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// $Id: TaxonController.java 5473 2009-03-25 13:42:07Z a.kohlbecker $
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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.remote.controller;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.EnumSet;
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import java.util.HashSet;
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import java.util.Hashtable;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import org.apache.commons.lang.BooleanUtils;
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import org.apache.log4j.Logger;
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import org.apache.lucene.queryParser.ParseException;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Controller;
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import org.springframework.web.bind.WebDataBinder;
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import org.springframework.web.bind.annotation.InitBinder;
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import org.springframework.web.bind.annotation.PathVariable;
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import org.springframework.web.bind.annotation.RequestMapping;
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import org.springframework.web.bind.annotation.RequestMethod;
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import org.springframework.web.bind.annotation.RequestParam;
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import org.springframework.web.servlet.ModelAndView;
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import eu.etaxonomy.cdm.api.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.IDescriptionService;
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import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.api.service.IOccurrenceService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.TaxaAndNamesSearchMode;
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import eu.etaxonomy.cdm.api.service.config.FindTaxaAndNamesConfiguratorImpl;
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import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
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import eu.etaxonomy.cdm.api.service.search.SearchResult;
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import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
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import eu.etaxonomy.cdm.database.UpdatableRoutingDataSource;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.remote.controller.util.ControllerUtils;
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import eu.etaxonomy.cdm.remote.controller.util.PagerParameters;
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import eu.etaxonomy.cdm.remote.editor.CdmTypePropertyEditor;
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import eu.etaxonomy.cdm.remote.editor.MatchModePropertyEditor;
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import eu.etaxonomy.cdm.remote.editor.NamedAreaPropertyEditor;
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import eu.etaxonomy.cdm.remote.editor.UUIDListPropertyEditor;
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import eu.etaxonomy.cdm.remote.editor.UuidList;
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/**
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* The TaxonPortalController class is a Spring MVC Controller.
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* <p>
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* The syntax of the mapped service URIs contains the the {datasource-name} path element.
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* The available {datasource-name}s are defined in a configuration file which
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* is loaded by the {@link UpdatableRoutingDataSource}. If the
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* UpdatableRoutingDataSource is not being used in the actual application
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* context any arbitrary {datasource-name} may be used.
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* <p>
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* Methods mapped at type level, inherited from super classes ({@link BaseController}):
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* <blockquote>
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* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}</b>
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*
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* Get the {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
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* The returned Taxon is initialized by
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* the following strategy {@link #TAXON_INIT_STRATEGY}
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* </blockquote>
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*
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* @author a.kohlbecker
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* @date 20.07.2009
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*
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*/
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@Controller
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@RequestMapping(value = {"/portal/taxon/{uuid}"})
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public class TaxonPortalController extends BaseController<TaxonBase, ITaxonService>
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{
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public static final Logger logger = Logger.getLogger(TaxonPortalController.class);
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@Autowired
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private INameService nameService;
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@Autowired
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private IDescriptionService descriptionService;
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@Autowired
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private IOccurrenceService occurrenceService;
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@Autowired
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private IClassificationService classificationService;
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@Autowired
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private ITaxonService taxonService;
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@Autowired
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private ITermService termService;
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@Autowired
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private IFeatureTreeService featureTreeService;
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private static final List<String> TAXON_INIT_STRATEGY = Arrays.asList(new String []{
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"*",
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// taxon relations
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"relationsToThisName.fromTaxon.name",
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// the name
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"name.$",
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"name.rank.representations",
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"name.status.type.representations",
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// taxon descriptions
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"descriptions.elements.area.$",
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"descriptions.elements.multilanguageText",
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"descriptions.elements.media",
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});
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private static final List<String> TAXON_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{
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"taxonNodes.$",
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"taxonNodes.classification.$",
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"taxonNodes.childNodes.$"
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});
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private static final List<String> SIMPLE_TAXON_INIT_STRATEGY = Arrays.asList(new String []{
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"*",
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// taxon relations
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"relationsToThisName.fromTaxon.name",
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// the name
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"name.$",
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"name.rank.representations",
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"name.status.type.representations",
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"name.nomenclaturalReference"
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});
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private static final List<String> SYNONYMY_INIT_STRATEGY = Arrays.asList(new String []{
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// initialize homotypical and heterotypical groups; needs synonyms
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"synonymRelations.$",
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"synonymRelations.synonym.$",
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"synonymRelations.synonym.name.status.type.representation",
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"synonymRelations.synonym.name.nomenclaturalReference.inReference",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",
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"synonymRelations.synonym.name.combinationAuthorTeam.$",
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"name.typeDesignations",
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"name.homotypicalGroup.$",
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"name.homotypicalGroup.typifiedNames.$",
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"name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",
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"name.homotypicalGroup.typifiedNames.taxonBases.$"
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});
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private static final List<String> SYNONYMY_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{
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// initialize homotypical and heterotypical groups; needs synonyms
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"synonymRelations.$",
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"synonymRelations.synonym.$",
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"synonymRelations.synonym.name.status.type.representation",
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"synonymRelations.synonym.name.nomenclaturalReference.inReference",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",
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"synonymRelations.synonym.name.combinationAuthorTeam.$",
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"name.homotypicalGroup.$",
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"name.homotypicalGroup.typifiedNames.$",
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"name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",
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"name.homotypicalGroup.typifiedNames.taxonBases.$",
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"taxonNodes.$",
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"taxonNodes.classification.$",
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"taxonNodes.childNodes.$"
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});
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private static final List<String> SIMPLE_TAXON_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{
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"*",
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// taxon relations
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"relationsToThisName.fromTaxon.name",
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// the name
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"name.$",
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"name.rank.representations",
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"name.status.type.representations",
