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

Class ExpressionExperimentController

    • Constructor Detail

      • ExpressionExperimentController

        public ExpressionExperimentController()

    • Method Detail

      • 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

      • 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

        @Secured("GROUP_USER")
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("/filterExpressionExperiments.html")
public ModelAndView filter​(javax.servlet.http.HttpServletRequest request,
                           javax.servlet.http.HttpServletResponse response)

      • 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

      • 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)

      • getQCTagHTML

        public String getQCTagHTML​(ExpressionExperiment ee)
        Used to include the html for the qc table in an ext panel (without using a tag) (This method should probably be in a service?)

      • 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)

      • recalculateBatchEffect

        public void recalculateBatchEffect​(Long id)

      • runGeeq

        public void runGeeq​(Long id,
                    String mode)

      • 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

      • 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

        @Secured("GROUP_USER")
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:
        taxonId - if the search should not be limited by taxon, pass in null
        query - query
        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({"/showAllExpressionExperiments.html","/showAll"})
public ModelAndView showAllExpressionExperiments​(javax.servlet.http.HttpServletRequest request,
                                                 javax.servlet.http.HttpServletResponse response)
        Show all experiments (optionally conditioned on either a taxon, a list of ids, or a platform)
        Parameters:
        request - request
        response - response
        Returns:
        model and view

      • showAllLinkSummaries

        @RequestMapping({"/showAllExpressionExperimentLinkSummaries.html","/manage.html"})
public ModelAndView showAllLinkSummaries​(javax.servlet.http.HttpServletRequest request,
                                         javax.servlet.http.HttpServletResponse response)

      • showSubSet

        @RequestMapping({"/showExpressionExperimentSubSet.html","/showSubset"})
public ModelAndView showSubSet​(javax.servlet.http.HttpServletRequest request,
                               javax.servlet.http.HttpServletResponse response)
        shows a list of BioAssays for an expression experiment subset
        Parameters:
        request - request
        response - response
        Returns:
        model and view

      • 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

      • updatePubMed

        @Secured("GROUP_USER")
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

      • handleRequestInternal

        @RequestMapping("/downloadExpressionExperimentList.html")
public ModelAndView handleRequestInternal​(javax.servlet.http.HttpServletRequest request)