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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.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.log4j.Logger;
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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 com.wordnik.swagger.annotations.Api;
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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.pager.Pager;
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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.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.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.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.remote.controller.util.ControllerUtils;
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import eu.etaxonomy.cdm.remote.editor.CdmTypePropertyEditor;
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import eu.etaxonomy.cdm.remote.editor.DefinedTermBaseList;
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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.TermBaseListPropertyEditor;
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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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@Api("portal_taxon")
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@RequestMapping(value = {"/portal/taxon/{uuid}"})
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public class TaxonPortalController extends TaxonController
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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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"$",
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"sources",
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// taxon relations
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// "relationsToThisName.fromTaxon.name",
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// the name
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"name.$",
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"name.nomenclaturalReference.authorship",
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"name.nomenclaturalReference.inReference",
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"name.rank.representations",
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"name.status.type.representations",
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// "descriptions" // TODO remove
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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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// the name
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"name.$",
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"name.rank.representations",
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"name.status.type.representations",
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"name.nomenclaturalReference.authorship",
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"name.nomenclaturalReference.inReference",
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"taxonNodes.classification",
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});
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private static final List<String> SYNONYMY_INIT_STRATEGY = Arrays.asList(new String []{
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// initialize homotypical and heterotypical groups; needs synonyms
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"synonymRelations.$",
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"synonymRelations.synonym.$",
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"synonymRelations.synonym.name.status.type.representation",
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"synonymRelations.synonym.name.nomenclaturalReference.authorship",
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"synonymRelations.synonym.name.nomenclaturalReference.inReference",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",
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"synonymRelations.synonym.name.combinationAuthorship.$",
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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.authorship",
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"name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",
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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.$",
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"synonymRelations.synonym.name.status.type.representation",
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"synonymRelations.synonym.name.nomenclaturalReference.authorship",
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"synonymRelations.synonym.name.nomenclaturalReference.inReference",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",
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"synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",
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"synonymRelations.synonym.name.combinationAuthorship.$",
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"name.homotypicalGroup.$",
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"name.homotypicalGroup.typifiedNames.$",
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"name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorship",
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"name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",
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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.$",
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"name.rank.representations",
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"name.status.type.representations",
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"name.nomenclaturalReference.authorship",
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"name.nomenclaturalReference.inReference",
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"taxonNodes.$",
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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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"toName.$",
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"toName.nomenclaturalReference.authorship",
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"toName.nomenclaturalReference.inReference",
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"fromName.$",
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"fromName.nomenclaturalReference.authorship",
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"fromName.nomenclaturalReference.inReference",
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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.stateData.$",
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"elements.sources.citation.authorship",
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"elements.sources.nameUsedInSource",
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"elements.multilanguageText",
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"elements.media",
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"elements.modifyingText",
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"elements.modifiers",
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"elements.kindOfUnit",
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"name.$",
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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.authorship",
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"sources.nameUsedInSource",
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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.authorship.$",
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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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binder.registerCustomEditor(DefinedTermBaseList.class, new TermBaseListPropertyEditor<NamedArea>(termService));
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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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/**
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* Get the synonymy for a taxon identified by the <code>{taxon-uuid}</code>.