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"name.nomenclaturalReference",
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"taxonNodes.$",
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"taxonNodes.classification.$",
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"taxonNodes.childNodes.$"
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});
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private static final List<String> TAXONRELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{
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"$",
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"type.inverseRepresentations",
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"fromTaxon.sec",
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"fromTaxon.name",
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"toTaxon.sec",
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"toTaxon.name"
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});
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private static final List<String> NAMERELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{
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"$",
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"type.inverseRepresentations",
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"fromName",
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"toName.$",
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});
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protected static final List<String> TAXONDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String [] {
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"$",
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"elements.$",
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"elements.states.$",
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"elements.sources.citation.authorTeam",
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"elements.sources.nameUsedInSource.originalNameString",
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"elements.multilanguageText",
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"elements.media",
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"name.$",
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"name.rank.representations",
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"name.status.type.representations",
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"sources.$",
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});
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protected static final List<String> DESCRIPTION_ELEMENT_INIT_STRATEGY = Arrays.asList(new String []{
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"$",
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"sources.citation.authorTeam",
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"sources.nameUsedInSource.originalNameString",
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"multilanguageText",
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"media",
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});
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// private static final List<String> NAMEDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{
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// "uuid",
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// "feature",
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// "elements.$",
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// "elements.multilanguageText",
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// "elements.media",
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// });
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protected static final List<String> TAXONDESCRIPTION_MEDIA_INIT_STRATEGY = Arrays.asList(new String []{
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"elements.media"
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});
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private static final List<String> TYPEDESIGNATION_INIT_STRATEGY = Arrays.asList(new String []{
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"typeSpecimen.$",
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"citation.authorTeam.$",
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"typeName",
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"typeStatus"
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});
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protected static final List<String> TAXONNODE_WITHTAXON_INIT_STRATEGY = Arrays.asList(new String []{
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"childNodes.taxon",
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});
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protected static final List<String> TAXONNODE_INIT_STRATEGY = Arrays.asList(new String []{
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"taxonNodes.classification"
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});
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private static final String featureTreeUuidPattern = "^/taxon(?:(?:/)([^/?#&\\.]+))+.*";
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public TaxonPortalController(){
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super();
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setInitializationStrategy(TAXON_INIT_STRATEGY);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.remote.controller.GenericController#setService(eu.etaxonomy.cdm.api.service.IService)
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*/
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@Autowired
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@Override
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public void setService(ITaxonService service) {
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this.service = service;
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}
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@InitBinder
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@Override
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public void initBinder(WebDataBinder binder) {
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super.initBinder(binder);
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binder.registerCustomEditor(NamedArea.class, new NamedAreaPropertyEditor());
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binder.registerCustomEditor(MatchMode.class, new MatchModePropertyEditor());
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binder.registerCustomEditor(Class.class, new CdmTypePropertyEditor());
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binder.registerCustomEditor(UuidList.class, new UUIDListPropertyEditor());
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.remote.controller.BaseController#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
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@Override
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@RequestMapping(method = RequestMethod.GET)
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public TaxonBase doGet(HttpServletRequest request, HttpServletResponse response)throws IOException {
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logger.info("doGet()");
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TaxonBase tb = getCdmBase(request, response, TAXON_INIT_STRATEGY, TaxonBase.class);
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return tb;
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}
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*/
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@RequestMapping(method = RequestMethod.GET,
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value = {"/portal/taxon/find"}) //TODO map to path /*/portal/taxon/
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public Pager<IdentifiableEntity> doFind(
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@RequestParam(value = "query", required = false) String query,
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@RequestParam(value = "tree", required = false) UUID treeUuid,
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@RequestParam(value = "area", required = false) Set<NamedArea> areas,
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@RequestParam(value = "pageNumber", required = false) Integer pageNumber,
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@RequestParam(value = "pageSize", required = false) Integer pageSize,
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@RequestParam(value = "doTaxa", required = false) Boolean doTaxa,
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@RequestParam(value = "doSynonyms", required = false) Boolean doSynonyms,
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@RequestParam(value = "doMisappliedNames", required = false) Boolean doMisappliedNames,
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@RequestParam(value = "doTaxaByCommonNames", required = false) Boolean doTaxaByCommonNames,
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@RequestParam(value = "matchMode", required = false) MatchMode matchMode,
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HttpServletRequest request,
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HttpServletResponse response
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)
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throws IOException {
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logger.info("doFind : " + request.getRequestURI() + "?" + request.getQueryString() );
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PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);
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pagerParams.normalizeAndValidate(response);
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IFindTaxaAndNamesConfigurator config = new FindTaxaAndNamesConfiguratorImpl();
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config.setPageNumber(pagerParams.getPageIndex());
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config.setPageSize(pagerParams.getPageSize());
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config.setTitleSearchString(query);
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config.setDoTaxa(doTaxa!= null ? doTaxa : Boolean.FALSE );
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config.setDoSynonyms(doSynonyms != null ? doSynonyms : Boolean.FALSE );
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config.setDoMisappliedNames(doMisappliedNames != null ? doMisappliedNames : Boolean.FALSE);
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config.setDoTaxaByCommonNames(doTaxaByCommonNames != null ? doTaxaByCommonNames : Boolean.FALSE );
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config.setMatchMode(matchMode != null ? matchMode : MatchMode.BEGINNING);
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config.setTaxonPropertyPath(SIMPLE_TAXON_INIT_STRATEGY);
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config.setNamedAreas(areas);
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if(treeUuid != null){
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Classification classification = classificationService.find(treeUuid);
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config.setClassification(classification);
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}
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return service.findTaxaAndNames(config);
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}
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/**
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* <b>NOTE and TODO</b>: this method is a direct copy of the same method in {@link TaxonListController},
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* refactorting needed to avoid method dublication
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* <p>
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* Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.
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* <p>
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* URI: <b>/{datasource-name}/portal/taxon/find</b>
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*
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* @param query
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* the string to query for. Since the wildcard character '*'
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* internally always is appended to the query string, a search
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* always compares the query string with the beginning of a name.
