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

Class AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

java.lang.Object

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

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

ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao<C,VO>

ubic.gemma.persistence.service.AbstractQueryFilteringVoEnabledDao<C,VO>

ubic.gemma.persistence.service.common.auditAndSecurity.curation.AbstractCuratableDao<C,VO>

All Implemented Interfaces:

org.springframework.beans.factory.InitializingBean, BaseDao<C>, BaseVoEnabledDao<C,VO>, CachedFilteringDao<C>, CachedFilteringVoEnabledDao<C,VO>, CuratableDao<C>, FilteringDao<C>, FilteringVoEnabledDao<C,VO>

Direct Known Subclasses:

ArrayDesignDaoImpl, ExpressionExperimentDaoImpl

public abstract class AbstractCuratableDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>
extends AbstractQueryFilteringVoEnabledDao<C,VO>
implements CuratableDao<C>

Created by tesarst on 07/03/17. DAO covering methods common to all Curatable objects.

Author:

tesarst

Nested Class Summary

Nested classes/interfaces inherited from class ubic.gemma.persistence.service.AbstractFilteringVoEnabledDao

AbstractFilteringVoEnabledDao.FilterablePropertiesConfigurer, AbstractFilteringVoEnabledDao.FilterablePropertyMeta

Field Summary

Fields

Modifier and Type	Field	Description
protected static final String	CURATION_DETAILS_ALIAS	HQL alias for Curatable.getCurationDetails().

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	AbstractCuratableDao(String objectAlias, Class<C> elementClass, SessionFactory sessionFactory)

Method Summary

Modifier and Type	Method	Description
protected void	addEventsToMap(Map<Long,Collection<AuditEvent>> eventMap, Long id, AuditEvent event)
protected void	addNonTroubledFilter(Filters filters, String objectAlias)	Restrict results to non-troubled curatable entities for non-administrators
protected void	configureFilterableProperties(AbstractFilteringVoEnabledDao<C,VO>.FilterablePropertiesConfigurer configurer)	Register filterable properties.
protected String	distinctIfNecessary()	If the filters or sort refer to one of the one-to-many relations, multiple rows will be returned per datasets, so the query has to use a "distinct" clause make pagination work properly.
protected String	formNativeNonTroubledClause(String idColumn, Class<? extends Curatable> clazz)	Form a native non-troubled clause.
protected String	formNonTroubledClause(String objectAlias, Class<? extends Curatable> clazz)	Form a non-troubled clause.
protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta	getFilterablePropertyMeta(String propertyName)	Obtain various meta-information used to infer what to use in a Filter or Sort.
protected String	groupByIfNecessary(Sort sort, String... oneToManyAliases)	Similar logic to distinctIfNecessary(), but using a group by since it's more efficient.
List<Long>	loadTroubledIds()	Load IDs of troubled entities.
void	updateCurationDetailsFromAuditEvent(C curatable, AuditEvent auditEvent)	Update the curation details of a given curatable entity.

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

count, countWithCache, getEntityTransformer, getFilteringCountQuery, getFilteringIdQuery, getFilteringQuery, getValueObjectTransformer, initializeCachedFilteringResult, load, load, loadIds, loadIdsWithCache, loadValueObjects, loadValueObjects, loadValueObjectsWithCache, loadValueObjectsWithCache, loadWithCache, loadWithCache

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

afterPropertiesSet, getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyMeta, getFilterablePropertyType, getSort

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

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

getFilter, getFilter, getFilter, getFilter, getFilter, getFilter, getFilterableProperties, getFilterablePropertyAllowedValues, getFilterablePropertyDescription, getFilterablePropertyIsUsingSubquery, getFilterablePropertyType, getSort

Field Details

CURATION_DETAILS_ALIAS

protected static final String CURATION_DETAILS_ALIAS

HQL alias for Curatable.getCurationDetails().