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* The synonymy consists
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* of two parts: The group of homotypic synonyms of the taxon and the
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* heterotypic synonymy groups of the taxon. The synonymy is ordered
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* historically by the type designations and by the publication date of the
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* nomenclatural reference
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* <p>
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* URI:
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* <b>/{datasource-name}/portal/taxon/{taxon-uuid}/synonymy</b>
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*
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*
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* @param request
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* @param response
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* @return a Map with to entries which are mapped by the following keys:
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* "homotypicSynonymsByHomotypicGroup", "heterotypicSynonymyGroups",
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* containing lists of {@link Synonym}s which are initialized using the
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* following initialization strategy: {@link #SYNONYMY_INIT_STRATEGY}
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*
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* @throws IOException
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*/
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@RequestMapping(
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value = {"synonymy"},
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method = RequestMethod.GET)
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public ModelAndView doGetSynonymy(@PathVariable("uuid") UUID uuid,
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HttpServletRequest request, HttpServletResponse response)throws IOException {
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if(request != null){
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logger.info("doGetSynonymy() " + requestPathAndQuery(request));
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}
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ModelAndView mv = new ModelAndView();
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Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
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Map<String, List<?>> synonymy = new Hashtable<String, List<?>>();
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//new
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List<List<Synonym>> synonymyGroups = service.getSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY);
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synonymy.put("homotypicSynonymsByHomotypicGroup", synonymyGroups.get(0));
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synonymyGroups.remove(0);
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synonymy.put("heterotypicSynonymyGroups", synonymyGroups);
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//old
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// synonymy.put("homotypicSynonymsByHomotypicGroup", service.getHomotypicSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY));
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// synonymy.put("heterotypicSynonymyGroups", service.getHeterotypicSynonymyGroups(taxon, SYNONYMY_INIT_STRATEGY));
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mv.addObject(synonymy);
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return mv;
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}
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/**
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* Get the list of {@link TaxonRelationship}s for the given
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* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
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* <p>
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* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/taxonRelationships</b>
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*
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* @param request
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* @param response
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* @return a List of {@link TaxonRelationship} entities which are initialized
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* using the following initialization strategy:
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* {@link #TAXONRELATIONSHIP_INIT_STRATEGY}
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* @throws IOException
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*/
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@RequestMapping(
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value = {"taxonRelationships"},
|
403
|
method = RequestMethod.GET)
|
404
|
public List<TaxonRelationship> doGetTaxonRelations(@PathVariable("uuid") UUID uuid,
|
405
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
406
|
|
407
|
logger.info("doGetTaxonRelations()" + requestPathAndQuery(request));
|
408
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
409
|
List<TaxonRelationship> toRelationships = service.listToTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
|
410
|
List<TaxonRelationship> fromRelationships = service.listFromTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
|
411
|
|
412
|
List<TaxonRelationship> allRelationships = new ArrayList<TaxonRelationship>(toRelationships.size() + fromRelationships.size());
|
413
|
allRelationships.addAll(toRelationships);
