Package ubic.gemma.persistence.service

Class AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

java.lang.Object

ubic.gemma.persistence.service.AbstractDao<O>

ubic.gemma.persistence.service.AbstractVoEnabledDao<O,VO>

ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao<O,VO>

All Implemented Interfaces:

BaseDao<O>, BaseVoEnabledDao<O,VO>, FilteringDao<O>, FilteringVoEnabledDao<O,VO>

Direct Known Subclasses:

BioAssayDaoImpl, CharacteristicDaoImpl, DatabaseEntryDaoImpl, FactorValueDaoImpl

public abstract class AbstractNoopFilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>
extends AbstractVoEnabledDao<O,VO>
implements FilteringVoEnabledDao<O,VO>

Base class to use to pretend to offer filtering, but actually supporting no filterable properties.

This is necessary because AbstractFilteringVoEnabledDao reroutes VO loading methods from BaseVoEnabledDao through the Filter-based mechanism for consistency, so it is not a suitable base class if you don't want or need to implement the filtering aspect of the interface.

Field Summary

Fields inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

REPORT_SLOW_QUERY_AFTER_MS

Fields inherited from class ubic.gemma.persistence.service.AbstractDao

log

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractNoopFilteringVoEnabledDao(Class<? extends O> elementClass, SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
final long	count(Filters filters)	Count VOs matching the given filters.
final <T> Filter	getFilter(String property, Class<T> propertyType, Filter.Operator operator, Collection<T> values)	Obtain a Filter with an already parsed collection of values.
final <T> Filter	getFilter(String property, Class<T> propertyType, Filter.Operator operator, T value)	Obtain a Filter with an already parsed value.
final Filter	getFilter(String property, Filter.Operator operator, String value)	Obtain an Filter for the entity this DAO is providing.
Filter	getFilter(String property, Filter.Operator operator, String value, SubqueryMode subqueryMode)
final Filter	getFilter(String property, Filter.Operator operator, Collection<String> values)	Similar to FilteringDao.getFilter(String, Filter.Operator, String), but with a collection of values.
Filter	getFilter(String property, Filter.Operator operator, Collection<String> values, SubqueryMode subqueryMode)
final Set<String>	getFilterableProperties()	List all properties availble for filtering.
List<Object>	getFilterablePropertyAllowedValues(String property)	Obtain a short list of allowed values for the given property, or null if unrestricted.
final String	getFilterablePropertyDescription(String propertyName)	Obtain a short description for a given filterable property.
boolean	getFilterablePropertyIsUsingSubquery(String property)	Indicate if the given property is using a subquery for filtering.
final Class<?>	getFilterablePropertyType(String propertyName)	Obtain the type of the given filterable property.
final Sort	getSort(String property, Sort.Direction direction, Sort.NullMode nullMode)	Obtain a Sort object for a property of the FilteringDao.
final List<O>	load(Filters filters, Sort sort)	Load entities matching the given filters.
final Slice<O>	load(Filters filters, Sort sort, int offset, int limit)	Load a slice of entities matching the given filters.
final List<Long>	loadIds(Filters filters, Sort sort)	Load IDs of entities matching the given filters.
final List<VO>	loadValueObjects(Filters filters, Sort sort)	Load VOs with minimal ordering and filtering.
final Slice<VO>	loadValueObjects(Filters filters, Sort sort, int offset, int limit)	Load VOs with ordering, filtering and offset/limit.

Methods inherited from class ubic.gemma.persistence.service.AbstractVoEnabledDao

doLoadValueObject, doLoadValueObjects, loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds, postProcessValueObjects

Methods inherited from class ubic.gemma.persistence.service.AbstractDao

countAll, create, create, find, findByProperty, findByPropertyIn, findOneByProperty, findOrCreate, getBatchSize, getElementClass, getIdentifierPropertyName, getSessionFactory, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, streamQuery, update, update

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ubic.gemma.persistence.service.BaseDao

countAll, create, create, find, findOrCreate, getElementClass, getIdentifierPropertyName, load, load, loadAll, loadReference, loadReference, reload, reload, remove, remove, remove, save, save, streamAll, streamAll, update, update

Methods inherited from interface ubic.gemma.persistence.service.BaseVoEnabledDao

loadAllValueObjects, loadValueObject, loadValueObjectById, loadValueObjects, loadValueObjectsByIds

Constructor Details

AbstractNoopFilteringVoEnabledDao

protected AbstractNoopFilteringVoEnabledDao(Class<? extends O> elementClass,
 SessionFactory sessionFactory)

Method Details

getFilterableProperties

public final Set<String> getFilterableProperties()

Description copied from interface: FilteringDao

List all properties availble for filtering.

Specified by:

getFilterableProperties in interface FilteringDao<O extends Identifiable>

getFilterablePropertyType

public final Class<?> getFilterablePropertyType(String propertyName)
                                         throws IllegalArgumentException

Description copied from interface: FilteringDao

Obtain the type of the given filterable property.

Specified by:

getFilterablePropertyType in interface FilteringDao<O extends Identifiable>

Throws:

IllegalArgumentException - if no such property exists, the cause will be a NoSuchFieldException

getFilterablePropertyDescription

@Nullable
public final String getFilterablePropertyDescription(String propertyName)
                                              throws IllegalArgumentException

Description copied from interface: FilteringDao

Obtain a short description for a given filterable property.

Specified by:

getFilterablePropertyDescription in interface FilteringDao<O extends Identifiable>

Throws:

IllegalArgumentException - if no such property exists

getFilterablePropertyAllowedValues

@Nullable
public List<Object> getFilterablePropertyAllowedValues(String property)

Description copied from interface: FilteringDao

Obtain a short list of allowed values for the given property, or null if unrestricted.