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* - <i>required parameter</i>
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* @param treeUuid
|
392
|
* the {@link UUID} of a {@link Classification} to which the
|
393
|
* search is to be restricted. - <i>optional parameter</i>
|
394
|
* @param areas
|
395
|
* restrict the search to a set of geographic {@link NamedArea}s.
|
396
|
* The parameter currently takes a list of TDWG area labels.
|
397
|
* - <i>optional parameter</i>
|
398
|
* @param pageNumber
|
399
|
* the number of the page to be returned, the first page has the
|
400
|
* pageNumber = 1 - <i>optional parameter</i>
|
401
|
* @param pageSize
|
402
|
* the maximum number of entities returned per page (can be -1
|
403
|
* to return all entities in a single page) - <i>optional parameter</i>
|
404
|
* @param doTaxa
|
405
|
* weather to search for instances of {@link Taxon} - <i>optional parameter</i>
|
406
|
* @param doSynonyms
|
407
|
* weather to search for instances of {@link Synonym} - <i>optional parameter</i>
|
408
|
* @param doTaxaByCommonNames
|
409
|
* for instances of {@link Taxon} by a common name used - <i>optional parameter</i>
|
410
|
* @return a Pager on a list of {@link IdentifiableEntity}s initialized by
|
411
|
* the following strategy {@link #SIMPLE_TAXON_INIT_STRATEGY}
|
412
|
* @throws IOException
|
413
|
* @throws LuceneMultiSearchException
|
414
|
* @throws ParseException
|
415
|
*/
|
416
|
@RequestMapping(method = RequestMethod.GET, value={"/portal/taxon/search"})
|
417
|
public Pager<SearchResult<TaxonBase>> doSearch(
|
418
|
@RequestParam(value = "query", required = true) String query,
|
419
|
@RequestParam(value = "tree", required = false) UUID treeUuid,
|
420
|
@RequestParam(value = "area", required = false) Set<NamedArea> areas,
|
421
|
@RequestParam(value = "status", required = false) Set<PresenceAbsenceTermBase<?>> status,
|
422
|
@RequestParam(value = "pageNumber", required = false) Integer pageNumber,
|
423
|
@RequestParam(value = "pageSize", required = false) Integer pageSize,
|
424
|
@RequestParam(value = "doTaxa", required = false) Boolean doTaxa,
|
425
|
@RequestParam(value = "doSynonyms", required = false) Boolean doSynonyms,
|
426
|
@RequestParam(value = "doMisappliedNames", required = false) Boolean doMisappliedNames,
|
427
|
@RequestParam(value = "doTaxaByCommonNames", required = false) Boolean doTaxaByCommonNames,
|
428
|
HttpServletRequest request,
|
429
|
HttpServletResponse response
|
430
|
)
|
431
|
throws IOException, ParseException, LuceneMultiSearchException {
|
432
|
|
433
|
|
434
|
logger.info("search : " + requestPathAndQuery(request) );
|
435
|
|
436
|
PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);
|
437
|
pagerParams.normalizeAndValidate(response);
|
438
|
|
439
|
// TODO change type of do* parameters to TaxaAndNamesSearchMode
|
440
|
EnumSet<TaxaAndNamesSearchMode> searchModes = EnumSet.noneOf(TaxaAndNamesSearchMode.class);
|
441
|
if(BooleanUtils.toBoolean(doTaxa)) {
|
442
|
searchModes.add(TaxaAndNamesSearchMode.doTaxa);
|
443
|
}
|
444
|
if(BooleanUtils.toBoolean(doSynonyms)) {
|
445
|
searchModes.add(TaxaAndNamesSearchMode.doSynonyms);
|
446
|
}
|
447
|
if(BooleanUtils.toBoolean(doMisappliedNames)) {
|
448
|
searchModes.add(TaxaAndNamesSearchMode.doMisappliedNames);
|
449
|
}
|
450
|
if(BooleanUtils.toBoolean(doTaxaByCommonNames)) {
|
451
|
searchModes.add(TaxaAndNamesSearchMode.doTaxaByCommonNames);
|
452
|
}
|
453
|
|
454
|
Classification classification = null;
|
455
|
if(treeUuid != null){
|
456
|
classification = classificationService.find(treeUuid);
|
457
|
}
|
458
|
|
459
|
return service.findTaxaAndNamesByFullText(searchModes, query,
|
460
|
classification, areas, status, null,
|
461
|
false, pagerParams.getPageSize(), pagerParams.getPageIndex(),
|
462
|
null, SIMPLE_TAXON_INIT_STRATEGY);
|
463
|
}
|
464
|
|
465
|
/**
|
466
|
* @param clazz
|
467
|
* @param queryString
|
468
|
* @param treeUuid
|
469
|
* @param languages
|
470
|
* @param features one or more feature uuids
|
471
|
* @param pageNumber
|
472
|
* @param pageSize
|
473
|
* @param request
|
474
|
* @param response
|
475
|
* @return
|
476
|
* @throws IOException
|
477
|
* @throws ParseException
|
478
|
*/
|
479
|
@SuppressWarnings("rawtypes")
|
480
|
@RequestMapping(method = RequestMethod.GET, value={"/portal/taxon/findByDescriptionElementFullText"})
|
481
|
public Pager<SearchResult<TaxonBase>> dofindByDescriptionElementFullText(
|
482
|
@RequestParam(value = "clazz", required = false) Class clazz,
|
483
|
@RequestParam(value = "query", required = true) String queryString,
|
484
|
@RequestParam(value = "tree", required = false) UUID treeUuid,
|
485
|
@RequestParam(value = "features", required = false) UuidList featureUuids,
|
486
|
@RequestParam(value = "languages", required = false) List<Language> languages,
|
487
|
@RequestParam(value = "hl", required = false) Boolean highlighting,
|
488
|
@RequestParam(value = "pageNumber", required = false) Integer pageNumber,
|
489
|
@RequestParam(value = "pageSize", required = false) Integer pageSize,
|
490
|
HttpServletRequest request,
|
491
|
HttpServletResponse response
|
492
|
)
|
493
|
throws IOException, ParseException {
|
494
|
|
495
|
logger.info("findByDescriptionElementFullText : " + requestPathAndQuery(request) );
|
496
|
|
497
|
PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);
|
498
|
pagerParams.normalizeAndValidate(response);
|
499
|
|
500
|
if(highlighting == null){
|
501
|
highlighting = false;
|
502
|
}
|
503
|
|
504
|
Classification classification = null;
|
505
|
if(treeUuid != null){
|
506
|
classification = classificationService.find(treeUuid);
|
507
|
}
|
508
|
|
509
|
List<Feature> features = null;
|
510
|
if(featureUuids != null){
|
511
|
features = new ArrayList<Feature>(featureUuids.size());
|
512
|
for(UUID uuid : featureUuids){
|
513
|
features.add((Feature) termService.find(uuid));
|
514
|
}
|
515
|
}
|
516
|
|
517
|
Pager<SearchResult<TaxonBase>> pager = service.findByDescriptionElementFullText(clazz, queryString, classification, features, languages, highlighting, pagerParams.getPageSize(), pagerParams.getPageIndex(), ((List<OrderHint>)null), SIMPLE_TAXON_INIT_STRATEGY);
|
518
|
return pager;
|
519
|
}
|
520
|
|
521
|
/**
|
522
|
* Get the synonymy for a taxon identified by the <code>{taxon-uuid}</code>.
