAccession

Identifier in a second database, if available. For example, if the data are in GEO and in ArrayExpress, this might be a link to the ArrayExpress version.

secondaryExternalDatabase

String secondaryExternalDatabase

secondaryExternalUri

String secondaryExternalUri

Class ubic.gemma.model.expression.experiment.ExpressionExperimentReferenceValueObject

class ExpressionExperimentReferenceValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

Gemma-internal dataset id, suitable for GET /datasets/{id}.

name

String name

Full title. A split part's title is of the form Split part 3 of: … [organism part = …], which is the only place the distinguishing factor value appears, so a reference carrying only the short name cannot tell one sibling from another.

shortName

String shortName

Short name, e.g. GSE1234 or Rexach-2024.3. This is what a page displays.

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSetValueObject

class ExpressionExperimentSetValueObject extends IdentifiableValueObject<ExpressionExperimentSet> implements Serializable

serialVersionUID:

-6852364688337216390L

Serialized Fields

description

String description

expressionExperimentIds

Collection<Long> expressionExperimentIds

isPublic

boolean isPublic

Accessor names are constrained by SecureValueObject; keep these getters/setters manual.

modifiable

boolean modifiable

If modifying the set is constrained by existing analyses.

name

String name

numWithCoexpressionAnalysis

Integer numWithCoexpressionAnalysis

numWithDifferentialExpressionAnalysis

Integer numWithDifferentialExpressionAnalysis

shared

boolean shared

Accessor names are constrained by SecureValueObject; keep these getters/setters manual.

size

Integer size

taxonId

Long taxonId

taxonName

String taxonName

userCanWrite

boolean userCanWrite

Accessor names are constrained by SecureValueObject; keep these getters/setters manual.

userOwned

boolean userOwned

Accessor names are constrained by SecureValueObject; keep these getters/setters manual.

Class ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject

class ExpressionExperimentSubsetValueObject extends IdentifiableValueObject<ExpressionExperimentSubSet> implements Serializable

Serialized Fields

bioAssays

Collection<BioAssayValueObject> bioAssays

characteristics

Collection<CharacteristicValueObject> characteristics

description

String description

isPublic

boolean isPublic

isShared

boolean isShared

minPvalue

Double minPvalue

name

String name

numberOfBioAssays

Integer numberOfBioAssays

sourceExperimentId

Long sourceExperimentId

The ID of the ExpressionExperiment this is a subset of.

sourceExperimentShortName

String sourceExperimentShortName

The short name of the ExpressionExperiment this is a subset of.

userCanWrite

boolean userCanWrite

userOwned

boolean userOwned

Class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

class ExpressionExperimentValueObject extends AbstractCuratableValueObject<ExpressionExperiment> implements Serializable

serialVersionUID:

-6861385216096602508L

Serialized Fields

accession

String accession

See Also:

• DatabaseEntryValueObject.getAccession()

arrayDesignCount

Long arrayDesignCount

batchConfound

String batchConfound

batchEffect

String batchEffect

Batch effect type. See BatchEffectType enum for possible values.

batchEffectStatistics

String batchEffectStatistics

Summary statistics of a batch effect is present.

bioMaterialCount

Integer bioMaterialCount

characteristics

Set<CharacteristicValueObject> characteristics

dateCreated

Date dateCreated

When the dataset was created in Gemma — loaded, not published.

Read from the C audit event, which is the only record of it: there is no creation column on the dataset (a CURATION_DETAILS.CREATED backfill was proposed and deferred, 2026-08-21). Measured universal — 200 of 200 sampled datasets carry the event — but null is still possible and means the event is missing, never "created just now".