The returned values must be of the type outlined by FilteringDao.getFilterablePropertyType(String), generally a list of String or Integer to denote possible values for an enumerated type.

Specified by:

getFilterablePropertyAllowedValues in interface FilteringDao<O extends Identifiable>

getFilterablePropertyIsUsingSubquery

public boolean getFilterablePropertyIsUsingSubquery(String property)

Description copied from interface: FilteringDao

Indicate if the given property is using a subquery for filtering.

When this is the case, the filter will only check if at least one related entity is matching.

Specified by:

getFilterablePropertyIsUsingSubquery in interface FilteringDao<O extends Identifiable>

getFilter

public final Filter getFilter(String property,
 Filter.Operator operator,
 String value)
                       throws IllegalArgumentException

Description copied from interface: FilteringDao

Obtain an Filter for the entity this DAO is providing.

It is the responsibility of the DAO to infer the filter property type as well as the alias to use.

If the filter refers to a related entity (i.e. a BioAssay of an ExpressionExperiment), then the DAO should inject the corresponding DAO and delegate it the work of creating the filter.

In the frontend, that correspond to a FilterArg, but since the definition is not available here, we unpack its attributes.

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

Parameters:

property - property name in the entity use as a left-hand side of the operator

operator - an operator

value - the corresponding, unparsed value, to the right-hand side of the operator

Returns:

a filter filled with the object alias, property, inferred type, operator and parsed value

Throws:

IllegalArgumentException - if the property does not exist in FilteringDao, or if the operator cannot be applied, or if the value cannot apply to the property an operator see Filter.parse(String, String, Class, Filter.Operator, String, String) for more details

getFilter

public Filter getFilter(String property,
 Filter.Operator operator,
 String value,
 SubqueryMode subqueryMode)

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

getFilter

public final Filter getFilter(String property,
 Filter.Operator operator,
 Collection<String> values)
                       throws IllegalArgumentException

Description copied from interface: FilteringDao

Similar to FilteringDao.getFilter(String, Filter.Operator, String), but with a collection of values.

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

Throws:

IllegalArgumentException

getFilter

public Filter getFilter(String property,
 Filter.Operator operator,
 Collection<String> values,
 SubqueryMode subqueryMode)

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

getFilter

public final <T> Filter getFilter(String property,
 Class<T> propertyType,
 Filter.Operator operator,
 T value)

Description copied from interface: FilteringDao

Obtain a Filter with an already parsed value.

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

See Also:

• FilteringDao.getFilter(String, Filter.Operator, String)

getFilter

public final <T> Filter getFilter(String property,
 Class<T> propertyType,
 Filter.Operator operator,
 Collection<T> values)

Description copied from interface: FilteringDao

Obtain a Filter with an already parsed collection of values.

Specified by:

getFilter in interface FilteringDao<O extends Identifiable>

See Also:

• FilteringDao.getFilter(String, Filter.Operator, Collection)

getSort

public final Sort getSort(String property,
 @Nullable
 Sort.Direction direction,
 Sort.NullMode nullMode)
                   throws IllegalArgumentException

Description copied from interface: FilteringDao

Obtain a Sort object for a property of the FilteringDao.

Specified by:

getSort in interface FilteringDao<O extends Identifiable>

Parameters:

property - a property of FilteringDao to sort by

direction - a sorting direction, or null if the default direction applies

nullMode - behavior for null values when sorting

Returns:

a Sort object that can be used, for example, on FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)

Throws:

IllegalArgumentException - if no such field exists in FilteringDao

loadIds

public final List<Long> loadIds(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringDao

Load IDs of entities matching the given filters.

Specified by:

loadIds in interface FilteringDao<O extends Identifiable>

load

public final List<O> load(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringDao

Load entities matching the given filters.

Specified by:

load in interface FilteringDao<O extends Identifiable>

load

public final Slice<O> load(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Description copied from interface: FilteringDao

Load a slice of entities matching the given filters.

Specified by:

load in interface FilteringDao<O extends Identifiable>

count

public final long count(@Nullable
 Filters filters)

Description copied from interface: FilteringDao

Count VOs matching the given filters.

Specified by:

count in interface FilteringDao<O extends Identifiable>

loadValueObjects

public final Slice<VO> loadValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort,
 int offset,
 int limit)

Description copied from interface: FilteringVoEnabledDao

Load VOs with ordering, filtering and offset/limit.

Consider using FilteringDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode) to produce the filters and sort safely from user input.

Specified by:

loadValueObjects in interface FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

Parameters:

filters - filters applied on the search. The properties mentioned in the Filter must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

sort - an object property and direction to order by. This property must exist and be visible to Hibernate. You can use nested properties such as "curationDetails.lastUpdated".

offset - an offset from which entities are retrieved when sorted according to the sort argument, or 0 to ignore

limit - a limit on the number of returned results, or -1 to ignore

Returns:

a slice of the relevant data

See Also:

• FilteringDao.load(Filters, Sort, int, int)

loadValueObjects

public final List<VO> loadValueObjects(@Nullable
 Filters filters,
 @Nullable
 Sort sort)

Description copied from interface: FilteringVoEnabledDao

Load VOs with minimal ordering and filtering.

Use this as an alternative to FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int) if you do not intend to provide pagination capabilities.

Specified by:

loadValueObjects in interface FilteringVoEnabledDao<O extends Identifiable,VO extends IdentifiableValueObject<O>>

See Also:

• FilteringDao.load(Filters, Sort)
• FilteringVoEnabledDao.loadValueObjects(Filters, Sort, int, int)