|
414
|
allRelationships.addAll(fromRelationships);
|
415
|
|
416
|
return allRelationships;
|
417
|
}
|
418
|
|
419
|
/**
|
420
|
* Get the list of {@link NameRelationship}s of the Name associated with the
|
421
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
422
|
* <p>
|
423
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/nameRelationships</b>
|
424
|
*
|
425
|
* @param request
|
426
|
* @param response
|
427
|
* @return a List of {@link NameRelationship} entities which are initialized
|
428
|
* using the following initialization strategy:
|
429
|
* {@link #NAMERELATIONSHIP_INIT_STRATEGY}
|
430
|
* @throws IOException
|
431
|
*/
|
432
|
@RequestMapping(
|
433
|
value = {"toNameRelationships"},
|
434
|
method = RequestMethod.GET)
|
435
|
public List<NameRelationship> doGetToNameRelations(@PathVariable("uuid") UUID uuid,
|
436
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
437
|
logger.info("doGetNameRelations()" + request.getRequestURI());
|
438
|
TaxonBase taxonBase = getCdmBaseInstance(TaxonBase.class, uuid, response, (List<String>)null);
|
439
|
List<NameRelationship> list = nameService.listNameRelationships(taxonBase.getName(), Direction.relatedTo, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
440
|
//List<NameRelationship> list = nameService.listToNameRelationships(taxonBase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
441
|
return list;
|
442
|
}
|
443
|
|
444
|
/**
|
445
|
* Get the list of {@link NameRelationship}s of the Name associated with the
|
446
|
* {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
|
447
|
* <p>
|
448
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/nameRelationships</b>
|
449
|
*
|
450
|
* @param request
|
451
|
* @param response
|
452
|
* @return a List of {@link NameRelationship} entities which are initialized
|
453
|
* using the following initialization strategy:
|
454
|
* {@link #NAMERELATIONSHIP_INIT_STRATEGY}
|
455
|
* @throws IOException
|
456
|
*/
|
457
|
@RequestMapping(
|
458
|
value = {"fromNameRelationships"},
|
459
|
method = RequestMethod.GET)
|
460
|
public List<NameRelationship> doGetFromNameRelations(@PathVariable("uuid") UUID uuid,
|
461
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
462
|
logger.info("doGetNameFromNameRelations()" + requestPathAndQuery(request));
|
463
|
|
464
|
TaxonBase taxonbase = getCdmBaseInstance(TaxonBase.class, uuid, response, SIMPLE_TAXON_INIT_STRATEGY);
|
465
|
List<NameRelationship> list = nameService.listNameRelationships(taxonbase.getName(), Direction.relatedFrom, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
466
|
//List<NameRelationship> list = nameService.listFromNameRelationships(taxonbase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);
|
467
|
return list;
|
468
|
}
|
469
|
|
470
|
@Override
|
471
|
@RequestMapping(value = "taxonNodes", method = RequestMethod.GET)
|
472
|
public Set<TaxonNode> doGetTaxonNodes(
|
473
|
@PathVariable("uuid") UUID uuid,
|
474
|
HttpServletRequest request,
|
475
|
HttpServletResponse response) throws IOException {
|
476
|
logger.info("doGetTaxonNodes" + requestPathAndQuery(request));
|
477
|
TaxonBase taxon = service.load(uuid, TAXONNODE_INIT_STRATEGY);
|
478
|
if(taxon instanceof Taxon){
|
479
|
return ((Taxon)taxon).getTaxonNodes();
|
480
|
} else {
|
481
|
HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);
|
482
|
return null;
|
483
|
}
|
484
|
}
|
485
|
|
486
|
/**
|
487
|
* Get the list of {@link TaxonDescription}s of the
|
488
|
* {@link Taxon} instance identified by the <code>{taxon-uuid}</code>.
|
489
|
* <p>
|
490
|
* URI: <b>/{datasource-name}/portal/taxon/{taxon-uuid}/descriptions</b>
|
491
|
*
|
492
|
* @param request
|
493
|
* @param response
|
494
|
* @return a List of {@link TaxonDescription} entities which are initialized
|
495
|
* using the following initialization strategy:
|
496
|
* {@link #TAXONDESCRIPTION_INIT_STRATEGY}
|
497
|
* @throws IOException
|
498
|
*/
|
499
|
@RequestMapping(
|
500
|
value = {"descriptions"},
|
501
|
method = RequestMethod.GET)
|
502
|
public List<TaxonDescription> doGetDescriptions(
|
503
|
@PathVariable("uuid") UUID uuid,
|
504
|
@RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,
|
505
|
HttpServletRequest request,
|
506
|
HttpServletResponse response)throws IOException {
|
507
|
if(request != null){
|
508
|
logger.info("doGetDescriptions()" + requestPathAndQuery(request));
|
509
|
}
|
510
|
List<DefinedTermBase> markerTypeTerms = null;
|
511
|
Set<UUID> sMarkerTypeUUIDs = null;
|
512
|
|
513
|
if(markerTypeUUIDs != null && !markerTypeUUIDs.isEmpty()){
|
514
|
sMarkerTypeUUIDs = new HashSet<UUID>(markerTypeUUIDs);
|
515
|
markerTypeTerms = termService.find(sMarkerTypeUUIDs);
|
516
|
} else if(markerTypeUUIDs != null && markerTypeUUIDs.isEmpty()){
|
517
|
markerTypeTerms = new ArrayList<DefinedTermBase>();
|
518
|
}
|
519
|
Set<MarkerType> markerTypes = new HashSet<MarkerType>();
|
520
|
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>();
|
521
|
if (markerTypeTerms != null) {
|
522
|
for (DefinedTermBase markerTypeTerm : markerTypeTerms) {
|
523
|
markerTypes.add((MarkerType)markerTypeTerm);
|
524
|
}
|
525
|
}
|
526
|
Taxon t = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
527
|
if (markerTypeTerms == null) {
|
528
|
|
529
|
Pager<TaxonDescription> p = descriptionService.pageTaxonDescriptions(t, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
530
|
descriptions = p.getRecords();
|
531
|
}
|
532
|
|
533
|
else if (markerTypeTerms != null && markerTypeTerms.isEmpty()) {
|
534
|
descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
535
|
|
536
|
}
|
537
|
else {
|
538
|
descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
539
|
/*for (TaxonDescription description: descriptions) {
|
540
|
for (IdentifiableSource source :description.getSources()) {
|
541
|
if (source.getOriginalNameString() != null) {
|
542
|
description.
