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

Class ExperimentalDesignController

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.expression.experiment.ExperimentalDesignController

@Controller
@RequestMapping("/experimentalDesign")
public class ExperimentalDesignController
extends BaseController

Main entry point to editing and viewing experimental designs. Note: do not use parametrized collections as parameters for ajax methods in this class! Type information is lost during proxy creation so DWR can't figure out what type of collection the method should take. See bug 2756. Use arrays instead.

Author:

keshav

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignController()

Method Summary

Modifier and Type	Method	Description
void	clearFactorValuesNeedsAttention(Long[] fvvos, String note)
void	createDesignFromFile(Long eeid, String filePath)
void	createExperimentalFactor(EntityDelegator<ExperimentalDesign> e, ExperimentalFactorValueWebUIObject efvo)	Create an experimental factor.
void	createFactorValue(EntityDelegator<ExperimentalFactor> e)
void	createFactorValueCharacteristic(EntityDelegator<FactorValue> e, CharacteristicValueObject cvo)
void	deleteExperimentalFactors(EntityDelegator<ExperimentalDesign> e, Long[] efIds)
void	deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)
void	deleteFactorValues(EntityDelegator<ExperimentalFactor> e, Long[] fvIds)
void	duplicateFactorValue(EntityDelegator<ExperimentalFactor> e, Long fvId)	Make an exact copy of a factorvalue and add it to the experiment.
Collection<CharacteristicValueObject>	getBioMaterialCharacteristicCategories(Long experimentalDesignID)	Extract just the categories from the biomaterial's characteristics.
Collection<BioMaterialValueObject>	getBioMaterials(EntityDelegator<ExpressionExperiment> e)
Collection<ExperimentalFactorValueObject>	getExperimentalFactors(EntityDelegator<?> e)
Collection<FactorValueValueObject>	getFactorValues(EntityDelegator<ExperimentalFactor> e)
Collection<FactorValueValueObject>	getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor> e)
void	markFactorValuesAsNeedsAttention(Long[] fvvos, String note)
org.springframework.web.servlet.ModelAndView	showByExperimentId(Long eeId)
org.springframework.web.servlet.ModelAndView	showByExperimentShortName(String shortName)
org.springframework.web.servlet.ModelAndView	showById(Long edId)
void	updateBioMaterials(BioMaterialValueObject[] bmvos)
void	updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)
void	updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)

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

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMessageUtil

Methods inherited from class java.lang.Object

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

Constructor Detail

ExperimentalDesignController

public ExperimentalDesignController()

Method Detail

createDesignFromFile

public void createDesignFromFile(Long eeid,
                                 String filePath)

createExperimentalFactor

public void createExperimentalFactor(EntityDelegator<ExperimentalDesign> e,
                                     ExperimentalFactorValueWebUIObject efvo)

Create an experimental factor.

Parameters:

e - experimentalDesign to add the factor to

efvo - non-null if we are pre-populating the factor values based on an existing set of BioMaterialCharacteristic, see #987

createFactorValue

public void createFactorValue(EntityDelegator<ExperimentalFactor> e)

createFactorValueCharacteristic

public void createFactorValueCharacteristic(EntityDelegator<FactorValue> e,
                                            CharacteristicValueObject cvo)

deleteExperimentalFactors

public void deleteExperimentalFactors(EntityDelegator<ExperimentalDesign> e,
                                      Long[] efIds)

deleteFactorValueCharacteristics

public void deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)

duplicateFactorValue

public void duplicateFactorValue(EntityDelegator<ExperimentalFactor> e,
                                 Long fvId)

Make an exact copy of a factorvalue and add it to the experiment. As per https://github.com/PavlidisLab/Gemma/issues/1160

Parameters:

e - the experimental factor

fvId - the id of the FV to duplicate

deleteFactorValues

public void deleteFactorValues(EntityDelegator<ExperimentalFactor> e,
                               Long[] fvIds)

getBioMaterials

public Collection<BioMaterialValueObject> getBioMaterials(EntityDelegator<ExpressionExperiment> e)

getBioMaterialCharacteristicCategories

public Collection<CharacteristicValueObject> getBioMaterialCharacteristicCategories(Long experimentalDesignID)

Extract just the categories from the biomaterial's characteristics.

Returns:

Collection of CharacteristicValueObjects but all we care about is the category

getExperimentalFactors

public Collection<ExperimentalFactorValueObject> getExperimentalFactors(EntityDelegator<?> e)

getFactorValues

public Collection<FactorValueValueObject> getFactorValues(EntityDelegator<ExperimentalFactor> e)

getFactorValuesWithCharacteristics

public Collection<FactorValueValueObject> getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor> e)

showById

@RequestMapping(value="/showExperimentalDesign.html",
                params="edid",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView showById(@RequestParam("edid")
                                                             Long edId)

showByExperimentId

@RequestMapping(value="/showExperimentalDesign.html",
                params="eeid",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView showByExperimentId(@RequestParam("eeid")
                                                                       Long eeId)

showByExperimentShortName

@RequestMapping(value="/showExperimentalDesign.html",
                params="shortName",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView showByExperimentShortName(@RequestParam("shortName")
                                                                              String shortName)

updateBioMaterials

public void updateBioMaterials(BioMaterialValueObject[] bmvos)

updateExperimentalFactors

public void updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)

updateFactorValueCharacteristics

public void updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)

markFactorValuesAsNeedsAttention

public void markFactorValuesAsNeedsAttention(Long[] fvvos,
                                             String note)

clearFactorValuesNeedsAttention

public void clearFactorValuesNeedsAttention(Long[] fvvos,
                                            String note)