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

Class ExperimentalDesignController

java.lang.Object

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

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

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

Modifier and Type	Field	Description
protected final org.apache.commons.logging.Log	log
protected org.springframework.context.MessageSource	messageSource
protected MessageUtil	messageUtil

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignController()

Method Summary

Modifier and Type	Method	Description
void	clearFactorValuesNeedsAttention(Long[] fvvos, String note)	AJAX
void	createDesignFromFile(Long eeid, String filename)	AJAX
void	createExperimentalFactor(EntityDelegator<ExperimentalDesign> e, ExperimentalFactorValueWebUIObject efvo)	Create an experimental factor.
void	createFactorValue(EntityDelegator<ExperimentalFactor> e)	AJAX
void	createFactorValueCharacteristic(EntityDelegator<FactorValue> e, CharacteristicValueObject cvo)	AJAX
void	deleteExperimentalFactors(EntityDelegator<ExperimentalDesign> e, Long[] efIds)	AJAX
void	deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)	AJAX
void	deleteFactorValues(EntityDelegator<ExperimentalFactor> e, Long[] fvIds)	AJAX
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)	AJAX
Collection<ExperimentalFactorValueObject>	getExperimentalFactors(EntityDelegator<?> e)	AJAX
Collection<FactorValueValueObject>	getFactorValues(EntityDelegator<ExperimentalFactor> e)	AJAX
Collection<FactorValueValueObject>	getFactorValuesWithCharacteristics(EntityDelegator<ExperimentalFactor> e)	AJAX
void	markFactorValuesAsNeedsAttention(Long[] fvvos, String note)	AJAX
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)	AJAX
void	updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)	AJAX
void	updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)	AJAX

Methods inherited from class java.lang.Object

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

Field Details

log

protected final org.apache.commons.logging.Log log

messageSource

@Autowired
protected org.springframework.context.MessageSource messageSource

messageUtil

@Autowired
protected MessageUtil messageUtil

Constructor Details

ExperimentalDesignController

public ExperimentalDesignController()

Method Details

createDesignFromFile

public void createDesignFromFile(Long eeid,
 String filename)

AJAX

createExperimentalFactor

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

Create an experimental factor.

AJAX

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)

AJAX

createFactorValueCharacteristic

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

AJAX

deleteExperimentalFactors

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

AJAX

deleteFactorValueCharacteristics

public void deleteFactorValueCharacteristics(FactorValueValueObject[] fvvos)

AJAX

duplicateFactorValue

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

Make an exact copy of a factorvalue and add it to the experiment. As per #1160

AJAX

Parameters:

e - the experimental factor

fvId - the id of the FV to duplicate

deleteFactorValues

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

AJAX

getBioMaterials

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

AJAX

getBioMaterialCharacteristicCategories

public Collection<CharacteristicValueObject> getBioMaterialCharacteristicCategories(Long experimentalDesignID)

Extract just the categories from the biomaterial's characteristics.

AJAX

Returns:

Collection of CharacteristicValueObjects but all we care about is the category

getExperimentalFactors

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

AJAX

getFactorValues

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

AJAX

getFactorValuesWithCharacteristics

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

AJAX

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)

AJAX

updateExperimentalFactors

public void updateExperimentalFactors(ExperimentalFactorValueObject[] efvos)

AJAX

updateFactorValueCharacteristics

public void updateFactorValueCharacteristics(FactorValueValueObject[] fvvos)

AJAX

markFactorValuesAsNeedsAttention

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

AJAX

clearFactorValuesNeedsAttention

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

AJAX