See Also:

• Constant Field Values

Constructor Details

AbstractCuratableDao

protected AbstractCuratableDao(String objectAlias,
 Class<C> elementClass,
 SessionFactory sessionFactory)

Method Details

loadTroubledIds

public List<Long> loadTroubledIds()

Description copied from interface: CuratableDao

Load IDs of troubled entities.

Specified by:

loadTroubledIds in interface CuratableDao<C extends Curatable>

updateCurationDetailsFromAuditEvent

public void updateCurationDetailsFromAuditEvent(C curatable,
 AuditEvent auditEvent)

Description copied from interface: CuratableDao

Update the curation details of a given curatable entity.

This method should only be called from AuditTrailService, as the passed event has to already exist in the audit trail of the curatable object.

Only use this method directly if you do not want the event to show up in the curatable objects audit trail.

This is marked as ignored for audit purposes since we don't want to audit the curation details update when it originated from an audit event.

Specified by:

updateCurationDetailsFromAuditEvent in interface CuratableDao<C extends Curatable>

Parameters:

curatable - curatable

auditEvent - the event containing information about the update. Method only accepts audit events whose type is one of CurationDetailsEvent extensions.

See Also:

• CuratableDao.updateCurationDetailsFromAuditEvent(Curatable, AuditEvent)

addEventsToMap

protected void addEventsToMap(Map<Long,Collection<AuditEvent>> eventMap,
 Long id,
 AuditEvent event)

addNonTroubledFilter

protected void addNonTroubledFilter(Filters filters,
 String objectAlias)

Restrict results to non-troubled curatable entities for non-administrators

distinctIfNecessary

protected String distinctIfNecessary()

If the filters or sort refer to one of the one-to-many relations, multiple rows will be returned per datasets, so the query has to use a "distinct" clause make pagination work properly.

Using "distinct" otherwise has a steep performance penalty when combined with "order by".

Note that non-admin users always need a group by because of the jointure on ACL entries.

FIXME: remove the need for a distinct altogether by using a sub-query to apply ACLs (see #784)

groupByIfNecessary

@Nullable
protected String groupByIfNecessary(@Nullable
 Sort sort,
 String... oneToManyAliases)

Similar logic to distinctIfNecessary(), but using a group by since it's more efficient. It does not work for the counting queries, however.

FIXME: remove the need for a group by altogether by using a sub-query to apply ACLs (see #784)

formNonTroubledClause

protected String formNonTroubledClause(String objectAlias,
 Class<? extends Curatable> clazz)

Form a non-troubled clause.

formNativeNonTroubledClause

protected String formNativeNonTroubledClause(String idColumn,
 Class<? extends Curatable> clazz)

Form a native non-troubled clause.

configureFilterableProperties

@OverridingMethodsMustInvokeSuper
protected void configureFilterableProperties(AbstractFilteringVoEnabledDao<C,VO>.FilterablePropertiesConfigurer configurer)

Description copied from class: AbstractFilteringVoEnabledDao

Register filterable properties.

Overrides:

configureFilterableProperties in class AbstractFilteringVoEnabledDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

getFilterablePropertyMeta

protected AbstractFilteringVoEnabledDao.FilterablePropertyMeta getFilterablePropertyMeta(String propertyName)
                                                                                  throws IllegalArgumentException

Obtain various meta-information used to infer what to use in a Filter or Sort.

This is used by AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String) and FilteringDao.getSort(String, Sort.Direction, Sort.NullMode).

Include filtering by lastUpdated, troubled and needsAttention from the associated curation details.

Overrides:

getFilterablePropertyMeta in class AbstractFilteringVoEnabledDao<C extends Curatable,VO extends AbstractCuratableValueObject<C>>

Throws:

IllegalArgumentException - if no such propertyName exists in AbstractFilteringVoEnabledDao

See Also:

• AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, String)
• AbstractFilteringVoEnabledDao.getFilter(String, Filter.Operator, Collection)
• FilteringDao.getSort(String, Sort.Direction, Sort.NullMode)