cdmlib-remote/src/main/java/eu/etaxonomy/cdm/remote/controller/TaxonPortalController.java

   1 // $Id: TaxonController.java 5473 2009-03-25 13:42:07Z a.kohlbecker $
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.remote.controller;
  12
  13 import java.io.IOException;
  14 import java.util.ArrayList;
  15 import java.util.Arrays;
  16 import java.util.HashSet;
  17 import java.util.Hashtable;
  18 import java.util.List;
  19 import java.util.Map;
  20 import java.util.NoSuchElementException;
  21 import java.util.Set;
  22 import java.util.SortedMap;
  23 import java.util.TreeMap;
  24 import java.util.UUID;
  25 import java.util.regex.Matcher;
  26 import java.util.regex.Pattern;
  27
  28 import javax.servlet.http.HttpServletRequest;
  29 import javax.servlet.http.HttpServletResponse;
  30
  31 import org.apache.commons.lang.ObjectUtils;
  32 import org.apache.log4j.Logger;
  33 import org.springframework.beans.factory.annotation.Autowired;
  34 import org.springframework.stereotype.Controller;
  35 import org.springframework.web.bind.WebDataBinder;
  36 import org.springframework.web.bind.annotation.InitBinder;
  37 import org.springframework.web.bind.annotation.RequestMapping;
  38 import org.springframework.web.bind.annotation.RequestMethod;
  39 import org.springframework.web.bind.annotation.RequestParam;
  40 import org.springframework.web.servlet.ModelAndView;
  41
  42 import eu.etaxonomy.cdm.api.service.IDescriptionService;
  43 import eu.etaxonomy.cdm.api.service.INameService;
  44 import eu.etaxonomy.cdm.api.service.IReferenceService;
  45 import eu.etaxonomy.cdm.api.service.ITaxonService;
  46 import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
  47 import eu.etaxonomy.cdm.api.service.config.impl.TaxonServiceConfiguratorImpl;
  48 import eu.etaxonomy.cdm.api.service.pager.Pager;
  49 import eu.etaxonomy.cdm.database.UpdatableRoutingDataSource;
  50 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  51 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  52 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  53 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  54 import eu.etaxonomy.cdm.model.location.NamedArea;
  55 import eu.etaxonomy.cdm.model.media.Media;
  56 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  57 import eu.etaxonomy.cdm.model.name.NameRelationship;
  58 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  59 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  60 import eu.etaxonomy.cdm.model.taxon.Synonym;
  61 import eu.etaxonomy.cdm.model.taxon.Taxon;
  62 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  63 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  64 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  65 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  66 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  67 import eu.etaxonomy.cdm.remote.editor.NamedAreaPropertyEditor;
  68 import eu.etaxonomy.cdm.remote.editor.UUIDPropertyEditor;
  69
  70 /**
  71  * The TaxonPortalController class is a Spring MVC Controller.
  72  * <p>
  73  * The syntax of the mapped service URIs contains the the {datasource-name} path element.
  74  * The available {datasource-name}s are defined in a configuration file which
  75  * is loaded by the {@link UpdatableRoutingDataSource}. If the
  76  * UpdatableRoutingDataSource is not being used in the actual application
  77  * context any arbitrary {datasource-name} may be used.
