Package ubic.gemma.web.controller.expression.experiment

Class ExpressionExperimentSetController

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.expression.experiment.ExpressionExperimentSetController

@Controller
@RequestMapping("/expressionExperimentSet")
public class ExpressionExperimentSetController
extends BaseController

For fetching and manipulating ExpressionExperimentSets. Methods take collections to be compatible with Store interfaces.

Author:

paul

Field Summary

Fields inherited from class ubic.gemma.web.controller.BaseController

log

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSetController()

Method Summary

Modifier and Type	Method	Description
SessionBoundExpressionExperimentSetValueObject	addSessionGroup(SessionBoundExpressionExperimentSetValueObject eesvo, Boolean modificationBased)	AJAX adds the Expression Experiment group to the session
Collection<SessionBoundExpressionExperimentSetValueObject>	addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> eeSetVos, Boolean modificationBased)	Deprecated.
Collection<ExpressionExperimentSetValueObject>	addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> sets)	AJAX adds the experiment group to the session
String	canCurrentUserEditGroup(ExpressionExperimentSetValueObject eesvo)	AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed
Collection<ExpressionExperimentSetValueObject>	create(Collection<ExpressionExperimentSetValueObject> entities)
Collection<Long>	getExperimentIdsInSet(Long id)
Collection<ExpressionExperimentDetailsValueObject>	getExperimentsInSet(Long groupId, Integer limit)
ExpressionExperimentSetValueObject	load(Long id)	AJAX
Collection<ExpressionExperimentSetValueObject>	loadAll()	AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments
Collection<SessionBoundExpressionExperimentSetValueObject>	loadAllSessionGroups()	AJAX
Collection<ExpressionExperimentSetValueObject>	loadAllUserAndSessionGroups()	AJAX
Collection<ExpressionExperimentSetValueObject>	loadAllUserOwnedAndSessionGroups()	AJAX
ExpressionExperimentSetValueObject	loadByName(String name)
Collection<ExpressionExperimentSetValueObject>	remove(Collection<ExpressionExperimentSetValueObject> entities)
Collection<SessionBoundExpressionExperimentSetValueObject>	removeSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> vos)	AJAX Given a valid experiment group will remove it from the session.
Collection<ExpressionExperimentSetValueObject>	removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Given valid experiment groups will remove them from the session or the database appropriately.
ModelAndView	showExpressionExperimentSet(javax.servlet.http.HttpServletRequest request, javax.servlet.http.HttpServletResponse response)
Collection<ExpressionExperimentSetValueObject>	update(Collection<ExpressionExperimentSetValueObject> entities)
String	updateMembers(Long groupId, Collection<Long> eeIds)	AJAX Updates the given group (permission permitting) with the given list of memberIds.
ExpressionExperimentSetValueObject	updateNameDesc(ExpressionExperimentSetValueObject eeSetVO)	AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.
Collection<SessionBoundExpressionExperimentSetValueObject>	updateSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> vos)	AJAX Updates the session group.
Collection<ExpressionExperimentSetValueObject>	updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)	AJAX Updates the session group and user database groups.

Methods inherited from class ubic.gemma.web.controller.BaseController

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMailEngine, setMessageSource, setMessageUtil

Methods inherited from class java.lang.Object

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

Constructor Detail

ExpressionExperimentSetController

public ExpressionExperimentSetController()

Method Detail

addSessionGroups

@Deprecated
public Collection<SessionBoundExpressionExperimentSetValueObject> addSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> eeSetVos,
                                                                                   Boolean modificationBased)

Deprecated.

