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

Class 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

    • Constructor Detail

      • ExperimentalDesignController

        public ExperimentalDesignController()

    • Method Detail

      • createDesignFromFile

        public void createDesignFromFile​(Long eeid,
                                 String filePath)

      • createExperimentalFactor

        public void createExperimentalFactor​(EntityDelegator<ubic.gemma.model.expression.experiment.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<ubic.gemma.model.expression.experiment.ExperimentalFactor> e)

      • createFactorValueCharacteristic

        public void createFactorValueCharacteristic​(EntityDelegator<ubic.gemma.model.expression.experiment.FactorValue> e,
                                            ubic.gemma.model.common.description.CharacteristicValueObject cvo)

      • deleteExperimentalFactors

        public void deleteExperimentalFactors​(EntityDelegator<ubic.gemma.model.expression.experiment.ExperimentalDesign> e,
                                      Long[] efIds)

      • deleteFactorValueCharacteristics

        public void deleteFactorValueCharacteristics​(ubic.gemma.model.expression.experiment.FactorValueValueObject[] fvvos)

      • duplicateFactorValue

        public void duplicateFactorValue​(EntityDelegator<ubic.gemma.model.expression.experiment.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<ubic.gemma.model.expression.experiment.ExperimentalFactor> e,
                               Long[] fvIds)

      • getBioMaterials

        public Collection<ubic.gemma.model.expression.biomaterial.BioMaterialValueObject> getBioMaterials​(EntityDelegator<ubic.gemma.model.expression.experiment.ExpressionExperiment> e)

      • getBioMaterialCharacteristicCategories

        public Collection<ubic.gemma.model.common.description.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<ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject> getExperimentalFactors​(EntityDelegator<?> e)

      • getFactorValues

        public Collection<ubic.gemma.model.expression.experiment.FactorValueValueObject> getFactorValues​(EntityDelegator<ubic.gemma.model.expression.experiment.ExperimentalFactor> e)

      • getFactorValuesWithCharacteristics

        public Collection<ubic.gemma.model.expression.experiment.FactorValueValueObject> getFactorValuesWithCharacteristics​(EntityDelegator<ubic.gemma.model.expression.experiment.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​(ubic.gemma.model.expression.biomaterial.BioMaterialValueObject[] bmvos)

      • updateExperimentalFactors

        public void updateExperimentalFactors​(ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject[] efvos)

      • updateFactorValueCharacteristics

        public void updateFactorValueCharacteristics​(ubic.gemma.model.expression.experiment.FactorValueValueObject[] fvvos)

      • markFactorValuesAsNeedsAttention

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

      • clearFactorValuesNeedsAttention

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