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

Class ExpressionExperimentController

java.lang.Object
ubic.gemma.web.controller.expression.experiment.ExpressionExperimentController
@Controller @RequestMapping({"/expressionExperiment","/ee"}) public class ExpressionExperimentController extends Object
Author:
keshav

  • Constructor Details

    • ExpressionExperimentController

      public ExpressionExperimentController()

  • Method Details

    • browse

      public JsonReaderResponse<ExpressionExperimentDetailsValueObject> browse(ListBatchCommand batch)
      AJAX call for remote paging store security isn't incorporated in db query, so paging needs to occur at higher level.
      1. a db call returns all experiments, which are filtered by the service method
      2. if the user is an admin, we filter out the troubled experiments
      3. an appropriate page-sized chunk is then taken from this (filtered) list
      4. another round of db calls create and fill value objects for this chunk
      5. value objects are returned

    • browseByTaxon

      public JsonReaderResponse<ExpressionExperimentDetailsValueObject> browseByTaxon(ListBatchCommand batch, Long taxonId)
      AJAX

    • browseSpecificIds

      public JsonReaderResponse<ExpressionExperimentDetailsValueObject> browseSpecificIds(ListBatchCommand batch, Collection<Long> ids)
      AJAX call for remote paging store

    • canCurrentUserEditExperiment

      public boolean canCurrentUserEditExperiment(Long eeId)
      AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it

    • clearFromCaches

      public void clearFromCaches(Long eeId)
      AJAX clear entries in caches relevant to experimental design for the experiment passed in. The caches cleared are the processedDataVectorCache and the caches held in ExperimentalDesignVisualizationService

    • deleteById

      public String deleteById(Long id)
      Exposed for AJAX calls.

    • doesCurrentUserOwnExperiment

      public boolean doesCurrentUserOwnExperiment(Long eeId)
      AJAX returns a JSON string encoding whether the current user owns the experiment and whether they can edit it

    • filter

      @RequestMapping(value="/filterExpressionExperiments.html", method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView filter(@RequestParam("filter") String searchString)

    • find

      public Collection<Long> find(String query, Long taxonId)
      AJAX TODO --- include a search of subsets. NOTE: only used via DataSetSearchAndGrabToolbar -> DatasetGroupEditor?
      Parameters:
      query - search string
      taxonId - (if null, all taxa are searched)
      Returns:
      EE ids that match

    • getAllTaxonExperimentGroup

      public List<SearchResultDisplayObject> getAllTaxonExperimentGroup(Long taxonId)
      AJAX

    • getAnnotation

      public Collection<AnnotationValueObject> getAnnotation(EntityDelegator<ExpressionExperiment> e)
      AJAX

    • getDescription

      public String getDescription(Long id)
      AJAX call
      Returns:
      a more informative description than the regular description 1st 120 characters of ee.description + Experimental Design information returned string contains HTML tags. TODO: Would be more generic if passed back a DescriptionValueObject that contains all the info necessary to reconstruct the HTML on the client side Currently only used by ExpressionExperimentGrid.js (row expander)

    • getDesignMatrixRows

      public Collection<DesignMatrixRowValueObject> getDesignMatrixRows(EntityDelegator<ExpressionExperiment> e)
      AJAX

    • getExperimentalFactors

      public Collection<ExperimentalFactorValueObject> getExperimentalFactors(EntityDelegator<ExpressionExperiment> e)
      AJAX
      Returns:
      a collection of factor value objects that represent the factors of a given experiment

    • getFactorValues

      public Collection<FactorValueValueObject> getFactorValues(EntityDelegator<ExperimentalFactor> e)
      AJAX
      Returns:
      A collection of factor value objects for the specified experimental factor

    • loadCountsForDataSummaryTable

      public Map<String,Object> loadCountsForDataSummaryTable()
      AJAX method to get data for database summary table, returned as a JSON object the slow part here is loading each new or updated object in whatsNewService.retrieveReport() -> fetch()
      Returns:
      json

    • loadExpressionExperimentDetails

      public ExpressionExperimentDetailsValueObject loadExpressionExperimentDetails(Long id)
      AJAX; Populate all the details.
      Parameters:
      id - Identifier for the experiment
      Returns:
      ee details vo

    • recalculateBatchConfound

      public void recalculateBatchConfound(Long id)
      AJAX

    • recalculateBatchEffect

      public void recalculateBatchEffect(Long id)
      AJAX

    • runGeeq

      public void runGeeq(Long id, String mode)
      AJAX

    • loadExpressionExperiments

      public Collection<ExpressionExperimentDetailsValueObject> loadExpressionExperiments(List<Long> ids)
      AJAX - for display in tables. Don't retrieve too much detail.
      Parameters:
      ids - of EEs to load
      Returns:
      security-filtered set of value objects.

    • loadExperimentsForPlatform

      public Collection<ExpressionExperimentDetailsValueObject> loadExperimentsForPlatform(Long id)
      AJAX get experiments that used a given platform. Don't retrieve too much detail.
      Parameters:
      id - of platform
      Returns:
      collection of experiments that use this platform -- including those that were switched

    • loadDetailedExpressionExperiments

      public Collection<ExpressionExperimentDetailsValueObject> loadDetailedExpressionExperiments(Collection<Long> ids)
      AJAX - for display in tables. Get more details.
      Parameters:
      ids - of EEs to load
      Returns:
      security-filtered set of value objects.

    • loadExpressionExperimentsWithQcIssues

      public JsonReaderResponse<Map<String,Object>> loadExpressionExperimentsWithQcIssues()
      AJAX; get a collection of experiments that have had samples removed due to outliers TODO: and experiment that have possible batch effects detected
      Returns:
      json reader response

    • loadQuantitationTypes

      public Collection<QuantitationTypeValueObject> loadQuantitationTypes(Long eeId)
      AJAX - for display in tables
      Parameters:
      eeId - ee id
      Returns:
      security-filtered set of value objects.