|
543
|
}
|
544
|
|
545
|
}
|
546
|
|
547
|
|
548
|
}*/
|
549
|
}
|
550
|
return descriptions;
|
551
|
}
|
552
|
|
553
|
@RequestMapping(value = "useDescriptions", method = RequestMethod.GET)
|
554
|
public List<TaxonDescription> doGetUseDescriptions(
|
555
|
@PathVariable("uuid") UUID uuid,
|
556
|
HttpServletRequest request,
|
557
|
HttpServletResponse response) throws IOException {
|
558
|
logger.info("doGetDescriptionElements() - " + requestPathAndQuery(request));
|
559
|
|
560
|
//ModelAndView mv = new ModelAndView();
|
561
|
Taxon t = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
562
|
|
563
|
//MarkerType useMarkerType = (MarkerType) markerTypeService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));
|
564
|
MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
565
|
|
566
|
//find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));
|
567
|
Set<MarkerType> markerTypes = new HashSet<MarkerType>();
|
568
|
markerTypes.add(useMarkerType);
|
569
|
List<TaxonDescription> descriptionElements = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
570
|
//getDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths) load(uuid);
|
571
|
|
572
|
/*if(!(description instanceof TaxonDescription)){
|
573
|
HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);
|
574
|
// will terminate thread
|
575
|
}*/
|
576
|
|
577
|
//boolean hasStructuredData = service. hasStructuredData(description);
|
578
|
|
579
|
//mv.addObject(hasStructuredData);
|
580
|
|
581
|
return descriptionElements;
|
582
|
}
|
583
|
|
584
|
@RequestMapping(value = "descriptions/elementsByType/{classSimpleName}", method = RequestMethod.GET)
|
585
|
public ModelAndView doGetDescriptionElementsByType(
|
586
|
@PathVariable("uuid") UUID uuid,
|
587
|
@PathVariable("classSimpleName") String classSimpleName,
|
588
|
@RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,
|
589
|
@RequestParam(value = "count", required = false, defaultValue = "false") Boolean doCount,
|
590
|
HttpServletRequest request,
|
591
|
HttpServletResponse response) throws IOException {
|
592
|
logger.info("doGetDescriptionElementsByType() - " + requestPathAndQuery(request));
|
593
|
|
594
|
ModelAndView mv = new ModelAndView();
|
595
|
|
596
|
List<DescriptionElementBase> allElements = new ArrayList<DescriptionElementBase>();
|
597
|
List<DescriptionElementBase> elements;
|
598
|
int count = 0;
|
599
|
|
600
|
List<String> initStrategy = doCount ? null : DESCRIPTION_ELEMENT_INIT_STRATEGY;
|
601
|
|
602
|
List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, markerTypeUUIDs, request, response);
|
603
|
try {
|
604
|
Class type;
|
605
|
type = Class.forName("eu.etaxonomy.cdm.model.description."