|
523
|
* The synonymy consists
|
524
|
* of two parts: The group of homotypic synonyms of the taxon and the
|
525
|
* heterotypic synonymy groups of the taxon. The synonymy is ordered
|
526
|
* historically by the type designations and by the publication date of the
|
527
|
* nomenclatural reference
|
528
|
* <p>
|
529
|
* URI:
|
530
|
* <b>/{datasource-name}/portal/taxon/{taxon-uuid}/synonymy</b>
|
531
|
*
|
532
|
*
|
533
|
* @param request
|
534
|
* @param response
|
535
|
* @return a Map with to entries which are mapped by the following keys:
|
536
|
* "homotypicSynonymsByHomotypicGroup", "heterotypicSynonymyGroups",
|
537
|
* containing lists of {@link Synonym}s which are initialized using the
|
538
|
* following initialization strategy: {@link #SYNONYMY_INIT_STRATEGY}
|
539
|
*
|
540
|
* @throws IOException
|
541
|
*/
|
542
|
@RequestMapping(
|
543
|
value = {"synonymy"},
|
544
|
method = RequestMethod.GET)
|
545
|
public ModelAndView doGetSynonymy(@PathVariable("uuid") UUID uuid,
|
546
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
547
|
|
548
|
if(request != null){
|
549
|
logger.info("doGetSynonymy() " + requestPathAndQuery(request));
|
550
|
}
|
551
|
ModelAndView mv = new ModelAndView();
|
552
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
553
|
Map<String, List<?>> synonymy = new Hashtable<String, List<?>>();
|
554
|
synonymy.put("homotypicSynonymsByHomotypicGroup", service.getHomotypicSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY));
|
555
|
synonymy.put("heterotypicSynonymyGroups", service.getHeterotypicSynonymyGroups(taxon, SYNONYMY_INIT_STRATEGY));
|
556
|
mv.addObject(synonymy);
|
557
|
return mv;
|
558
|
}
|
559
|
|
560
|
/**
|
561
|
* Get the set of accepted {@link Taxon} entities for a given
|
562
|
* {@link TaxonBase} entity identified by the <code>{taxon-uuid}</code>.
|
563
|
* <p>
|
564
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/accepted</b>
|
565
|
*
|
566
|
* @param request
|
567
|
* @param response
|
568
|
* @return a Set of {@link Taxon} entities which are initialized
|
569
|
* using the following initialization strategy:
|
570
|
* {@link #SYNONYMY_INIT_STRATEGY}
|
571
|
* @throws IOException
|
572
|
*/
|
573
|
@RequestMapping(value = "accepted/{classification_uuid}", method = RequestMethod.GET)
|
574
|
public Set<TaxonBase> getAccepted(
|
575
|
@PathVariable("uuid") UUID uuid,
|
576
|
@PathVariable("classification_uuid") UUID classification_uuid,
|
577
|
HttpServletRequest request,
|
578
|
HttpServletResponse response)
|
579
|
throws IOException {
|
580
|
|
581
|
if(request != null){
|
582
|
logger.info("getAccepted() " + requestPathAndQuery(request));
|
583
|
}
|
584
|
|
585
|
TaxonBase tb = service.load(uuid, SYNONYMY_WITH_NODES_INIT_STRATEGY);
|
586
|
if(tb == null){
|
587
|
response.sendError(HttpServletResponse.SC_NOT_FOUND, "A taxon with the uuid " + uuid + " does not exist");
|
588
|
return null;
|
589
|
}
|
590
|
|
591
|
HashSet<TaxonBase> resultset = new HashSet<TaxonBase>();
|
592
|
|
593
|
if (tb instanceof Taxon){
|
594
|
Taxon taxon = (Taxon) tb;
|
595
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
596
|
for (TaxonNode taxonNode : nodes) {
|
597
|
if (taxonNode.getClassification().compareTo(classification_uuid) == 0){
|
598
|
resultset.add(tb);
|
599
|
}
|
600
|
}
|
601
|
if (resultset.size() > 1){
|
602
|
//error!! A taxon is not allow to have more taxonnodes for a given classification
|
603
|
response.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
|
604
|
"A taxon with the uuid " + uuid + " has more than one taxon node for the given classification" + classification_uuid);
|
605
|
}
|
606
|
}else{
|
607
|
Synonym syn = (Synonym) tb;
|
608
|
for(TaxonBase accepted : syn.getAcceptedTaxa()){
|
609
|
tb = service.load(accepted.getUuid(), SIMPLE_TAXON_WITH_NODES_INIT_STRATEGY);
|
610
|
if (tb instanceof Taxon){
|
611
|
Taxon taxon = (Taxon) tb;
|
612
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
613
|
for (TaxonNode taxonNode : nodes) {
|
614
|
if (taxonNode.getClassification().compareTo(classification_uuid) == 0){
|
615
|
resultset.add(tb);
|
616
|
}
|
617
|
}
|
618
|
if (resultset.size() > 1){
|
619
|
//error!! A taxon is not allow to have more taxonnodes for a given classification
|
620
|
response.sendError(HttpServletResponse.SC_INTERNAL_SERVER_ERROR,
|
621
|
"A taxon with the uuid " + uuid + " has more than one taxon node for the given classification" + classification_uuid);
|
622
|
}
|
623
|
}else{
|
624
|
//ERROR!! perhaps missapplied name????
|
625
|
//syn.getRelationType((Taxon)accepted);
|
626
|
}
|
627
|
}
|
628
|
}
|
629
|
/**
|
630
|
* OLD CODE!!
|
631
|
if(tb instanceof Taxon){
|
632
|
//the taxon already is accepted
|
633
|
//FIXME take the current view into account once views are implemented!!!