🛑 Not filterable or sortable. AbstractCuratableDao unregisters auditTrail.* from the dataset filter surface, so this is a projection for display. Filtering on it is what the deferred migration was for.

description

String description

doi

String doi

DOI of the primary publication, when it is a preprint or otherwise identified by a DOI rather than a PubMed ID. See ExpressionExperimentValueObject.pubmedId.

experimentalDesign

Long experimentalDesign

externalDatabase

String externalDatabase

See Also:

• ExternalDatabaseValueObject.getName()

externalDatabaseUri

String externalDatabaseUri

See Also:

• ExternalDatabaseValueObject.getUri()

externalLabel

String externalLabel

See Also:

• DatabaseEntryValueObject.getLabel()

externalUri

String externalUri

See Also:

• DatabaseEntryValueObject.getUri()

geeq

GeeqValueObject geeq

isPublic

boolean isPublic

isShared

boolean isShared

isSingleCell

boolean isSingleCell

Whether this is a single-cell experiment, i.e. it has a preferred single-cell quantitation type.

That is the same condition every single-cell route resolves against (getPreferredSingleCellQuantitationType), so a dataset this reports true for is one /cellTypeAssignment and /singleCellDimension can actually serve. 546 datasets on prod — 29 more than SINGLE_CELL_DIMENSION_EXPERIMENT indexes, which is why the flag and not that table decides this.

It is here rather than on the details VO because technologyType does not answer the question — eid 79038 is single-cell and reads GENELIST, the generic-platform placeholder — which left clients inferring modality from a regex over platform and assay strings, blind to a dataset annotated with none of the expected words and fooled by a title that merely mentions single cell (uib, 2026-09-03).

metadata

String metadata

minPvalue

Double minPvalue

name

String name

numberOfBioAssays

Integer numberOfBioAssays

numberOfCellIds

Integer numberOfCellIds

Number of cell IDs in the preferred single-cell dimension, or null when there is none.

numberOfCells

Integer numberOfCells

Total number of cells, or null when this is not a single-cell experiment or the count has not been computed. Denormalized on the experiment itself, so it costs nothing to serve.

🛑 Not a substitute for ExpressionExperimentValueObject.isSingleCell: 63 of the 546 single-cell datasets on prod have no count.

originalPlatforms

List<ArrayDesignReferenceValueObject> originalPlatforms

The platforms this dataset's assays were run on BEFORE a platform switch, when one happened.

Empty for the great majority of datasets. A no-op switch — an original platform that is also a platform in use — is left out, so a non-empty list here means the dataset really was moved.

otherParts

List<ExpressionExperimentReferenceValueObject> otherParts

The other parts of the study this dataset was split off from, empty when it was not split.

Gemma splits an experiment by a factor — usually organism part for single-cell data — and names each part Split part N of: … [organism part = …]. That title tells a reader siblings exist and gives them no way to reach one: 52 of 100 sampled single-cell datasets are split parts over 32 parent studies, and neither the curation UI nor the browser could follow the link, because the field lived on a VO only /experiment-sets/{id}/datasets serves (uib, 2026-09-03).

References rather than whole VOs: a sibling is rendered as a name and a link, and the previous full-VO form cost a loadValueObjectsByIds per split experiment.

platforms

List<ArrayDesignReferenceValueObject> platforms

The platforms this dataset's assays were run on, as accession + full name.

A list because a dataset may use more than one; ExpressionExperimentValueObject.arrayDesignCount is the size of this list and is kept because clients read it. Populated on every filtered read out of the same query that produces the count — the join to the platform was already being paid for.

processedExpressionVectorCount

Integer processedExpressionVectorCount

pubmedId

String pubmedId

PubMed ID of the primary publication, when it is indexed by PubMed. Mutually exclusive with ExpressionExperimentValueObject.doi: the primary publication carries a single accession, so a PubMed-indexed paper populates this and a preprint (bioRxiv/arXiv/CrossRef DOI) populates ExpressionExperimentValueObject.doi.

shortName

String shortName

source

String source

suitableForDEA

Boolean suitableForDEA

taxonObject

TaxonValueObject taxonObject

FIXME: this should be named simply "taxon", but that field is already taken for Gemma Web, see ExpressionExperimentValueObject.getTaxon().

technologyType

String technologyType

userCanWrite

boolean userCanWrite

userOwned

boolean userOwned

Class ubic.gemma.model.expression.experiment.FactorValueBasicValueObject

class FactorValueBasicValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

value

String value

Deprecated.

use either AbstractFactorValueValueObject.getCharacteristics() or AbstractFactorValueValueObject.getMeasurementObject()

Class ubic.gemma.model.expression.experiment.FactorValueValueObject

class FactorValueValueObject extends AbstractFactorValueValueObject implements Serializable

serialVersionUID:

3378801249808036785L

Serialized Fields

category

String category

Deprecated.

categoryUri

String categoryUri

Deprecated.

charId

Long charId

Deprecated.