|
606
|
+ classSimpleName);
|
607
|
if (taxonDescriptions != null) {
|
608
|
for (TaxonDescription description : taxonDescriptions) {
|
609
|
elements = descriptionService.listDescriptionElements(description, null, type, null, 0, initStrategy);
|
610
|
allElements.addAll(elements);
|
611
|
count += elements.size();
|
612
|
}
|
613
|
|
614
|
}
|
615
|
} catch (ClassNotFoundException e) {
|
616
|
HttpStatusMessage.create(e.getLocalizedMessage(), 400).send(response);
|
617
|
}
|
618
|
if(doCount){
|
619
|
mv.addObject(count);
|
620
|
} else {
|
621
|
mv.addObject(allElements);
|
622
|
}
|
623
|
return mv;
|
624
|
}
|
625
|
|
626
|
// @RequestMapping(value = "specimens", method = RequestMethod.GET)
|
627
|
// public ModelAndView doGetSpecimens(
|
628
|
// @PathVariable("uuid") UUID uuid,
|
629
|
// HttpServletRequest request,
|
630
|
// HttpServletResponse response) throws IOException, ClassNotFoundException {
|
631
|
// logger.info("doGetSpecimens() - " + request.getRequestURI());
|
632
|
//
|
633
|
// ModelAndView mv = new ModelAndView();
|
634
|
//
|
635
|
// List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
|
636
|
//
|
637
|
// // find speciemens in the TaxonDescriptions
|
638
|
// List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, request, response);
|
639
|
// if (taxonDescriptions != null) {
|
640
|
//
|
641
|
// for (TaxonDescription description : taxonDescriptions) {
|
642
|
// derivedUnitFacadeList.addAll( occurrenceService.listDerivedUnitFacades(description, null) );
|
643
|
// }
|
644
|
// }
|
645
|
// // TODO find speciemens in the NameDescriptions ??
|
646
|
//
|
647
|
// // TODO also find type specimens
|
648
|
//
|
649
|
// mv.addObject(derivedUnitFacadeList);
|
650
|
//
|
651
|
// return mv;
|
652
|
// }
|
653
|
|
654
|
/**
|
655
|
* Get the {@link Media} attached to the {@link Taxon} instance
|
656
|
* identified by the <code>{taxon-uuid}</code>.
|
657
|
*
|
658
|
* Usage /{datasource-name}/portal/taxon/{taxon-
|
659
|
* uuid}/media/{mime type
|
660
|
* list}/{size}[,[widthOrDuration}][,{height}]/
|
661
|
*
|
662
|
* Whereas
|
663
|
* <ul>
|
664
|
* <li><b>{mime type list}</b>: a comma separated list of mime types, in the
|
665
|
* order of preference. The forward slashes contained in the mime types must
|
666
|
* be replaced by a colon. Regular expressions can be used. Each media
|
667
|
* associated with this given taxon is being searched whereas the first
|
668
|
* matching mime type matching a representation always rules.</li>
|
669
|
* <li><b>{size},{widthOrDuration},{height}</b>: <i>not jet implemented</i>
|
670
|
* valid values are an integer or the asterisk '*' as a wildcard</li>
|
671
|
* </ul>
|
672
|
*
|
673
|
* @param request
|
674
|
* @param response
|
675
|
* @return a List of {@link Media} entities which are initialized
|
676
|
* using the following initialization strategy:
|
677
|
* {@link #TAXONDESCRIPTION_INIT_STRATEGY}
|
678
|
* @throws IOException
|
679
|
*/
|
680
|
@RequestMapping(
|
681
|
value = {"media"},
|
682
|
method = RequestMethod.GET)
|
683
|
public List<Media> doGetMedia(
|
684
|
@PathVariable("uuid") UUID uuid,
|
685
|
@RequestParam(value = "type", required = false) Class<? extends MediaRepresentationPart> type,
|
686
|
@RequestParam(value = "mimeTypes", required = false) String[] mimeTypes,
|
687
|
@RequestParam(value = "relationships", required = false) UuidList relationshipUuids,
|
688
|
@RequestParam(value = "relationshipsInvers", required = false) UuidList relationshipInversUuids,
|
689
|
@RequestParam(value = "includeTaxonDescriptions", required = true) Boolean includeTaxonDescriptions,
|
690
|
@RequestParam(value = "includeOccurrences", required = true) Boolean includeOccurrences,