  78  * <p>
  79  * Methods mapped at type level, inherited from super classes ({@link BaseController}):
  80  * <blockquote>
  81  * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}</b>
  82  *
  83  * Get the {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
  84  * The returned Taxon is initialized by
  85  * the following strategy {@link #TAXON_INIT_STRATEGY}
  86  * </blockquote>
  87  *
  88  * @author a.kohlbecker
  89  * @date 20.07.2009
  90  *
  91  */
  92 @Controller
  93 @RequestMapping(value = {"/*/portal/taxon/*", "/*/portal/taxon/*/*", "/*/portal/name/*/*", "/*/portal/taxon/*/media/*/*"})
  94 public class TaxonPortalController extends BaseController<TaxonBase, ITaxonService>
  95 {
  96         public static final Logger logger = Logger.getLogger(TaxonPortalController.class);
  97
  98         @Autowired
  99         private INameService nameService;
 100         @Autowired
 101         private IDescriptionService descriptionService;
 102         @Autowired
 103         private IReferenceService referenceService;
 104
 105
 106         private static final List<String> TAXON_INIT_STRATEGY = Arrays.asList(new String []{
 107                         "*",
 108                         // taxon relations
 109                         "relationsToThisName.fromTaxon.name.taggedName",
 110                         // the name
 111                         "name.$",
 112                         "name.taggedName",
 113                         "name.rank.representations",
 114                         "name.status.type.representations",
 115
 116                         // taxon descriptions
 117                         "descriptions.elements.$",
 118                         "descriptions.elements.area",
 119                         "descriptions.elements.area.$",
 120                         "descriptions.elements.multilanguageText",
 121                         "descriptions.elements.media.representations.parts",
 122
 123 //                      // typeDesignations
 124 //                      "name.typeDesignations.$",
 125 //                      "name.typeDesignations.citation.authorTeam",
 126 //                      "name.typeDesignations.typeName.$",
 127 //                      "name.typeDesignations.typeStatus.representations",
 128 //                      "name.typeDesignations.typeSpecimen.media.representations.parts"
 129
 130                         });
 131
 132         private static final List<String> SIMPLE_TAXON_INIT_STRATEGY = Arrays.asList(new String []{
 133                         "*",
 134                         // taxon relations
 135                         "relationsToThisName.fromTaxon.name.taggedName",
 136                         // the name
 137                         "name.$",
 138                         "name.taggedName",
 139                         "name.rank.representations",
 140                         "name.status.type.representations"
 141                         });
 142
 143         private static final List<String> SYNONYMY_INIT_STRATEGY = Arrays.asList(new String []{
 144                         // initialize homotypical and heterotypical groups; needs synonyms
 145                         "synonymRelations.$",
 146                         "synonymRelations.synonym.$",
 147                         "synonymRelations.synonym.name.taggedName",
 148                         "synonymRelations.synonym.name.nomenclaturalReference.inBook.authorTeam",
 149                         "synonymRelations.synonym.name.nomenclaturalReference.inJournal",
 150                         "synonymRelations.synonym.name.nomenclaturalReference.inProceedings",
 151                         "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",
 152                         "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.name.taggedName",
 153                         "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",
 154                         "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.name.taggedName",
 155
 156                         "name.homotypicalGroup.$",
 157                         "name.homotypicalGroup.typifiedNames.$",
 158                         "name.homotypicalGroup.typifiedNames.name.taggedName",
 159
 160                         "name.homotypicalGroup.typifiedNames.taxonBases.$",
 161                         "name.homotypicalGroup.typifiedNames.taxonBases.name.taggedName"
 162
 163         });
 164
 165         private static final List<String> TAXONRELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{
 166                         "$",
 167                         "type.inverseRepresentations",
 168                         "fromTaxon.sec.authorTeam",
 169                         "fromTaxon.name.taggedName"
 170         });
 171
 172         private static final List<String> NAMERELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{
 173                         "$",
 174                         "type.inverseRepresentations",