AJAX adds the Expression Experiment group to the session

Parameters:

eeSetVos - value object constructed on the client.

modificationBased - whether the set was modified by the user

Returns:

collection of added session groups (with updated reference.id etc)

addSessionGroup

public SessionBoundExpressionExperimentSetValueObject addSessionGroup(SessionBoundExpressionExperimentSetValueObject eesvo,
                                                                      Boolean modificationBased)

AJAX adds the Expression Experiment group to the session

addUserAndSessionGroups

public Collection<ExpressionExperimentSetValueObject> addUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> sets)

AJAX adds the experiment group to the session

Returns:

the new gene groups

canCurrentUserEditGroup

public String canCurrentUserEditGroup(ExpressionExperimentSetValueObject eesvo)

AJAX returns a JSON string encoding whether the current user owns the group and whether the group is db-backed

create

public Collection<ExpressionExperimentSetValueObject> create(Collection<ExpressionExperimentSetValueObject> entities)

getExperimentIdsInSet

public Collection<Long> getExperimentIdsInSet(Long id)

getExperimentsInSet

public Collection<ExpressionExperimentDetailsValueObject> getExperimentsInSet(Long groupId,
                                                                              Integer limit)

Parameters:

limit - to return only up to a given number of experiments, e.g. for a preview of the set.

load

public ExpressionExperimentSetValueObject load(Long id)

AJAX

Parameters:

id - of the set

Returns:

the ExpressionExperimentSetValueObject for the id param

Throws:

IllegalArgumentException - if the id param is null

org.springframework.security.access.AccessDeniedException - if the id param is not null but the loading function returns a null value

loadAll

public Collection<ExpressionExperimentSetValueObject> loadAll()

AJAX returns all available sets that have a taxon value (so not really all) sets can have *any* number of experiments

Returns:

all available sets that have a taxon value

loadAllSessionGroups

public Collection<SessionBoundExpressionExperimentSetValueObject> loadAllSessionGroups()

AJAX

Returns:

all available session backed sets

loadAllUserAndSessionGroups

public Collection<ExpressionExperimentSetValueObject> loadAllUserAndSessionGroups()

AJAX

Returns:

all available sets from db and also session backed sets

loadAllUserOwnedAndSessionGroups

public Collection<ExpressionExperimentSetValueObject> loadAllUserOwnedAndSessionGroups()

AJAX

Returns:

all available sets that have a taxon value from db and also session backed sets

loadByName

public ExpressionExperimentSetValueObject loadByName(String name)

remove

public Collection<ExpressionExperimentSetValueObject> remove(Collection<ExpressionExperimentSetValueObject> entities)

Returns:

the entities which were removed.

removeSessionGroups

public Collection<SessionBoundExpressionExperimentSetValueObject> removeSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> vos)

AJAX Given a valid experiment group will remove it from the session.

removeUserAndSessionGroups

public Collection<ExpressionExperimentSetValueObject> removeUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)

AJAX Given valid experiment groups will remove them from the session or the database appropriately.

showExpressionExperimentSet

@RequestMapping(value="/showExpressionExperimentSet.html",
                method=GET)
public ModelAndView showExpressionExperimentSet(javax.servlet.http.HttpServletRequest request,
                                                javax.servlet.http.HttpServletResponse response)

update

public Collection<ExpressionExperimentSetValueObject> update(Collection<ExpressionExperimentSetValueObject> entities)

Returns:

the entities which were updated (even if they weren't actually updated)

updateMembers

public String updateMembers(Long groupId,
                            Collection<Long> eeIds)

AJAX Updates the given group (permission permitting) with the given list of memberIds. Will not allow the same experiment to be added to the set twice. Will not update name or description, just members.

Parameters:

groupId - id of the gene set being updated

Returns:

error message or null if no errors

updateNameDesc

public ExpressionExperimentSetValueObject updateNameDesc(ExpressionExperimentSetValueObject eeSetVO)

AJAX Updates the database record for the param experiment set value object (permission permitting) with the value object's name and description.

Parameters:

eeSetVO - the value object that represents the database record to update

Returns:

a value object for the updated set

updateSessionGroups

public Collection<SessionBoundExpressionExperimentSetValueObject> updateSessionGroups(Collection<SessionBoundExpressionExperimentSetValueObject> vos)

AJAX Updates the session group.

updateUserAndSessionGroups

public Collection<ExpressionExperimentSetValueObject> updateUserAndSessionGroups(Collection<ExpressionExperimentSetValueObject> vos)

AJAX Updates the session group and user database groups.