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 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<ubic.gemma.model.expression.experiment.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<ubic.gemma.model.expression.experiment.ExperimentalFactor> e)
      AJAX

    • createFactorValueCharacteristic

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

    • deleteExperimentalFactors

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

    • deleteFactorValueCharacteristics

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

    • 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 #1160

      AJAX

      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)
      AJAX

    • getBioMaterials

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

    • getBioMaterialCharacteristicCategories

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

    • getFactorValues

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

    • getFactorValuesWithCharacteristics

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

    • updateExperimentalFactors

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

    • updateFactorValueCharacteristics

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

    • markFactorValuesAsNeedsAttention

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

    • clearFactorValuesNeedsAttention

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