It could be the id of the measurement if there is no characteristic.

factorId

Long factorId

Deprecated.

ID of the experimental factor this FV belongs to.

needsAttention

Boolean needsAttention

Deprecated.

object

String object

Deprecated.

objectUri

String objectUri

Deprecated.

predicate

String predicate

Deprecated.

predicateUri

String predicateUri

Deprecated.

secondObject

String secondObject

Deprecated.

secondObjectUri

String secondObjectUri

Deprecated.

secondPredicate

String secondPredicate

Deprecated.

secondPredicateUri

String secondPredicateUri

Deprecated.

value

String value

Deprecated.

valueUri

String valueUri

Deprecated.

Class ubic.gemma.model.expression.experiment.FreeTextExpressionExperimentResultsValueObject

class FreeTextExpressionExperimentResultsValueObject extends SessionBoundExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.expression.experiment.GeeqAdminValueObject

class GeeqAdminValueObject extends GeeqValueObject implements Serializable

Serialized Fields

detectedQualityScore

double detectedQualityScore

manualBatchConfoundActive

boolean manualBatchConfoundActive

manualBatchEffectActive

boolean manualBatchEffectActive

manualHasBatchConfound

boolean manualHasBatchConfound

manualHasNoBatchEffect

boolean manualHasNoBatchEffect

manualHasStrongBatchEffect

boolean manualHasStrongBatchEffect

manualQualityOverride

boolean manualQualityOverride

manualQualityScore

double manualQualityScore

otherIssues

String otherIssues

qScoreBatchConfound

double qScoreBatchConfound

qScoreBatchEffect

double qScoreBatchEffect

Class ubic.gemma.model.expression.experiment.GeeqValueObject

class GeeqValueObject extends IdentifiableValueObject<Geeq> implements Serializable

Serialized Fields

batchCorrected

boolean batchCorrected

corrMatIssues

byte corrMatIssues

lastComputed

Date lastComputed

Timestamp of the last GeeqEvent for the experiment, populated by callers that have access to the audit log. null when unknown or never recorded.

noVectors

boolean noVectors

publicQualityScore

double publicQualityScore

qScoreBatchInfo

double qScoreBatchInfo

qScoreOutliers

double qScoreOutliers

qScorePlatformsTech

double qScorePlatformsTech

qScorePublicBatchConfound

double qScorePublicBatchConfound

qScorePublicBatchEffect

double qScorePublicBatchEffect

qScoreReplicates

double qScoreReplicates

qScoreSampleCorrelationVariance

double qScoreSampleCorrelationVariance

qScoreSampleMeanCorrelation

double qScoreSampleMeanCorrelation

qScoreSampleMedianCorrelation

double qScoreSampleMedianCorrelation

replicatesIssues

byte replicatesIssues

Class ubic.gemma.model.expression.experiment.GeoScrapeWatermark

class GeoScrapeWatermark extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

criteriaApplied

String criteriaApplied

errorMessage

String errorMessage

id

Long id

recordsMatched

int recordsMatched

recordsScanned

int recordsScanned

scanFrom

Date scanFrom

scannedAt

Date scannedAt

scanTo

Date scanTo

status

GeoScrapeWatermark.Status status

Class ubic.gemma.model.expression.experiment.SessionBoundExpressionExperimentSetValueObject

class SessionBoundExpressionExperimentSetValueObject extends ExpressionExperimentSetValueObject implements Serializable

serialVersionUID:

2068650886972222818L

Serialized Fields

modified

boolean modified

Class ubic.gemma.model.expression.experiment.StatementValueObject

class StatementValueObject extends IdentifiableValueObject<Statement> implements Serializable

Serialized Fields

category

String category

categoryUri

String categoryUri

evidenceCode

String evidenceCode

How this statement was arrived at, as a GOEvidenceCode name (IC, IEA, IIA, TAS, …). The uppercase enum name is the wire form this field carries everywhere it appears — AnnotationValueObject#evidenceCode and PublicationAssociationValueObject#evidenceCode spell it the same way.