 175                         "fromName.taggedName",
 176         });
 177
 178
 179         protected static final List<String> TAXONDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{
 180                         "$",
 181                         "elements.$",
 182                         "elements.citation.authorTeam",
 183                         "elements.multilanguageText",
 184                         "elements.media.representations.parts",
 185         });
 186
 187         private static final List<String> NAMEDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{
 188                         "uuid",
 189                         "feature",
 190                         "elements.$",
 191                         "elements.multilanguageText",
 192                         "elements.media.representations.parts",
 193         });
 194
 195         private static final List<String> TYPEDESIGNATION_INIT_STRATEGY = Arrays.asList(new String []{
 196                         //"$",
 197                         "typeSpecimen.$",
 198                         "typeStatus.representations",
 199                         "citation.authorTeam",
 200                         "typeName.taggedName"
 201         });
 202
 203
 204
 205         private static final String featureTreeUuidPattern = "^/(?:[^/]+)/taxon(?:(?:/)([^/?#&\\.]+))+.*";
 206
 207         public TaxonPortalController(){
 208                 super();
 209                 setUuidParameterPattern("^/(?:[^/]+)/portal/(?:[^/]+)/([^/?#&\\.]+).*");
 210         }
 211
 212         /* (non-Javadoc)
 213          * @see eu.etaxonomy.cdm.remote.controller.GenericController#setService(eu.etaxonomy.cdm.api.service.IService)
 214          */
 215         @Autowired
 216         @Override
 217         public void setService(ITaxonService service) {
 218                 this.service = service;
 219         }
 220
 221         @InitBinder
 222     public void initBinder(WebDataBinder binder) {
 223                 binder.registerCustomEditor(UUID.class, new UUIDPropertyEditor());
 224                 binder.registerCustomEditor(NamedArea.class, new NamedAreaPropertyEditor());
 225         }
 226
 227
 228         /* (non-Javadoc)
 229          * @see eu.etaxonomy.cdm.remote.controller.BaseController#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)
 230          */
 231         @Override
 232         @RequestMapping(method = RequestMethod.GET)
 233         public TaxonBase doGet(HttpServletRequest request, HttpServletResponse response)throws IOException {
 234                 logger.info("doGet()");
 235                 TaxonBase tb = getCdmBase(request, response, TAXON_INIT_STRATEGY, TaxonBase.class);
 236                 return tb;
 237         }
 238
 239         /**
 240          * Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.
 241          * <p>
 242          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;find</b>
 243          *
 244          * @param query
 245          *            the string to query for. Since the wildcard character '*'
 246          *            internally always is appended to the query string, a search
 247          *            always compares the query string with the beginning of a name.
 248          *            - <i>required parameter</i>
 249          * @param treeUuid
 250          *            the {@link UUID} of a {@link TaxonomicTree} to which the
 251          *            search is to be restricted. - <i>optional parameter</i>
 252          * @param areas
 253          *            restrict the search to a set of geographic {@link NamedArea}s.
 254          *            The parameter currently takes a list of TDWG area labels.
 255          *            - <i>optional parameter</i>
 256          * @param page
 257          *            the number of the page to be returned, the first page has the
 258          *            pageNumber = 1 - <i>optional parameter</i>
 259          * @param pageSize
 260          *            the maximum number of entities returned per page (can be null
 261          *            to return all entities in a single page) - <i>optional parameter</i>
 262          * @param doTaxa
 263          *            weather to search for instances of {@link Taxon} - <i>optional parameter</i>
 264          * @param doSynonyms
 265          *            weather to search for instances of {@link Synonym} - <i>optional parameter</i>
 266          * @param doTaxaByCommonNames
 267          *            for instances of {@link Taxon} by a common name used - <i>optional parameter</i>
 268          * @return a Pager on a list of {@link IdentifiableEntity}s initialized by
 269          *         the following strategy {@link #SIMPLE_TAXON_INIT_STRATEGY}
 270          * @throws IOException
 271          */
 272         @RequestMapping(method = RequestMethod.GET,
 273                         value = {"/*/portal/taxon/find"}) //TODO map to path /*/portal/taxon/
