Java tutorial
/* * Copyright 2008-2013 Microarray Informatics Team, EMBL-European Bioinformatics Institute * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * * * For further details of the Gene Expression Atlas project, including source code, * downloads and documentation, please see: * * http://gxa.github.com/gxa */ package uk.ac.ebi.atlas.search; import com.google.common.base.Optional; import org.apache.commons.lang3.StringUtils; import org.apache.log4j.Logger; import org.apache.solr.common.SolrException; import org.springframework.context.annotation.Scope; import org.springframework.http.HttpStatus; import org.springframework.stereotype.Controller; import org.springframework.ui.Model; import org.springframework.validation.BindingResult; import org.springframework.web.bind.MissingServletRequestParameterException; import org.springframework.web.bind.annotation.ExceptionHandler; import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.ResponseStatus; import org.springframework.web.servlet.ModelAndView; import uk.ac.ebi.atlas.bioentity.GeneSetUtil; import uk.ac.ebi.atlas.search.EFO.ConditionSearchEFOExpander; import uk.ac.ebi.atlas.search.baseline.BaselineExperimentAssayGroup; import uk.ac.ebi.atlas.search.baseline.BaselineExperimentAssayGroupSearchService; import uk.ac.ebi.atlas.search.diffanalytics.DiffAnalyticsList; import uk.ac.ebi.atlas.search.diffanalytics.DiffAnalyticsSearchService; import uk.ac.ebi.atlas.solr.BioentityProperty; import uk.ac.ebi.atlas.solr.BioentityType; import uk.ac.ebi.atlas.solr.query.SolrQueryService; import uk.ac.ebi.atlas.thirdpartyintegration.EBIGlobalSearchQueryBuilder; import uk.ac.ebi.atlas.web.DifferentialRequestPreferences; import uk.ac.ebi.atlas.web.GeneQuerySearchRequestParameters; import javax.inject.Inject; import javax.validation.Valid; import java.util.Set; import java.util.SortedSet; import static com.google.common.base.Preconditions.checkArgument; import static uk.ac.ebi.atlas.search.baseline.BaselineExperimentAssayGroups.*; @Controller @Scope("prototype") public class BioentitiesSearchController { private static final int DEFAULT_BASELINE_SPLIT = 10; private static final Logger LOGGER = Logger.getLogger(BioentitiesSearchController.class); private DiffAnalyticsSearchService diffAnalyticsSearchService; private BaselineExperimentAssayGroupSearchService baselineExperimentAssayGroupSearchService; private EBIGlobalSearchQueryBuilder ebiGlobalSearchQueryBuilder; private SolrQueryService solrQueryService; private ConditionSearchEFOExpander efoExpander; @Inject public BioentitiesSearchController(DiffAnalyticsSearchService diffAnalyticsSearchService, BaselineExperimentAssayGroupSearchService baselineExperimentAssayGroupSearchService, EBIGlobalSearchQueryBuilder ebiGlobalSearchQueryBuilder, SolrQueryService solrQueryService, ConditionSearchEFOExpander efoExpander) { this.diffAnalyticsSearchService = diffAnalyticsSearchService; this.baselineExperimentAssayGroupSearchService = baselineExperimentAssayGroupSearchService; this.ebiGlobalSearchQueryBuilder = ebiGlobalSearchQueryBuilder; this.solrQueryService = solrQueryService; this.efoExpander = efoExpander; } @RequestMapping(value = "/query") public String showGeneQueryResultPage(@Valid GeneQuerySearchRequestParameters requestParameters, Model model, BindingResult result) { checkArgument(requestParameters.hasGeneQuery() || requestParameters.hasCondition(), "Please specify a gene query or condition!"); String geneQuery = requestParameters.getGeneQuery().asString().trim(); String selectedSpecies = ""; if (requestParameters.hasOrganism()) { selectedSpecies = requestParameters.getOrganism().trim(); } if (requestParameters.hasGeneQuery() && !requestParameters.hasCondition()) { //If Query just for a single bioentityID Optional<String> geneIdRedirectString = getGeneIdRedirectString(geneQuery, selectedSpecies, requestParameters.isExactMatch()); if (geneIdRedirectString.isPresent()) { return geneIdRedirectString.get(); } } model.addAttribute("geneQuery", requestParameters.getGeneQuery()); model.addAttribute("searchDescription", requestParameters.getDescription()); String condition = efoExpander.addEfoAccessions(requestParameters.getConditionQuery()).asString(); SortedSet<BaselineExperimentAssayGroup> baselineExperimentAssayGroups = baselineExperimentAssayGroupSearchService .query(geneQuery, condition, selectedSpecies.toLowerCase(), requestParameters.isExactMatch()); boolean showWidget = hasAllSameSpecies(baselineExperimentAssayGroups) && hasAnyTissueExperiment(baselineExperimentAssayGroups) & !requestParameters.hasCondition(); if (showWidget) { model.addAttribute("widgetHasBaselineProfiles", true); model.addAttribute("species", baselineExperimentAssayGroups.iterator().next().getSpecies()); SortedSet<BaselineExperimentAssayGroup> nonTissueExperimentAssayGroups = selectNonTissueExperiments( baselineExperimentAssayGroups); model.addAttribute("firstBaselineCounts", removeFirstAssayGroups(nonTissueExperimentAssayGroups, DEFAULT_BASELINE_SPLIT)); model.addAttribute("remainingBaselineCounts", nonTissueExperimentAssayGroups); } else { model.addAttribute("firstBaselineCounts", removeFirstAssayGroups(baselineExperimentAssayGroups, DEFAULT_BASELINE_SPLIT)); model.addAttribute("remainingBaselineCounts", baselineExperimentAssayGroups); } // used to populate diff-heatmap-table DiffAnalyticsList bioentityExpressions = diffAnalyticsSearchService.fetchTop(geneQuery, condition, selectedSpecies, requestParameters.isExactMatch()); model.addAttribute("bioentities", bioentityExpressions); model.addAttribute("preferences", new DifferentialRequestPreferences()); model.addAttribute("requestParameters", requestParameters); model.addAttribute("exactMatch", requestParameters.isExactMatch()); String globalSearchTerm = ebiGlobalSearchQueryBuilder.buildGlobalSearchTerm(geneQuery, requestParameters.getConditionQuery()); model.addAttribute("globalSearchTerm", globalSearchTerm); return "bioEntities"; } private Optional<String> getGeneIdRedirectString(String geneQuery, String specie, boolean isExactMatch) { boolean singleTerm = !StringUtils.containsWhitespace(geneQuery); if (singleTerm && GeneSetUtil.isGeneSet(geneQuery.toUpperCase())) { return Optional.of("redirect:/genesets/" + geneQuery); } BioentityProperty bioentityProperty = solrQueryService.findBioentityIdentifierProperty(geneQuery); if (bioentityProperty != null) { String bioentityPageName = BioentityType.get(bioentityProperty.getBioentityType()) .getBioentityPageName(); return Optional.of("redirect:/" + bioentityPageName + "/" + geneQuery); } String species = ""; if (StringUtils.isNotBlank(specie)) { species = specie; } Optional<Set<String>> geneIdsOrSets = solrQueryService.expandGeneQueryIntoGeneIds(geneQuery, species, isExactMatch); if (geneIdsOrSets.isPresent() && geneIdsOrSets.get().size() == 1) { return Optional.of("redirect:/" + BioentityType.GENE.getBioentityPageName() + "/" + geneIdsOrSets.get().iterator().next()); } return Optional.absent(); } @ExceptionHandler(value = { MissingServletRequestParameterException.class, IllegalArgumentException.class }) @ResponseStatus(value = HttpStatus.UNPROCESSABLE_ENTITY) public ModelAndView handleException(Exception e) { ModelAndView mav = new ModelAndView("bioEntities"); mav.addObject("exceptionMessage", e.getMessage()); return mav; } @ExceptionHandler(value = { SolrException.class }) @ResponseStatus(value = HttpStatus.BAD_REQUEST) public ModelAndView InternalServerHandleException(Exception e) { ModelAndView mav = new ModelAndView("query-error-page"); mav.addObject("exceptionMessage", e.getMessage()); return mav; } }