|
634
|
resultset.add((Taxon)tb);
|
635
|
} else {
|
636
|
Synonym syn = (Synonym)tb;
|
637
|
for(TaxonBase accepted : syn.getAcceptedTaxa()){
|
638
|
accepted = service.load(accepted.getUuid(), SIMPLE_TAXON_INIT_STRATEGY);
|
639
|
resultset.add(accepted);
|
640
|
}
|
641
|
}
|
642
|
*/
|
643
|
return resultset;
|
644
|
}
|
645
|
|
646
|
/**
|
647
|
* Get the list of {@link TaxonRelationship}s for the given
|
648
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
649
|
* <p>
|
650
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/taxonRelationships</b>
|
651
|
*
|
652
|
* @param request
|
653
|
* @param response
|
654
|
* @return a List of {@link TaxonRelationship} entities which are initialized
|
655
|
* using the following initialization strategy:
|
656
|
* {@link #TAXONRELATIONSHIP_INIT_STRATEGY}
|
657
|
* @throws IOException
|
658
|
*/
|
659
|
@RequestMapping(
|
660
|
value = {"taxonRelationships"},
|
661
|
method = RequestMethod.GET)
|
662
|
public List<TaxonRelationship> doGetTaxonRelations(@PathVariable("uuid") UUID uuid,
|
663
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
664
|
|
665
|
logger.info("doGetTaxonRelations()" + requestPathAndQuery(request));
|
666
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
667
|
List<TaxonRelationship> toRelationships = service.listToTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
|
668
|
List<TaxonRelationship> fromRelationships = service.listFromTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
|
669
|
|
670
|
List<TaxonRelationship> allRelationships = new ArrayList<TaxonRelationship>(toRelationships.size() + fromRelationships.size());
|
671
|
allRelationships.addAll(toRelationships);
|
672
|
allRelationships.addAll(fromRelationships);
|
673
|
|
674
|
return allRelationships;
|
675
|
}
|
676
|
|
677
|
/**
|
678
|
* Get the list of {@link NameRelationship}s of the Name associated with the
|
679
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
680
|
* <p>
|
681
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/nameRelationships</b>
|
682
|
*
|
683
|
* @param request
|
684
|
* @param response
|
685
|
* @return a List of {@link NameRelationship} entities which are initialized
|
686
|
* using the following initialization strategy:
|
687
|
* {@link #NAMERELATIONSHIP_INIT_STRATEGY}
|
688
|
* @throws IOException
|
689
|
*/
|
690
|
@RequestMapping(
|
691
|
value = {"toNameRelationships"},
|
692
|
method = RequestMethod.GET)
|
693
|
public List<NameRelationship> doGetToNameRelations(@PathVariable("uuid") UUID uuid,
|
694
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
695
|
logger.info("doGetNameRelations()" + request.getRequestURI());
|
696
|
TaxonBase taxonBase = getCdmBaseInstance(TaxonBase.class, uuid, response, (List<String>)null);
|
697
|
List<NameRelationship> list = nameService.listNameRelationships(taxonBase.getName(), Direction.relatedTo, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
698
|
//List<NameRelationship> list = nameService.listToNameRelationships(taxonBase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
699
|
return list;
|
700
|
}
|
701
|
|
702
|
/**
|
703
|
* Get the list of {@link NameRelationship}s of the Name associated with the
|
704
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
705
|
* <p>
|
706
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/nameRelationships</b>
|
707
|
*
|
708
|
* @param request
|
709
|
* @param response
|
710
|
* @return a List of {@link NameRelationship} entities which are initialized
|
711
|
* using the following initialization strategy:
|
712
|
* {@link #NAMERELATIONSHIP_INIT_STRATEGY}
|
713
|
* @throws IOException
|
714
|
*/
|
715
|
@RequestMapping(
|
716
|
value = {"fromNameRelationships"},
|
717
|
method = RequestMethod.GET)
|
718
|
public List<NameRelationship> doGetFromNameRelations(@PathVariable("uuid") UUID uuid,
|
719
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
720
|
logger.info("doGetNameFromNameRelations()" + requestPathAndQuery(request));
|
721
|
|
722
|
TaxonBase taxonbase = getCdmBaseInstance(TaxonBase.class, uuid, response, SIMPLE_TAXON_INIT_STRATEGY);
|
723
|
List<NameRelationship> list = nameService.listNameRelationships(taxonbase.getName(), Direction.relatedFrom, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
724
|
//List<NameRelationship> list = nameService.listFromNameRelationships(taxonbase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
725
|
return list;
|
726
|
}
|
727
|
|
728
|
/**
|
729
|
* Get the list of {@link TypeDesignationBase}s of the
|
730
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
731
|
* <p>
|
732
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/nameTypeDesignations</b>
|
733
|
*
|
734
|
* @param request
|
735
|
* @param response
|
736
|
* @return a List of {@link TypeDesignationBase} entities which are initialized
|
737
|
* using the following initialization strategy:
|
738
|
* {@link #TYPEDESIGNATION_INIT_STRATEGY}
|
739
|
* @throws IOException
|
740
|
* @Deprecated use /name/{uuid}/typeDesignations & /derivedunitfacade/{uuid} instead
|
741
|
* also see http://dev.e-taxonomy.eu/trac/ticket/2280
|
742
|
*/
|
743
|
@Deprecated
|
744
|
@RequestMapping(
|
745
|
value = {"nameTypeDesignations"},
|
746
|
method = RequestMethod.GET)
|
747
|
public List<TypeDesignationBase> doGetNameTypeDesignations(@PathVariable("uuid") UUID uuid,
|
748
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
749
|
logger.info("doGetNameTypeDesignations()" + request.getRequestURI());
|
750
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, SIMPLE_TAXON_INIT_STRATEGY);
|
751
|
Pager<TypeDesignationBase> p = nameService.getTypeDesignations(taxon.getName(), null, null, null, TYPEDESIGNATION_INIT_STRATEGY);
|
752
|
return p.getRecords();
|
753
|
}
|
754
|
|
755
|
@RequestMapping(value = "taxonNodes", method = RequestMethod.GET)
|
756
|
public Set<TaxonNode> doGetTaxonNodes(
|
757
|
@PathVariable("uuid") UUID uuid,
|
758
|
HttpServletRequest request,
|
759
|
HttpServletResponse response) throws IOException {
|
760
|
logger.info("doGetTaxonNodes" + requestPathAndQuery(request));
|
761
|
TaxonBase taxon = service.load(uuid, TAXONNODE_INIT_STRATEGY);
|
762
|
if(taxon instanceof Taxon){
|
763
|
return ((Taxon)taxon).getTaxonNodes();
|
764
|
} else {
|
765
|
HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);
|
766
|
return null;
|
767
|
}
|
768
|
}
|
769
|
|
770
|
/**
|
771
|
* Get the list of {@link TaxonDescription}s of the
|
772
|
* {@link Taxon} instance identified by the <code>{taxon-uuid}</code>.