 274         public Pager<IdentifiableEntity> doFind(
 275                         @RequestParam(value = "query", required = false) String query,
 276                         @RequestParam(value = "tree", required = false) UUID treeUuid,
 277                         @RequestParam(value = "area", required = false) Set<NamedArea> areas,
 278                         @RequestParam(value = "page", required = false) Integer page,
 279                         @RequestParam(value = "pageSize", required = false) Integer pageSize,
 280                         @RequestParam(value = "doTaxa", required = false) Boolean doTaxa,
 281                         @RequestParam(value = "doSynonyms", required = false) Boolean doSynonyms,
 282                         @RequestParam(value = "doTaxaByCommonNames", required = false) Boolean doTaxaByCommonNames)
 283                          throws IOException {
 284
 285                 logger.info("doFind( " +
 286                         "query=\"" + ObjectUtils.toString(query) + "\", treeUuid=" + ObjectUtils.toString(treeUuid) +
 287                         ", area=" + ObjectUtils.toString(areas) +
 288                         ", pageSize=" + ObjectUtils.toString(pageSize) +  ", page=" + ObjectUtils.toString(page) +
 289                         ", doTaxa=" + ObjectUtils.toString(doTaxa) + ", doSynonyms=" + ObjectUtils.toString(doSynonyms) +")" );
 290
 291                 if(page == null){ page = BaseListController.DEFAULT_PAGE_NUMBER;}
 292                 if(pageSize == null){ pageSize = BaseListController.DEFAULT_PAGESIZE;}
 293
 294                 ITaxonServiceConfigurator config = new TaxonServiceConfiguratorImpl();
 295                 config.setPageNumber(page);
 296                 config.setPageSize(pageSize);
 297                 config.setSearchString(query);
 298                 config.setDoTaxa(doTaxa!= null ? doTaxa : Boolean.FALSE );
 299                 config.setDoSynonyms(doSynonyms != null ? doSynonyms : Boolean.FALSE );
 300                 config.setDoTaxaByCommonNames(doTaxaByCommonNames != null ? doTaxaByCommonNames : Boolean.FALSE );
 301                 config.setMatchMode(MatchMode.BEGINNING);
 302                 config.setTaxonPropertyPath(SIMPLE_TAXON_INIT_STRATEGY);
 303                 config.setNamedAreas(areas);
 304                 if(treeUuid != null){
 305                         TaxonomicTree taxonomicTree = service.getTaxonomicTreeByUuid(treeUuid);
 306                         config.setTaxonomicTree(taxonomicTree);
 307                 }
 308
 309                 return (Pager<IdentifiableEntity>) service.findTaxaAndNames(config);
 310         }
 311
 312         /**
 313          * Get the synonymy for a taxon identified by the <code>{taxon-uuid}</code>.
 314          * The synonymy consists
 315          * of two parts: The group of homotypic synonyms of the taxon and the
 316          * heterotypic synonymy groups of the taxon. The synonymy is ordered
 317          * historically by the type designations and by the publication date of the
 318          * nomenclatural reference
 319          * <p>
 320          * URI:
 321          * <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;synonymy</b>
 322          *
 323          *
 324          * @param request
 325          * @param response
 326          * @return a Map with to entries which are mapped by the following keys:
 327          *         "homotypicSynonymsByHomotypicGroup", "heterotypicSynonymyGroups",
 328          *         containing lists of {@link Synonym}s which are initialized using the
 329          *         following initialization strategy: {@link #SYNONYMY_INIT_STRATEGY}
 330          *
 331          * @throws IOException
 332          */
 333         @RequestMapping(
 334                         value = {"/*/portal/taxon/*/synonymy"},
 335                         method = RequestMethod.GET)
 336         public ModelAndView doGetSynonymy(HttpServletRequest request, HttpServletResponse response)throws IOException {
 337
 338                 logger.info("doGetSynonymy() " + request.getServletPath());
 339                 ModelAndView mv = new ModelAndView();
 340                 TaxonBase tb = getCdmBase(request, response, null, Taxon.class);
 341                 Taxon taxon = (Taxon)tb;
 342                 Map<String, List<?>> synonymy = new Hashtable<String, List<?>>();
 343                 synonymy.put("homotypicSynonymsByHomotypicGroup", service.getHomotypicSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY));
 344                 synonymy.put("heterotypicSynonymyGroups", service.getHeterotypicSynonymyGroups(taxon, SYNONYMY_INIT_STRATEGY));
 345                 mv.addObject(synonymy);
 346                 return mv;
 347         }
 348
 349         /**
 350          * Get the set of accepted {@link Taxon} entities for a given
 351          * {@link TaxonBase} entity identified by the <code>{taxon-uuid}</code>.