|
691
|
@RequestParam(value = "includeTaxonNameDescriptions", required = true) Boolean includeTaxonNameDescriptions,
|
692
|
@RequestParam(value = "widthOrDuration", required = false) Integer widthOrDuration,
|
693
|
@RequestParam(value = "height", required = false) Integer height,
|
694
|
@RequestParam(value = "size", required = false) Integer size,
|
695
|
HttpServletRequest request, HttpServletResponse response) throws IOException {
|
696
|
|
697
|
logger.info("doGetMedia() " + requestPathAndQuery(request));
|
698
|
|
699
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);
|
700
|
|
701
|
Set<TaxonRelationshipEdge> includeRelationships = ControllerUtils.loadIncludeRelationships(relationshipUuids, relationshipInversUuids, termService);
|
702
|
|
703
|
List<Media> returnMedia = getMediaForTaxon(taxon, includeRelationships,
|
704
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
705
|
type, mimeTypes, widthOrDuration, height, size);
|
706
|
return returnMedia;
|
707
|
}
|
708
|
|
709
|
@RequestMapping(
|
710
|
value = {"subtree/media"},
|
711
|
method = RequestMethod.GET)
|
712
|
public List<Media> doGetSubtreeMedia(
|
713
|
@PathVariable("uuid") UUID uuid,
|
714
|
@RequestParam(value = "type", required = false) Class<? extends MediaRepresentationPart> type,
|
715
|
@RequestParam(value = "mimeTypes", required = false) String[] mimeTypes,
|
716
|
@RequestParam(value = "relationships", required = false) UuidList relationshipUuids,
|
717
|
@RequestParam(value = "relationshipsInvers", required = false) UuidList relationshipInversUuids,
|
718
|
@RequestParam(value = "includeTaxonDescriptions", required = true) Boolean includeTaxonDescriptions,
|
719
|
@RequestParam(value = "includeOccurrences", required = true) Boolean includeOccurrences,
|
720
|
@RequestParam(value = "includeTaxonNameDescriptions", required = true) Boolean includeTaxonNameDescriptions,
|
721
|
@RequestParam(value = "widthOrDuration", required = false) Integer widthOrDuration,
|
722
|
@RequestParam(value = "height", required = false) Integer height,
|
723
|
@RequestParam(value = "size", required = false) Integer size,
|
724
|
HttpServletRequest request, HttpServletResponse response)throws IOException {
|
725
|
|
726
|
logger.info("doGetSubtreeMedia() " + requestPathAndQuery(request));
|
727
|
|
728
|
Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, TAXON_WITH_NODES_INIT_STRATEGY);
|
729
|
|
730
|
Set<TaxonRelationshipEdge> includeRelationships = ControllerUtils.loadIncludeRelationships(relationshipUuids, relationshipInversUuids, termService);
|
731
|
|
732
|
List<Media> returnMedia = getMediaForTaxon(taxon, includeRelationships,
|
733
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
734
|
type, mimeTypes, widthOrDuration, height, size);
|
735
|
TaxonNode node;
|
736
|
//looking for all medias of genus
|
737
|
if (taxon.getTaxonNodes().size()>0){
|
738
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
739
|
Iterator<TaxonNode> iterator = nodes.iterator();
|
740
|
//TaxonNode holen
|
741
|
node = iterator.next();
|
742
|
//Check if TaxonNode belongs to the current tree
|
743
|
|
744
|
node = classificationService.loadTaxonNode(node, TAXONNODE_WITHTAXON_INIT_STRATEGY);
|
745
|
List<TaxonNode> children = node.getChildNodes();
|
746
|
Taxon childTaxon;
|
747
|
for (TaxonNode child : children){
|
748
|
childTaxon = child.getTaxon();
|
749
|
if(childTaxon != null) {
|
750
|
childTaxon = (Taxon)taxonService.load(childTaxon.getUuid(), null);
|
751
|
returnMedia.addAll(getMediaForTaxon(childTaxon, includeRelationships,
|
752
|
includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
753
|
type, mimeTypes, widthOrDuration, height, size));