|
773
|
* <p>
|
774
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/descriptions</b>
|
775
|
*
|
776
|
* @param request
|
777
|
* @param response
|
778
|
* @return a List of {@link TaxonDescription} entities which are initialized
|
779
|
* using the following initialization strategy:
|
780
|
* {@link #TAXONDESCRIPTION_INIT_STRATEGY}
|
781
|
* @throws IOException
|
782
|
*/
|
783
|
@RequestMapping(
|
784
|
value = {"descriptions"},
|
785
|
method = RequestMethod.GET)
|
786
|
public List<TaxonDescription> doGetDescriptions(
|
787
|
@PathVariable("uuid") UUID uuid,
|
788
|
@RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,
|
789
|
HttpServletRequest request,
|
790
|
HttpServletResponse response)throws IOException {
|
791
|
if(request != null){
|
792
|
logger.info("doGetDescriptions()" + requestPathAndQuery(request));
|
793
|
}
|
794
|
List<DefinedTermBase> markerTypeTerms = null;
|
795
|
Set<UUID> sMarkerTypeUUIDs = null;
|
796
|
|
797
|
if(markerTypeUUIDs != null && !markerTypeUUIDs.isEmpty()){
|
798
|
sMarkerTypeUUIDs = new HashSet<UUID>(markerTypeUUIDs);
|
799
|
markerTypeTerms = termService.find(sMarkerTypeUUIDs);
|
800
|
} else if(markerTypeUUIDs != null && markerTypeUUIDs.isEmpty()){
|
801
|
markerTypeTerms = new ArrayList<DefinedTermBase>();
|
802
|
}
|
803
|
Set<MarkerType> markerTypes = new HashSet<MarkerType>();
|
804
|
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>();
|
805
|
if (markerTypeTerms != null) {
|
806
|
for (DefinedTermBase markerTypeTerm : markerTypeTerms) {
|
807
|
markerTypes.add((MarkerType)markerTypeTerm);
|
808
|
}
|
809
|
}
|
810
|
Taxon t = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
811
|
if (markerTypeTerms == null) {
|
812
|
|
813
|
Pager<TaxonDescription> p = descriptionService.pageTaxonDescriptions(t, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
814
|
descriptions = p.getRecords();
|
815
|
}
|
816
|
|
817
|
else if (markerTypeTerms != null && markerTypeTerms.isEmpty()) {
|
818
|
descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
819
|
|
820
|
}
|
821
|
else {
|
822
|
descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
823
|
/*for (TaxonDescription description: descriptions) {
|
824
|
for (IdentifiableSource source :description.getSources()) {
|
825
|
if (source.getOriginalNameString() != null) {
|
826
|
description.
|
827
|
}
|
828
|
|
829
|
}
|
830
|
|
831
|
|
832
|
}*/
|
833
|
}
|
834
|
return descriptions;
|
835
|
}
|
836
|
|
837
|
@RequestMapping(value = "useDescriptions", method = RequestMethod.GET)
|
838
|
public List<TaxonDescription> doGetUseDescriptions(
|
839
|
@PathVariable("uuid") UUID uuid,
|
840
|
HttpServletRequest request,
|
841
|
HttpServletResponse response) throws IOException {
|
842
|
logger.info("doGetDescriptionElements() - " + requestPathAndQuery(request));
|
843
|
|
844
|
//ModelAndView mv = new ModelAndView();
|
845
|
Taxon t = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
846
|
|
847
|
//MarkerType useMarkerType = (MarkerType) markerTypeService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));
|
848
|
MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
849
|
|
850
|
//find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));
|
851
|
Set<MarkerType> markerTypes = new HashSet<MarkerType>();
|
852
|
markerTypes.add(useMarkerType);
|
853
|
List<TaxonDescription> descriptionElements = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
854
|
//getDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths) load(uuid);
|
855
|
|
856
|
/*if(!(description instanceof TaxonDescription)){
|
857
|
HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);
|
858
|
// will terminate thread
|
859
|
}*/
|
860
|
|
861
|
//boolean hasStructuredData = service. hasStructuredData(description);
|
862
|
|
863
|
//mv.addObject(hasStructuredData);
|
864
|
|
865
|
return descriptionElements;
|
866
|
}
|
867
|
|
868
|
@RequestMapping(value = "descriptions/elementsByType/{classSimpleName}", method = RequestMethod.GET)
|
869
|
public ModelAndView doGetDescriptionElementsByType(
|
870
|
@PathVariable("uuid") UUID uuid,
|
871
|
@PathVariable("classSimpleName") String classSimpleName,
|
872
|
@RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,
|
873
|
@RequestParam(value = "count", required = false, defaultValue = "false") Boolean doCount,
|
874
|
HttpServletRequest request,
|
875
|
HttpServletResponse response) throws IOException {
|
876
|
logger.info("doGetDescriptionElementsByType() - " + requestPathAndQuery(request));
|
877
|
|
878
|
ModelAndView mv = new ModelAndView();
|
879
|
|
880
|
List<DescriptionElementBase> allElements = new ArrayList<DescriptionElementBase>();
|
881
|
List<DescriptionElementBase> elements;
|
882
|
int count = 0;
|
883
|
|
884
|
List<String> initStrategy = doCount ? null : DESCRIPTION_ELEMENT_INIT_STRATEGY;
|
885
|
|
886
|
List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, markerTypeUUIDs, request, response);
|
887
|
try {
|
888
|
Class type;
|
889
|
type = Class.forName("eu.etaxonomy.cdm.model.description."