 352          * <p>
 353          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;accepted</b>
 354          *
 355          * @param request
 356          * @param response
 357          * @return a Set of {@link Taxon} entities which are initialized
 358          *         using the following initialization strategy:
 359          *         {@link #SYNONYMY_INIT_STRATEGY}
 360          * @throws IOException
 361          */
 362         @RequestMapping(value = "/*/portal/taxon/*/accepted", method = RequestMethod.GET)
 363         public Set<TaxonBase> getAccepted(HttpServletRequest request, HttpServletResponse response) throws IOException {
 364
 365                 logger.info("getAccepted() " + request.getServletPath());
 366
 367                 UUID uuid = readValueUuid(request, null);
 368                 TaxonBase tb = service.load(uuid, SYNONYMY_INIT_STRATEGY);
 369                 if(tb == null){
 370                         response.sendError(HttpServletResponse.SC_NOT_FOUND, "A taxon with the uuid " + uuid + " does not exist");
 371                         return null;
 372                 }
 373                 HashSet<TaxonBase> resultset = new HashSet<TaxonBase>();
 374                 if(tb instanceof Taxon){
 375                         //the taxon already is accepted
 376                         //FIXME take the current view into account once views are implemented!!!
 377                         resultset.add((Taxon)tb);
 378                 } else {
 379                         Synonym syn = (Synonym)tb;
 380                         for(TaxonBase accepted : syn.getAcceptedTaxa()){
 381                                 accepted = service.load(accepted.getUuid(), SIMPLE_TAXON_INIT_STRATEGY);
 382                                 resultset.add(accepted);
 383                         }
 384                 }
 385                 return resultset;
 386         }
 387
 388         /**
 389      * Get the list of {@link TaxonRelationship}s for the given
 390          * {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
 391          * <p>
 392          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;taxonRelationships</b>
 393          *
 394          * @param request
 395          * @param response
 396          * @return a List of {@link TaxonRelationship} entities which are initialized
 397          *         using the following initialization strategy:
 398          *         {@link #TAXONRELATIONSHIP_INIT_STRATEGY}
 399          * @throws IOException
 400          */
 401         @RequestMapping(
 402                         value = {"/*/portal/taxon/*/taxonRelationships"},
 403                         method = RequestMethod.GET)
 404         public List<TaxonRelationship> doGetTaxonRelations(HttpServletRequest request, HttpServletResponse response)throws IOException {
 405
 406                 logger.info("doGetTaxonRelations()" + request.getServletPath());
 407                 TaxonBase tb = getCdmBase(request, response, null, Taxon.class);
 408                 Taxon taxon = (Taxon)tb;
 409                 List<TaxonRelationship> relations = new ArrayList<TaxonRelationship>();
 410                 List<TaxonRelationship> results = service.listToTaxonRelationships(taxon, TaxonRelationshipType.MISAPPLIED_NAME_FOR(), null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
 411                 relations.addAll(results);
 412                 results = service.listToTaxonRelationships(taxon, TaxonRelationshipType.INVALID_DESIGNATION_FOR(), null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);
 413                 relations.addAll(results);
 414
 415                 return relations;
 416         }
 417
 418         /**
 419      * Get the list of {@link NameRelationship}s of the Name associated with the
 420          * {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
 421          * <p>
 422          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;nameRelationships</b>
 423          *
 424          * @param request
 425          * @param response
 426          * @return a List of {@link NameRelationship} entities which are initialized
 427          *         using the following initialization strategy:
 428          *         {@link #NAMERELATIONSHIP_INIT_STRATEGY}
 429          * @throws IOException
 430          */
 431         @RequestMapping(
 432                         value = {"/*/portal/taxon/*/nameRelationships"},
 433                         method = RequestMethod.GET)
 434         public List<NameRelationship> doGetNameRelations(HttpServletRequest request, HttpServletResponse response)throws IOException {
 435                 logger.info("doGetNameRelations()" + request.getServletPath());
 436                 TaxonBase tb = getCdmBase(request, response, SIMPLE_TAXON_INIT_STRATEGY, Taxon.class);
 437                 List<NameRelationship> list = nameService.listToNameRelationships(tb.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);
 438                 return list;
 439         }
 440
 441         /**
 442      * Get the list of {@link TaxonNameDescription}s of the Name associated with the
 443          * {@link TaxonNameBase} instance identified by the <code>{name-uuid}</code>.