Storage is the EVIDENCE_CODE column Statement inherits from Characteristic; like StatementValueObject.supportingEvidence it was never surfaced here, so a design write could not say who decided and a design read could not tell a curator's call from a program's.

Provenance rather than identity, so it is excluded from equals/hashCode and from StatementValueObject.COMPARATOR for the same reason StatementValueObject.supportingEvidence is: the comparator's ordering assigns annotation ids.

object

String object

objectId

String objectId

A unique ontology identifier (i.e. IRI) for this object. Assigned and omitted on the same terms as StatementValueObject.subjectId.

objectUri

String objectUri

predicate

String predicate

The predicate and object halves are absent rather than null when nothing was said.

This is the rule AbstractFactorValueValueObjectSerializer#writeStatement already applies when it emits the same VO by hand on the factor-value path — "null reads as 'this was cleared', and a subject-only statement has nothing to clear" — and these four annotations make the bean path agree with it. Before, the two serializations of one type disagreed about the commonest statement there is.

The subject and category halves keep their nulls, on the same serializer's reasoning: they describe a term that IS there, and subjectUri: null says it is ungrounded.

Measured on GET /datasets/3937/samples: predicate, predicateUri, object, objectUri, objectId, subjectId and id were null on all 5,291 statements in the response, costing 587,301 of 5,265,852 bytes — 11.2% — to say nothing seven times over.

predicateUri

String predicateUri

secondObject

String secondObject

secondObjectUri

String secondObjectUri

secondPredicate

String secondPredicate

The second clause of a compound statement (e.g. the "for 12 weeks" of "HFD for 12 weeks").

These four are withheld because AbstractFactorValueValueObjectSerializer already puts them on the wire, flattened: a statement with a second object is emitted as two entries in the statements array sharing one subject, the second carrying this clause under the generic predicate / object keys. Serializing the raw fields as well would publish the same clause twice under two names. That flattening arrived with the fields' exposure in dff752727c ("Serialize statements", fix #814), which is why the first four slots are public here and these are not.

AnnotationValueObject exposes its own second* fields directly, and that is not an inconsistency: it is serialized as a plain bean with no flattener, so direct fields are the only way to carry the compound shape there.

secondPredicateUri

String secondPredicateUri

subject

String subject

subjectId

String subjectId

A unique ontology identifier (i.e. IRI) for this subject.

Assigned by AbstractFactorValueValueObjectSerializer, which is the only thing that populates it; nothing sets it on the bean path, so it is null on every statement GET /datasets/{id}/samples returns. Absent rather than null for that reason.

subjectUri

String subjectUri

supportingEvidence

com.fasterxml.jackson.databind.JsonNode supportingEvidence

Verbatim provenance backing this statement — a JSON array of {quote, source, location, …} items the curation agents emitted. Gemma stores and serves it opaquely; the agents repo owns the schema.

A Statement is a Characteristic, so the storage (the SUPPORTING_EVIDENCE column) has always existed — it was simply never surfaced here, which left the design read path unable to answer "where did this factor value's term come from" even for rows that recorded it. Null means "nothing recorded", the expected reading for most rows.

Provenance rather than identity, so it is excluded from equals/hashCode and from StatementValueObject.COMPARATOR: the same statement with and without recorded evidence is the same statement, and the comparator's ordering is relied upon to assign annotation ids.