|
890
|
+ classSimpleName);
|
891
|
if (taxonDescriptions != null) {
|
892
|
for (TaxonDescription description : taxonDescriptions) {
|
893
|
elements = descriptionService.listDescriptionElements(description, null, type, null, 0, initStrategy);
|
894
|
allElements.addAll(elements);
|
895
|
count += elements.size();
|
896
|
}
|
897
|
|
898
|
}
|
899
|
} catch (ClassNotFoundException e) {
|
900
|
HttpStatusMessage.fromString(e.getLocalizedMessage()).send(response);
|
901
|
}
|
902
|
if(doCount){
|
903
|
mv.addObject(count);
|
904
|
} else {
|
905
|
mv.addObject(allElements);
|
906
|
}
|
907
|
return mv;
|
908
|
}
|
909
|
|
910
|
// @RequestMapping(value = "specimens", method = RequestMethod.GET)
|
911
|
// public ModelAndView doGetSpecimens(
|
912
|
// @PathVariable("uuid") UUID uuid,
|
913
|
// HttpServletRequest request,
|
914
|
// HttpServletResponse response) throws IOException, ClassNotFoundException {
|
915
|
// logger.info("doGetSpecimens() - " + request.getRequestURI());
|
916
|
//
|
917
|
// ModelAndView mv = new ModelAndView();
|
918
|
//
|
919
|
// List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
|
920
|
//
|
921
|
// // find speciemens in the TaxonDescriptions
|
922
|
// List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, request, response);
|
923
|
// if (taxonDescriptions != null) {
|
924
|
//
|
925
|
// for (TaxonDescription description : taxonDescriptions) {
|
926
|
// derivedUnitFacadeList.addAll( occurrenceService.listDerivedUnitFacades(description, null) );
|
927
|
// }
|
928
|
// }
|
929
|
// // TODO find speciemens in the NameDescriptions ??
|
930
|
//
|
931
|
// // TODO also find type specimens
|
932
|
//
|
933
|
// mv.addObject(derivedUnitFacadeList);
|
934
|
//
|
935
|
// return mv;
|
936
|
// }
|
937
|
|
938
|
/**
|
939
|
* Get the {@link Media} attached to the {@link Taxon} instance
|
940
|
* identified by the <code>{taxon-uuid}</code>.
|
941
|
*
|
942
|
* Usage /{datasource-name}/portal/taxon/{taxon-
|
943
|
* uuid}/media/{mime type
|
944
|
* list}/{size}[,[widthOrDuration}][,{height}]/
|
945
|
*
|
946
|
* Whereas
|
947
|
* <ul>
|
948
|
* <li><b>{mime type list}</b>: a comma separated list of mime types, in the
|
949
|
* order of preference. The forward slashes contained in the mime types must
|
950
|
* be replaced by a colon. Regular expressions can be used. Each media
|
951
|
* associated with this given taxon is being searched whereas the first
|
952
|
* matching mime type matching a representation always rules.</li>
|
953
|
* <li><b>{size},{widthOrDuration},{height}</b>: <i>not jet implemented</i>
|
954
|
* valid values are an integer or the asterisk '*' as a wildcard</li>
|
955
|
* </ul>
|
956
|
*
|
957
|
* @param request
|
958
|
* @param response
|
959
|
* @return a List of {@link Media} entities which are initialized
|
960
|
* using the following initialization strategy:
|
961
|
* {@link #TAXONDESCRIPTION_INIT_STRATEGY}
|
962
|
* @throws IOException
|
963
|
*/
|
964
|
@RequestMapping(
|
965
|
value = {"media"},
|
966
|
method = RequestMethod.GET)
|
967
|
public List<Media> doGetMedia(
|
968
|
@PathVariable("uuid") UUID uuid,
|
969
|
@RequestParam(value = "type", required = false) Class<? extends MediaRepresentationPart> type,
|
970
|
@RequestParam(value = "mimeTypes", required = false) String[] mimeTypes,
|
971
|
@RequestParam(value = "relationships", required = false) UuidList relationshipUuids,
|
972
|
@RequestParam(value = "relationshipsInvers", required = false) UuidList relationshipInversUuids,
|
973
|
@RequestParam(value = "includeTaxonDescriptions", required = true) Boolean includeTaxonDescriptions,
|
974
|
@RequestParam(value = "includeOccurrences", required = true) Boolean includeOccurrences,
|
975
|
@RequestParam(value = "includeTaxonNameDescriptions", required = true) Boolean includeTaxonNameDescriptions,
|
976
|
@RequestParam(value = "widthOrDuration", required = false) Integer widthOrDuration,
|
977
|
@RequestParam(value = "height", required = false) Integer height,
|
978
|
@RequestParam(value = "size", required = false) Integer size,
|
979
|
HttpServletRequest request, HttpServletResponse response) throws IOException {
|
980
|
|
981
|
logger.info("doGetMedia() " + requestPathAndQuery(request));
|
982
|
|
983
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
984
|
|
985
|
Set<TaxonRelationshipEdge> includeRelationships = ControllerUtils.loadIncludeRelationships(relationshipUuids, relationshipInversUuids, termService);
|
986
|
|
987
|
List<Media> returnMedia = getMediaForTaxon(taxon, includeRelationships,
|
988
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
989
|
type, mimeTypes, widthOrDuration, height, size);
|
990
|
return returnMedia;
|
991
|
}
|
992
|
|
993
|
@RequestMapping(
|
994
|
value = {"subtree/media"},
|
995
|
method = RequestMethod.GET)
|
996
|
public List<Media> doGetSubtreeMedia(
|
997
|
@PathVariable("uuid") UUID uuid,
|
998
|
@RequestParam(value = "type", required = false) Class<? extends MediaRepresentationPart> type,
|
999
|
@RequestParam(value = "mimeTypes", required = false) String[] mimeTypes,
|
1000
|
@RequestParam(value = "relationships", required = false) UuidList relationshipUuids,
|
1001
|
@RequestParam(value = "relationshipsInvers", required = false) UuidList relationshipInversUuids,
|
1002
|
@RequestParam(value = "includeTaxonDescriptions", required = true) Boolean includeTaxonDescriptions,