 444          * <p>
 445          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;name&#x002F;{name-uuid}&#x002F;descriptions</b>
 446          *
 447          * @param request
 448          * @param response
 449          * @return a List of {@link TaxonNameDescription} entities which are initialized
 450          *         using the following initialization strategy:
 451          *         {@link #NAMEDESCRIPTION_INIT_STRATEGY}
 452          * @throws IOException
 453          */
 454         @RequestMapping(
 455                         value = {"/*/portal/name/*/descriptions"},
 456                         method = RequestMethod.GET)
 457         public List<TaxonNameDescription> doGetNameDescriptions(HttpServletRequest request, HttpServletResponse response)throws IOException {
 458                 logger.info("doGetNameDescriptions()" + request.getServletPath());
 459                 UUID nameUuuid = readValueUuid(request, null);
 460                 TaxonNameBase tnb = nameService.load(nameUuuid, null);
 461                 Pager<TaxonNameDescription> p = descriptionService.getTaxonNameDescriptions(tnb, null, null, NAMEDESCRIPTION_INIT_STRATEGY);
 462                 return p.getRecords();
 463         }
 464
 465         /**
 466      * Get the list of {@link TypeDesignationBase}s of the
 467          * {@link TaxonBase} instance identified by the <code>{taxon-uuid}</code>.
 468          * <p>
 469          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;nameTypeDesignations</b>
 470          *
 471          * @param request
 472          * @param response
 473          * @return a List of {@link TypeDesignationBase} entities which are initialized
 474          *         using the following initialization strategy:
 475          *         {@link #TYPEDESIGNATION_INIT_STRATEGY}
 476          * @throws IOException
 477          */
 478         @RequestMapping(
 479                         value = {"/*/portal/taxon/*/nameTypeDesignations"},
 480                         method = RequestMethod.GET)
 481         public List<TypeDesignationBase> doGetNameTypeDesignations(HttpServletRequest request, HttpServletResponse response)throws IOException {
 482                 logger.info("doGetNameTypeDesignations()" + request.getServletPath());
 483                 TaxonBase tb = getCdmBase(request, response, SIMPLE_TAXON_INIT_STRATEGY, Taxon.class);
 484                 Pager<TypeDesignationBase> p = nameService.getTypeDesignations(tb.getName(), null, null, null, TYPEDESIGNATION_INIT_STRATEGY);
 485                 return p.getRecords();
 486         }
 487
 488         /**
 489      * Get the list of {@link TaxonDescription}s of the
 490          * {@link Taxon} instance identified by the <code>{taxon-uuid}</code>.
 491          * <p>
 492          * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;descriptions</b>
 493          *
 494          * @param request
 495          * @param response
 496          * @return a List of {@link TaxonDescription} entities which are initialized
 497          *         using the following initialization strategy:
 498          *         {@link #TAXONDESCRIPTION_INIT_STRATEGY}
 499          * @throws IOException
 500          */
 501         @RequestMapping(
 502                         value = {"/*/portal/taxon/*/descriptions"},
 503                         method = RequestMethod.GET)
 504         public List<TaxonDescription> doGetDescriptions(HttpServletRequest request, HttpServletResponse response)throws IOException {
 505                 logger.info("doGetDescriptions()" + request.getServletPath());
 506                 Taxon t = getCdmBase(request, response, null, Taxon.class);
 507                 Pager<TaxonDescription> p = descriptionService.getTaxonDescriptions(t, null, null, null, null,
 508                         TAXONDESCRIPTION_INIT_STRATEGY);
 509                 return p.getRecords();
 510         }
 511
 512         /**
 513          * Get the {@link Media} attached to the {@link Taxon} instance
 514          * identified by the <code>{taxon-uuid}</code>.