Package ubic.gemma.model.genome

Class ubic.gemma.model.genome.GeneOntologyTermValueObject

class GeneOntologyTermValueObject extends Object implements Serializable

Serialized Fields

comment

String comment

goId

String goId

isObsolete

boolean isObsolete

label

String label

localName

String localName

term

String term

uri

String uri

Class ubic.gemma.model.genome.PhysicalLocationValueObject

class PhysicalLocationValueObject extends IdentifiableValueObject<PhysicalLocation> implements Serializable

Serialized Fields

bin

Integer bin

chromosome

String chromosome

nucleotide

Long nucleotide

nucleotideLength

Integer nucleotideLength

strand

String strand

taxon

TaxonValueObject taxon

Class ubic.gemma.model.genome.TaxonValueObject

class TaxonValueObject extends IdentifiableValueObject<Taxon> implements Serializable

Serialized Fields

commonName

String commonName

externalDatabase

ExternalDatabaseValueObject externalDatabase

isGenesUsable

Boolean isGenesUsable

Whether Gemma has gene records loaded for this taxon — a loader-maintained capability bit, written false at creation and flipped by NcbiGeneLoader.updateTaxaWithGenesUsable once genes actually land. Read internally by TaxonReadServiceImpl.loadAllTaxaWithGenes(), whose one consumer, GeneSearchServiceImpl.getGOGroupGenes, uses it to bound an untargeted GO search's fan-out.

Withheld because production only serves taxa that have genes loaded, so on the wire this would be a constant true: it invites clients to branch on a condition that never occurs. Note this is a claim about the data rather than the structure — GET /taxa serves every taxon unfiltered, and GeoConverterImpl still writes false for taxa imported from GEO, so a genes-less taxon reaching a client is possible in principle. If that becomes routine, the field is informative again and this reason no longer holds.

Distinct from TaxonValueObject.isSpecies, which is withheld because nothing populates it at all.

isSpecies

Boolean isSpecies

ncbiId

Integer ncbiId

scientificName

String scientificName

Package ubic.gemma.model.genome.gene

Class ubic.gemma.model.genome.gene.DatabaseBackedGeneSetValueObject

class DatabaseBackedGeneSetValueObject extends GeneSetValueObject implements Serializable

serialVersionUID:

-1360523793656012770L

Class ubic.gemma.model.genome.gene.FreeTextGeneResultsValueObject

class FreeTextGeneResultsValueObject extends SessionBoundGeneSetValueObject implements Serializable

serialVersionUID:

3557304710219740029L

Serialized Fields

queryString

String queryString

Class ubic.gemma.model.genome.gene.GeneProductValueObject

class GeneProductValueObject extends IdentifiableValueObject<GeneProduct> implements Serializable

serialVersionUID:

1156628868995566223L

Serialized Fields

chromosome

String chromosome

geneId

Long geneId

name

String name

ncbiId

String ncbiId

nucleotideEnd

Long nucleotideEnd

Deprecated.

nucleotideStart

Long nucleotideStart

strand

String strand

Class ubic.gemma.model.genome.gene.GeneReferenceValueObject

class GeneReferenceValueObject extends Object implements Serializable

serialVersionUID:

1L

Serialized Fields

id

Long id

Gemma-internal gene id, suitable for GET /genes/{id}.

ncbiId

Integer ncbiId

NCBI gene id. Null for genes Gemma tracks without one.

officialSymbol

String officialSymbol

Official gene symbol, e.g. BRCA1. Null for the (rare) gene rows that carry none.

Class ubic.gemma.model.genome.gene.GeneSetValueObject

class GeneSetValueObject extends IdentifiableValueObject<GeneSet> implements Serializable

serialVersionUID:

6212231006289412683L

Serialized Fields

description

String description

geneIds

Collection<Long> geneIds

Gene IDs part of this gene set.

isPublic

boolean isPublic

isShared

boolean isShared

name

String name

size

Long size

taxon

TaxonValueObject taxon

userOwned

boolean userOwned

Class ubic.gemma.model.genome.gene.GeneValueObject

class GeneValueObject extends IdentifiableValueObject<Gene> implements Serializable

serialVersionUID:

-7098036090107647318L

Serialized Fields

accessions

Set<DatabaseEntryValueObject> accessions

aliases

SortedSet<String> aliases

Gene aliases, sorted alphabetically.

associatedExperimentCount

Integer associatedExperimentCount

How many experiments "involve" (manipulate, etc.) this gene

compositeSequenceCount

Integer compositeSequenceCount

Number of probes (composite sequences) across all platforms that map to this gene.