|
1003
|
@RequestParam(value = "includeOccurrences", required = true) Boolean includeOccurrences,
|
1004
|
@RequestParam(value = "includeTaxonNameDescriptions", required = true) Boolean includeTaxonNameDescriptions,
|
1005
|
@RequestParam(value = "widthOrDuration", required = false) Integer widthOrDuration,
|
1006
|
@RequestParam(value = "height", required = false) Integer height,
|
1007
|
@RequestParam(value = "size", required = false) Integer size,
|
1008
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
1009
|
|
1010
|
logger.info("doGetSubtreeMedia() " + requestPathAndQuery(request));
|
1011
|
|
1012
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, TAXON_WITH_NODES_INIT_STRATEGY);
|
1013
|
|
1014
|
Set<TaxonRelationshipEdge> includeRelationships = ControllerUtils.loadIncludeRelationships(relationshipUuids, relationshipInversUuids, termService);
|
1015
|
|
1016
|
List<Media> returnMedia = getMediaForTaxon(taxon, includeRelationships,
|
1017
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
1018
|
type, mimeTypes, widthOrDuration, height, size);
|
1019
|
TaxonNode node;
|
1020
|
//looking for all medias of genus
|
1021
|
if (taxon.getTaxonNodes().size()>0){
|
1022
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
1023
|
Iterator<TaxonNode> iterator = nodes.iterator();
|
1024
|
//TaxonNode holen
|
1025
|
node = iterator.next();
|
1026
|
//Check if TaxonNode belongs to the current tree
|
1027
|
|
1028
|
node = classificationService.loadTaxonNode(node, TAXONNODE_WITHTAXON_INIT_STRATEGY);
|
1029
|
List<TaxonNode> children = node.getChildNodes();
|
1030
|
Taxon childTaxon;
|
1031
|
for (TaxonNode child : children){
|
1032
|
childTaxon = child.getTaxon();
|
1033
|
childTaxon = (Taxon)taxonService.load(childTaxon.getUuid(), null);
|
1034
|
returnMedia.addAll(getMediaForTaxon(childTaxon, includeRelationships,
|
1035
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
1036
|
type, mimeTypes, widthOrDuration, height, size));
|
1037
|
}
|
1038
|
}
|
1039
|
return returnMedia;
|
1040
|
}
|
1041
|
|
1042
|
/**
|
1043
|
*
|
1044
|
* @param taxon
|
1045
|
* @param includeRelationships
|
1046
|
* @param type
|
1047
|
* @param mimeTypes
|
1048
|
* @param widthOrDuration
|
1049
|
* @param height
|
1050
|
* @param size
|
1051
|
* @return
|
1052
|
*/
|
1053
|
private List<Media> getMediaForTaxon(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
|
1054
|
Boolean includeTaxonDescriptions, Boolean includeOccurrences, Boolean includeTaxonNameDescriptions,
|
1055
|
Class<? extends MediaRepresentationPart> type, String[] mimeTypes, Integer widthOrDuration, Integer height,
|
1056
|
Integer size) {
|
1057
|
|
1058
|
List<Media> taxonGalleryMedia = service.listMedia(taxon, includeRelationships, false, includeTaxonDescriptions,
|
1059
|
includeOccurrences, includeTaxonNameDescriptions, TAXONDESCRIPTION_MEDIA_INIT_STRATEGY);
|
1060
|
|
1061
|
Map<Media, MediaRepresentation> mediaRepresentationMap = MediaUtils.findPreferredMedia(taxonGalleryMedia, type,
|
1062
|
mimeTypes, null, widthOrDuration, height, size);
|
1063
|
|
1064
|
List<Media> filteredMedia = new ArrayList<Media>(mediaRepresentationMap.size());
|
1065
|
for (Media media : mediaRepresentationMap.keySet()) {
|
1066
|
media.getRepresentations().clear();
|
1067
|
media.addRepresentation(mediaRepresentationMap.get(media));
|
1068
|
filteredMedia.add(media);
|
1069
|
}
|
1070
|
|
1071
|
return filteredMedia;
|
1072
|
}
|
1073
|
|
1074
|
// ---------------------- code snippet preserved for possible later use --------------------
|
1075
|
// @RequestMapping(
|
1076
|
// value = {"/*/portal/taxon/*/descriptions"},
|
1077
|
// method = RequestMethod.GET)
|
1078
|
// public List<TaxonDescription> doGetDescriptionsbyFeatureTree(HttpServletRequest request, HttpServletResponse response)throws IOException {
|
1079
|
// TaxonBase tb = getCdmBase(request, response, null, Taxon.class);
|
1080
|
// if(tb instanceof Taxon){
|
1081
|
// //T O D O this is a quick and dirty implementation -> generalize
|
1082
|
// UUID featureTreeUuid = readValueUuid(request, featureTreeUuidPattern);
|
1083
|
//
|
1084
|
// FeatureTree featureTree = descriptionService.getFeatureTreeByUuid(featureTreeUuid);
|
1085
|
// Pager<TaxonDescription> p = descriptionService.getTaxonDescriptions((Taxon)tb, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
1086
|
// List<TaxonDescription> descriptions = p.getRecords();
|
1087
|
//
|
1088
|
// if(!featureTree.isDescriptionSeparated()){
|
1089
|
//
|
1090
|
// TaxonDescription superDescription = TaxonDescription.NewInstance();
|
1091
|
// //put all descriptionElements in superDescription and make it invisible
|
1092
|
// for(TaxonDescription description: descriptions){
|
1093
|
// for(DescriptionElementBase element: description.getElements()){
|
1094
|
// superDescription.addElement(element);
|
1095
|
// }
|
1096
|
// }
|
1097
|
// List<TaxonDescription> separatedDescriptions = new ArrayList<TaxonDescription>(descriptions.size());
|
1098
|
// separatedDescriptions.add(superDescription);
|
1099
|
// return separatedDescriptions;
|
1100
|
// }else{
|
1101
|
// return descriptions;
|
1102
|
// }
|
1103
|
// } else {
|
1104
|
// response.sendError(HttpServletResponse.SC_NOT_FOUND, "invalid type; Taxon expected but " + tb.getClass().getSimpleName() + " found.");
|
1105
|
// return null;
|
1106
|
// }
|
1107
|
// }
|
1108
|
|
1109
|
}
|