 515          *
 516          * Usage &#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-
 517          * uuid}&#x002F;media&#x002F;{mime type
 518          * list}&#x002F;{size}[,[widthOrDuration}][,{height}]&#x002F;
 519          *
 520          * Whereas
 521          * <ul>
 522          * <li><b>{mime type list}</b>: a comma separated list of mime types, in the
 523          * order of preference. The forward slashes contained in the mime types must
 524          * be replaced by a colon. Regular expressions can be used. Each media
 525          * associated with this given taxon is being searched whereas the first
 526          * matching mime type matching a representation always rules.</li>
 527          * <li><b>{size},{widthOrDuration},{height}</b>: <i>not jet implemented</i>
 528          * valid values are an integer or the asterisk '*' as a wildcard</li>
 529          * </ul>
 530          *
 531          * @param request
 532          * @param response
 533          * @return a List of {@link Media} entities which are initialized
 534          *         using the following initialization strategy:
 535          *         {@link #TAXONDESCRIPTION_INIT_STRATEGY}
 536          * @throws IOException
 537          */
 538         @RequestMapping(
 539                 value = {"/*/portal/taxon/*/media/*/*"},
 540                 method = RequestMethod.GET)
 541         public List<Media> doGetMedia(HttpServletRequest request, HttpServletResponse response)throws IOException {
 542                 logger.info("doGetMedia()" + request.getServletPath());
 543                 Taxon t = getCdmBase(request, response, null, Taxon.class);
 544                 Pager<TaxonDescription> p =
 545                         descriptionService.getTaxonDescriptions(t, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
 546
 547                 // pars the media and quality parameters
 548
 549
 550                 // collect all media of the given taxon
 551                 boolean limitToGalleries = false;
 552                 List<Media> taxonMedia = new ArrayList<Media>();
 553                 for(TaxonDescription desc : p.getRecords()){
 554                         if(!limitToGalleries || desc.isImageGallery()){
 555                                 for(DescriptionElementBase element : desc.getElements()){
 556                                         for(Media media : element.getMedia()){
 557                                                 taxonMedia.add(media);
 558                                         }
 559                                 }
 560                         }
 561                 }
 562
 563                 // move into media ...
 564
 565                 // find best matching representations of each media
 566                 String path = request.getServletPath();
 567                 String[] pathTokens = path.split("/");
 568                 String[] mimeTypes = pathTokens[6].split(",");
 569                 String[] sizeTokens = pathTokens[7].split(",");
 570                 Integer widthOrDuration = null;
 571                 Integer height = null;
 572                 Integer size = null;
 573
 574                 for(int i=0; i<mimeTypes.length; i++){
 575                         mimeTypes[i] = mimeTypes[i].replace(':', '/');
 576                 }
 577
 578                 if(sizeTokens.length > 0){
 579                         try {
 580                                 size = Integer.valueOf(sizeTokens[0]);
 581                         } catch (NumberFormatException nfe) {
 582                                 /* IGNORE */
 583                         }
 584                 }
 585                 if(sizeTokens.length > 1){
 586                         try {
 587                                 widthOrDuration = Integer.valueOf(sizeTokens[1]);
 588                         } catch (NumberFormatException nfe) {
 589                                 /* IGNORE */
 590                         }
 591                 }
 592                 if(sizeTokens.length > 2){
 593                         try {
 594                                 height = Integer.valueOf(sizeTokens[2]);
 595                         } catch (NumberFormatException nfe) {
 596                                 /* IGNORE */
 597                         }
 598                 }
 599
 600                 List<Media> returnMedia = new ArrayList<Media>(taxonMedia.size());
 601                 for(Media media : taxonMedia){
 602                         SortedMap<String, MediaRepresentation> prefRepresentations
 603                                 = orderMediaRepresentations(media, mimeTypes, size, widthOrDuration, height);
 604                         try {
 605                                 // take first one and remove all other representations
 606                                 MediaRepresentation prefOne = prefRepresentations.get(prefRepresentations.firstKey());
 607                                 for (MediaRepresentation representation : media.getRepresentations()) {
 608                                         if (representation != prefOne) {
 609                                                 media.removeRepresentation(representation);
 610                                         }
 611                                 }
 612                                 returnMedia.add(media);
 613                         } catch (NoSuchElementException nse) {
 614                                 /* IGNORE */