Only GeneServiceImpl.loadFullyPopulatedValueObject fills this in, so it is null on every gene value object that does not come from GET /genes/{gene}/overview. It must stay null-initialised: a 0 default would serialize on every gene in every list response and read as "this gene has no probes".

description

String description

ensemblId

String ensemblId

geneSets

Collection<GeneSetValueObject> geneSets

Gene sets this gene belongs to, in their light form (no members). Populated only by GeneServiceImpl.loadFullyPopulatedValueObject; null elsewhere.

homologues

Collection<GeneValueObject> homologues

Homologues of this gene across taxa. Populated only by GeneServiceImpl.loadFullyPopulatedValueObject; null elsewhere.

This field is self-referential, and serialization only terminates because the homologue value objects are built through loadValueObjects, i.e. the plain GeneValueObject(Gene) constructor, which leaves their own homologues null. Populating homologues recursively would turn this into an unbounded serialization loop.

includeTaxon

boolean includeTaxon

isQuery

Boolean isQuery

Was this gene directly used in a query? Or is it inferred somehow. The default is true, use this when you need to differentiate

matchType

String matchType

How this gene matched the search query (e.g. exact_symbol, alias, prefix), when the VO originates from a search. Populated by GeneWebService.searchGenes; null outside a search context. Lets a client distinguish a safe alias hit from a low-trust prefix look-alike. See SearchMatchType.

multifunctionalityRank

Double multifunctionalityRank

name

String name

ncbiId

Integer ncbiId

nodeDegreeNegRanks

double[] nodeDegreeNegRanks

nodeDegreePosRanks

double[] nodeDegreePosRanks

nodeDegreesNeg

int[] nodeDegreesNeg

Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for negative correlation coexpression

nodeDegreesPos

int[] nodeDegreesPos

Array containing number of links supported by 0,1,2, .... data sets (value in first index is always 0) for positive coexpression

numGoTerms

Integer numGoTerms

Number of GO terms associated with this gene. Filled in by GeneWebService.getGeneOverview; null elsewhere. Null-initialised for the same reason as GeneValueObject.compositeSequenceCount.

officialName

String officialName

officialSymbol

String officialSymbol

platformCount

Integer platformCount

Number of platforms carrying at least one probe for this gene. Populated only by GeneServiceImpl.loadFullyPopulatedValueObject; null elsewhere.

score

Double score

taxon

TaxonValueObject taxon

Class ubic.gemma.model.genome.gene.GOGroupValueObject

class GOGroupValueObject extends SessionBoundGeneSetValueObject implements Serializable

serialVersionUID:

-185326197992950287L

Serialized Fields

goId

String goId

searchTerm

String searchTerm

Class ubic.gemma.model.genome.gene.SessionBoundGeneSetValueObject

class SessionBoundGeneSetValueObject extends GeneSetValueObject implements Serializable

serialVersionUID:

5073203626044664184L

Serialized Fields

modified

boolean modified

Package ubic.gemma.model.genome.sequenceAnalysis

Class ubic.gemma.model.genome.sequenceAnalysis.BioSequenceValueObject

class BioSequenceValueObject extends IdentifiableValueObject<BioSequence> implements Serializable

Serialized Fields

description

String description

fractionRepeats

Double fractionRepeats

length

Long length

name

String name

sequence

String sequence

sequenceDatabaseEntry

DatabaseEntryValueObject sequenceDatabaseEntry

taxon

TaxonValueObject taxon

type

SequenceTypeValueObject type

Class ubic.gemma.model.genome.sequenceAnalysis.BlatResultValueObject

class BlatResultValueObject extends IdentifiableValueObject<BlatResult> implements Serializable