|
754
|
}
|
755
|
}
|
756
|
}
|
757
|
return returnMedia;
|
758
|
}
|
759
|
|
760
|
/**
|
761
|
*
|
762
|
* @param taxon
|
763
|
* @param includeRelationships
|
764
|
* @param type
|
765
|
* @param mimeTypes
|
766
|
* @param widthOrDuration
|
767
|
* @param height
|
768
|
* @param size
|
769
|
* @return
|
770
|
*/
|
771
|
private List<Media> getMediaForTaxon(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
|
772
|
Boolean includeTaxonDescriptions, Boolean includeOccurrences, Boolean includeTaxonNameDescriptions,
|
773
|
Class<? extends MediaRepresentationPart> type, String[] mimeTypes, Integer widthOrDuration,
|
774
|
Integer height, Integer size) {
|
775
|
|
776
|
// list the media
|
777
|
logger.trace("getMediaForTaxon() - list the media");
|
778
|
List<Media> taxonGalleryMedia = service.listMedia(taxon, includeRelationships,
|
779
|
false, includeTaxonDescriptions, includeOccurrences, includeTaxonNameDescriptions,
|
780
|
TAXONDESCRIPTION_MEDIA_INIT_STRATEGY);
|
781
|
|
782
|
// filter by preferred size and type
|
783
|
|
784
|
logger.trace("getMediaForTaxon() - filter the media");
|
785
|
Map<Media, MediaRepresentation> mediaRepresentationMap = MediaUtils.findPreferredMedia(
|
786
|
taxonGalleryMedia, type, mimeTypes, null, widthOrDuration, height, size);
|
787
|
|
788
|
List<Media> filteredMedia = new ArrayList<Media>(mediaRepresentationMap.size());
|
789
|
for (Media media : mediaRepresentationMap.keySet()) {
|
790
|
media.getRepresentations().clear();
|
791
|
media.addRepresentation(mediaRepresentationMap.get(media));
|
792
|
filteredMedia.add(media);
|
793
|
}
|
794
|
|
795
|
logger.trace("getMediaForTaxon() - END ");
|
796
|
|
797
|
return filteredMedia;
|
798
|
}
|
799
|
|
800
|
// ---------------------- code snippet preserved for possible later use --------------------
|
801
|
// @RequestMapping(
|
802
|
// value = {"//*/portal/taxon/*/descriptions"}, // mapped as absolute path, see CdmAntPathMatcher
|
803
|
// method = RequestMethod.GET)
|
804
|
// public List<TaxonDescription> doGetDescriptionsbyFeatureTree(HttpServletRequest request, HttpServletResponse response)throws IOException {
|
805
|
// TaxonBase tb = getCdmBase(request, response, null, Taxon.class);
|
806
|
// if(tb instanceof Taxon){
|
807
|
// //T O D O this is a quick and dirty implementation -> generalize
|
808
|
// UUID featureTreeUuid = readValueUuid(request, featureTreeUuidPattern);
|
809
|
//
|
810
|
// FeatureTree featureTree = descriptionService.getFeatureTreeByUuid(featureTreeUuid);
|
811
|
// Pager<TaxonDescription> p = descriptionService.getTaxonDescriptions((Taxon)tb, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
|
812
|
// List<TaxonDescription> descriptions = p.getRecords();
|
813
|
//
|
814
|
// if(!featureTree.isDescriptionSeparated()){
|
815
|
//
|
816
|
// TaxonDescription superDescription = TaxonDescription.NewInstance();
|
817
|
// //put all descriptionElements in superDescription and make it invisible
|
818
|
// for(TaxonDescription description: descriptions){
|
819
|
// for(DescriptionElementBase element: description.getElements()){
|
820
|
// superDescription.addElement(element);
|
821
|
// }
|
822
|
// }
|
823
|
// List<TaxonDescription> separatedDescriptions = new ArrayList<TaxonDescription>(descriptions.size());
|
824
|
// separatedDescriptions.add(superDescription);
|
825
|
// return separatedDescriptions;
|
826
|
// }else{
|
827
|
// return descriptions;
|
828
|
// }
|
829
|
// } else {
|
830
|
// response.sendError(HttpServletResponse.SC_NOT_FOUND, "invalid type; Taxon expected but " + tb.getClass().getSimpleName() + " found.");
|
831
|
// return null;
|
832
|
// }
|
833
|
// }
|
834
|
|
835
|
}
|