    • loadStatusSummaries

      public Collection<ExpressionExperimentDetailsValueObject> loadStatusSummaries(Long taxonId, List<Long> ids, Integer limit, Integer filter, Boolean showPublic)
      AJAX. Data summarizing the status of experiments.
      Parameters:
      taxonId - can be null
      limit - If >0, get the most recently updated N experiments, where N <= limit; or if < 0, get the least recently updated; if 0, or null, return all.
      filter - if non-null, limit data sets to ones meeting criteria.
      showPublic - return user's public datasets too
      Returns:
      ee details vos

    • removePrimaryPublication

      public String removePrimaryPublication(Long eeId)
      Remove the primary publication for the given expression experiment (by id). The reference is not actually deleted from the system. AJAX
      Parameters:
      eeId - ee id
      Returns:
      string

    • searchExperimentsAndExperimentGroups

      public List<SearchResultDisplayObject> searchExperimentsAndExperimentGroups(String query, Long taxonId)
      AJAX (used by experimentAndExperimentGroupCombo.js)
      Parameters:
      query - query
      taxonId - if the search should not be limited by taxon, pass in null
      Returns:
      Collection of SearchResultDisplayObjects

    • searchExpressionExperiments

      public Collection<ExpressionExperimentValueObject> searchExpressionExperiments(String query)
      AJAX (used by ExperimentCombo.js)
      Parameters:
      query - query
      Returns:
      Collection of expression experiment entity objects

    • showAllExpressionExperiments

      @RequestMapping(value={"/showAllExpressionExperiments.html","/showAll"}, method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showAllExpressionExperiments()
      Show all experiments (optionally conditioned on either a taxon, a list of ids, or a platform)

    • showAllLinkSummaries

      @RequestMapping(value={"/showAllExpressionExperimentLinkSummaries.html","/manage.html"}, method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showAllLinkSummaries()

    • showBioAssays

      @RequestMapping(value={"/showBioAssaysFromExpressionExperiment.html","/bioAssays"}, method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showBioAssays(@RequestParam("id") Long id, @RequestParam(value="platform",required=false) Long platformId)

    • showBioMaterials

      @RequestMapping(value={"/showBioMaterialsFromExpressionExperiment.html","/bioMaterials"}, method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showBioMaterials(@RequestParam("id") Long id)

    • showExpressionExperimentById

      @RequestMapping(value={"/showExpressionExperiment.html","/","/show"}, params="id", method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showExpressionExperimentById(@RequestParam("id") Long id)

    • showExpressionExperimentByShortName

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

    • showAllSubSets

      @RequestMapping(value={"/showAllExpressionExperimentSubSets.html","/showSubsets"}, method={GET,HEAD}, params="id") public org.springframework.web.servlet.ModelAndView showAllSubSets(@RequestParam("id") Long id, @RequestParam(value="dimension",required=false) Long dimensionId, javax.servlet.http.HttpServletRequest request)

    • showAllSubSets

      @RequestMapping(value={"/showAllExpressionExperimentSubSets.html","/showSubsets"}, method={GET,HEAD}, params="shortName") public org.springframework.web.servlet.ModelAndView showAllSubSets(@RequestParam("shortName") String shortName, @RequestParam(value="dimension",required=false) Long dimensionId, javax.servlet.http.HttpServletRequest request)

    • showSubSet

      @RequestMapping(value={"/showExpressionExperimentSubSet.html","/showSubset"}, method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showSubSet(@RequestParam("id") Long id, @RequestParam(value="dimension",required=false) Long dimensionId, javax.servlet.http.HttpServletRequest request)
      Shows a list of BioAssays for an expression experiment subset.

    • showSingleCellExpressionData

      @RequestMapping(value="/showSingleCellExpressionData.html", method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView showSingleCellExpressionData(@RequestParam("id") Long id, @RequestParam(value="quantitationType",required=false) @Nullable Long quantitationTypeId, @RequestParam("designElement") Long designElementId, @RequestParam(value="assays",required=false) @Nullable Long[] assayIds, @RequestParam(value="cellTypeAssignment",required=false) @Nullable Long cellTypeAssignmentId, @RequestParam(value="cellLevelCharacteristics",required=false) @Nullable Long cellLevelCharacteristicsId, @RequestParam(value="focusedCharacteristic",required=false) @Nullable Long focusedCharacteristicId, javax.servlet.http.HttpServletRequest request)

    • unmatchAllBioAssays

      public void unmatchAllBioAssays(Long eeId)
      Completely reset the pairing of bioassays to biomaterials, so they are no longer paired. New biomaterials are constructed where necessary; they retain the characteristics of the original. Experimental design might need to be redone after this operation. (AJAX)
      Parameters:
      eeId - ee id

    • updateBasics

      public ExpressionExperimentDetailsValueObject updateBasics(UpdateEEDetailsCommand command)

    • updatePubMed

      public String updatePubMed(Long eeId, String pubmedId)
      AJAX. Associate the given pubmedId with the given expression experiment.
      Parameters:
      eeId - ee id
      pubmedId - pubmed id
      Returns:
      string

    • downloadExpressionExperimentList

      @RequestMapping(value="/downloadExpressionExperimentList.html", method={GET,HEAD}) public void downloadExpressionExperimentList(@RequestParam(value="e",required=false) String e, @RequestParam(value="es",required=false) String es, javax.servlet.http.HttpServletResponse response) throws IOException
      Throws:
      IOException