Serialized Fields

blockCount

Integer blockCount

blockSizes

String blockSizes

identity

Double identity

matches

Integer matches

mismatches

Integer mismatches

ns

Integer ns

queryEnd

Integer queryEnd

queryGapBases

Integer queryGapBases

queryGapCount

Integer queryGapCount

querySequence

BioSequenceValueObject querySequence

queryStart

Integer queryStart

queryStarts

String queryStarts

repMatches

Integer repMatches

score

Double score

strand

String strand

targetChromosomeName

String targetChromosomeName

targetDatabase

String targetDatabase

targetEnd

Long targetEnd

targetGapBases

Integer targetGapBases

targetGapCount

Integer targetGapCount

targetStart

Long targetStart

targetStarts

String targetStarts

taxon

TaxonValueObject taxon

Class ubic.gemma.model.genome.sequenceAnalysis.SequenceTypeValueObject

class SequenceTypeValueObject extends Object implements Serializable

Serialized Fields

value

String value

Package ubic.gemma.model.util

Exception Class ubic.gemma.model.util.UninitializedCollectionException

class UninitializedCollectionException extends RuntimeException implements Serializable

Package ubic.gemma.persistence.hibernate

Class ubic.gemma.persistence.hibernate.XSDEntityResolver

class XSDEntityResolver extends DTDEntityResolver implements Serializable

Package ubic.gemma.persistence.service

Exception Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithMessage

class ExceptionWithMessage extends Exception implements Serializable

Exception Class ubic.gemma.persistence.service.AbstractServiceTest.ExceptionWithoutMessage

class ExceptionWithoutMessage extends Exception implements Serializable

Package ubic.gemma.persistence.service.analysis.expression.diff

Class ubic.gemma.persistence.service.analysis.expression.diff.MissingResult

class MissingResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

-2868418055346274525L

Class ubic.gemma.persistence.service.analysis.expression.diff.NonRetainedResult

class NonRetainedResult extends DiffExprGeneSearchResult implements Serializable

serialVersionUID:

3501605965895623139L

Package ubic.gemma.persistence.service.common.auditAndSecurity.curation

Exception Class ubic.gemma.persistence.service.common.auditAndSecurity.curation.CurationLockService.CurationLockedException

class CurationLockedException extends RuntimeException implements Serializable

serialVersionUID:

1L

Serialized Fields

heldBy

String heldBy

Package ubic.gemma.persistence.service.common.description

Exception Class ubic.gemma.persistence.service.common.description.PublicationAssociationConflictException

class PublicationAssociationConflictException extends IllegalArgumentException implements Serializable

Package ubic.gemma.persistence.service.common.quantitationtype

Exception Class ubic.gemma.persistence.service.common.quantitationtype.NonUniqueQuantitationTypeByNameException

class NonUniqueQuantitationTypeByNameException extends Exception implements Serializable

Package ubic.gemma.persistence.service.expression.bioAssayData

Class ubic.gemma.persistence.service.expression.bioAssayData.NegativeBinomialDistribution

class NegativeBinomialDistribution extends org.apache.commons.math3.distribution.AbstractIntegerDistribution implements Serializable

Serialized Fields

distribution

NegativeBinomial distribution

i

int i

v

double v

Package ubic.gemma.persistence.service.expression.experiment

Exception Class ubic.gemma.persistence.service.expression.experiment.DisallowedWorkflowTransitionException

class DisallowedWorkflowTransitionException extends RuntimeException implements Serializable

Serialized Fields

allowedNextStates

Set<WorkflowState> allowedNextStates

currentState

WorkflowState currentState

targetState

WorkflowState targetState

Exception Class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.AccessionAlreadyExistsException

class AccessionAlreadyExistsException extends Exception implements Serializable

Serialized Fields

existingId

Long existingId

existingType

String existingType

Exception Class ubic.gemma.persistence.service.expression.experiment.PreboardedExperimentService.PreboardedAlreadyPromotedException

class PreboardedAlreadyPromotedException extends Exception implements Serializable

Serialized Fields

preboardedId

Long preboardedId

Package ubic.gemma.persistence.service.maintenance

Class ubic.gemma.persistence.service.maintenance.Gene2CsStatus

class Gene2CsStatus extends Object implements Serializable

serialVersionUID:

1956861185764899312L

Serialized Fields

annotation

String annotation

error

Exception error

lastUpdate

Date lastUpdate

Package ubic.gemma.persistence.util

Exception Class ubic.gemma.persistence.util.UnsupportedEntityUrlException

class UnsupportedEntityUrlException extends RuntimeException implements Serializable

Serialized Fields

entityType

Class<? extends Identifiable> entityType