 615                         }
 616                 }
 617
 618                 return returnMedia;
 619         }
 620
 621         /**
 622          * @param media
 623          * @param mimeTypeRegexes
 624          * @param size
 625          * @param widthOrDuration
 626          * @param height
 627          * @return
 628          *
 629          * TODO move into a media utils class
 630          * TODO implement the quality filter
 631          */
 632         private SortedMap<String, MediaRepresentation> orderMediaRepresentations(Media media, String[] mimeTypeRegexes,
 633                         Integer size, Integer widthOrDuration, Integer height) {
 634                 SortedMap<String, MediaRepresentation> prefRepr = new TreeMap<String, MediaRepresentation>();
 635                 for (String mimeTypeRegex : mimeTypeRegexes) {
 636                         // getRepresentationByMimeType
 637                         Pattern mimeTypePattern = Pattern.compile(mimeTypeRegex);
 638                         int representationCnt = 0;
 639                         for (MediaRepresentation representation : media.getRepresentations()) {
 640                                 Matcher mather = mimeTypePattern.matcher(representation.getMimeType());
 641                                 if (mather.matches()) {
 642                                         int dwa = 0;
 643
 644                                         /* TODO the quality filter part is being skipped
 645                                          * // look for representation with the best matching parts
 646                                         for (MediaRepresentationPart part : representation.getParts()) {
 647                                                 if (part instanceof ImageFile) {
 648                                                         ImageFile image = (ImageFile) part;
 649                                                         int dw = image.getWidth() * image.getHeight() - height * widthOrDuration;
 650                                                         if (dw < 0) {
 651                                                                 dw *= -1;
 652                                                         }
 653                                                         dwa += dw;
 654                                                 }
 655                                                 dwa = (representation.getParts().size() > 0 ? dwa / representation.getParts().size() : 0);
 656                                         }*/
 657                                         prefRepr.put((dwa + representationCnt++) + '_' + representation.getMimeType(), representation);
 658
 659                                         // preferred mime type found => end loop
 660                                         break;
 661                                 }
 662                         }
 663                 }
 664                 return prefRepr;
 665         }
 666
 667 // ---------------------- code snippet preserved for possible later use --------------------
 668 //      @RequestMapping(
 669 //                      value = {"/*/portal/taxon/*/descriptions"},
 670 //                      method = RequestMethod.GET)
 671 //      public List<TaxonDescription> doGetDescriptionsbyFeatureTree(HttpServletRequest request, HttpServletResponse response)throws IOException {
 672 //              TaxonBase tb = getCdmBase(request, response, null, Taxon.class);
 673 //              if(tb instanceof Taxon){
 674 //                      //T O D O this is a quick and dirty implementation -> generalize
 675 //                      UUID featureTreeUuid = readValueUuid(request, featureTreeUuidPattern);
 676 //
 677 //                      FeatureTree featureTree = descriptionService.getFeatureTreeByUuid(featureTreeUuid);
 678 //                      Pager<TaxonDescription> p = descriptionService.getTaxonDescriptions((Taxon)tb, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);
 679 //                      List<TaxonDescription> descriptions = p.getRecords();
 680 //
 681 //                      if(!featureTree.isDescriptionSeparated()){
 682 //
 683 //                              TaxonDescription superDescription = TaxonDescription.NewInstance();
 684 //                              //put all descriptionElements in superDescription and make it invisible
 685 //                              for(TaxonDescription description: descriptions){
 686 //                                      for(DescriptionElementBase element: description.getElements()){
 687 //                                              superDescription.addElement(element);
 688 //                                      }
 689 //                              }
 690 //                              List<TaxonDescription> separatedDescriptions = new ArrayList<TaxonDescription>(descriptions.size());
 691 //                              separatedDescriptions.add(superDescription);
 692 //                              return separatedDescriptions;
 693 //                      }else{
 694 //                              return descriptions;
 695 //                      }
 696 //              } else {
 697 //                      response.sendError(HttpServletResponse.SC_NOT_FOUND, "invalid type; Taxon expected but " + tb.getClass().getSimpleName() + " found.");
 698 //                      return null;
 699 //              }
 700 //      }
 701
 702 }