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

   1
   2 package eu.etaxonomy.cdm.remote.controller;
   3
   4 import java.io.File;
   5 import java.io.IOException;
   6 import java.io.InputStream;
   7 import java.io.PrintWriter;
   8 import java.util.ArrayList;
   9 import java.util.Arrays;
  10 import java.util.HashMap;
  11 import java.util.HashSet;
  12 import java.util.Iterator;
  13 import java.util.LinkedHashMap;
  14 import java.util.List;
  15 import java.util.Map;
  16 import java.util.Set;
  17 import java.util.TreeMap;
  18 import java.util.UUID;
  19
  20 import javax.servlet.http.HttpServletRequest;
  21 import javax.servlet.http.HttpServletResponse;
  22
  23 import java.util.Hashtable;
  24
  25 import org.springframework.beans.factory.annotation.Autowired;
  26 import org.springframework.context.ResourceLoaderAware;
  27 import org.springframework.core.io.Resource;
  28 import org.springframework.core.io.ResourceLoader;
  29 import org.springframework.stereotype.Controller;
  30 import org.springframework.web.bind.annotation.RequestMapping;
  31 import org.springframework.web.bind.annotation.RequestMethod;
  32 import org.springframework.web.bind.annotation.RequestParam;
  33 import org.springframework.web.servlet.ModelAndView;
  34
  35 import eu.etaxonomy.cdm.api.service.IClassificationService;
  36 import eu.etaxonomy.cdm.api.service.INameService;
  37 import eu.etaxonomy.cdm.api.service.ITaxonService;
  38 import eu.etaxonomy.cdm.common.DocUtils;
  39
  40 import eu.etaxonomy.cdm.remote.dto.common.ErrorResponse;
  41 import eu.etaxonomy.cdm.remote.dto.common.RemoteResponse;
  42 import eu.etaxonomy.cdm.remote.dto.namecatalogue.NameInformation;
  43 import eu.etaxonomy.cdm.remote.dto.namecatalogue.NameSearch;
  44 import eu.etaxonomy.cdm.remote.dto.namecatalogue.TaxonInformation;
  45 import eu.etaxonomy.cdm.remote.view.HtmlView;
  46 import eu.etaxonomy.cdm.model.common.CdmBase;
  47 import eu.etaxonomy.cdm.model.common.Language;
  48 import eu.etaxonomy.cdm.model.name.NonViralName;
  49 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  50 import eu.etaxonomy.cdm.model.reference.Reference;
  51 import eu.etaxonomy.cdm.model.taxon.Classification;
  52 import eu.etaxonomy.cdm.model.taxon.Synonym;
  53 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  54 import eu.etaxonomy.cdm.model.taxon.Taxon;
  55 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  56 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  57 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  58 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  59 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  60 import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
  61
  62 /**
  63  * The controller class for the namespace 'name_catalogue'. This web service namespace
  64  * is an add-on to the already existing CDM REST API and provides information relating
  65  * to scientific names as well as taxa present in the underlying datasource.
  66  *
  67  * @author c.mathew
  68  * @version 1.1.0
  69  * @created 15-Apr-2012
  70  */
  71
  72 @Controller
  73 @RequestMapping(value = { "/name_catalogue" })
  74 public class NameCatalogueController extends BaseController<TaxonNameBase, INameService> implements ResourceLoaderAware {
  75
  76     private ResourceLoader resourceLoader;
  77
  78     /** Taxonomic status 'accepted' string */
  79     public static final String ACCEPTED_NAME_STATUS = "accepted";
  80
  81     /** Taxonpmic status 'synonym' string */
  82     public static final String SYNONYM_STATUS = "synonym";
  83
  84     /** Flag 'doubtful' strings */
  85     public static final String DOUBTFUL_FLAG = "doubtful";
  86
  87     /** Base scientific name search type */
  88     public static final String NAME_SEARCH = "name";
  89
  90     /** Complete scientific name search type */
  91     public static final String TITLE_SEARCH = "title";
  92
  93     /** Default name search type */
  94     public static final String DEFAULT_SEARCH_TYPE = NAME_SEARCH;
  95
  96     /** Classifcation 'default' key */
  97     public static final String CLASSIFICATION_DEFAULT = "default";
  98
  99     /** Classifcation 'all' key */
 100     public static final String CLASSIFICATION_ALL = "all";
 101
 102     @Autowired
 103     private ITaxonService taxonService;
 104
 105     @Autowired
 106     private IClassificationService classificationService;
 107
 108     /** Hibernate name search initialisation strategy */
 109     private static final List<String> NAME_SEARCH_INIT_STRATEGY = Arrays.asList(new String[] {
 110             "combinationAuthorTeam.$",
 111             "exCombinationAuthorTeam.$",
 112             "basionymAuthorTeam.$",
 113             "exBasionymAuthorTeam.$",
 114             "nameCache",
 115             "taxonBases",
 116             "taxonBases.synonymRelations.type.$"});
 117
 118     /** Hibernate name information initialisation strategy */
 119     private static final List<String> NAME_INFORMATION_INIT_STRATEGY = Arrays.asList(new String[] {
 120             "taxonBases",
 121             "status",
 122             "nomenclaturalReference.$",
 123             "combinationAuthorTeam.$",
 124             "exCombinationAuthorTeam.$",
 125             "basionymAuthorTeam.$",
 126             "exBasionymAuthorTeam.$",
 127             "relationsToThisName.fromName.$",
 128             "relationsToThisName.nomenclaturalReference.$",
 129             "relationsToThisName.type.$",
 130             "relationsFromThisName.toName.$",
 131             "relationsFromThisName.nomenclaturalReference.$",
 132             "relationsFromThisName.type.$"});
 133
 134     /** Hibernate taxon information initialisation strategy */
 135     private static final List<String> TAXON_INFORMATION_INIT_STRATEGY = Arrays.asList(new String[] {
 136             "name.titleCache",
 137             "name.rank.titleCache",
 138             "synonymRelations.synonym.name.rank.titleCache",
 139             "synonymRelations.acceptedTaxon.name.rank.titleCache",
 140             "synonymRelations.type.$",
 141             "taxonRelations.toTaxon.$",
 142             "taxonRelations.fromTaxon.$",
 143             "taxonRelations.type.$",
 144             "synonymRelations.relatedTo.name.rank.titleCache",
 145             "relationsFromThisTaxon.type.$",
 146             "relationsFromThisTaxon.relatedTo.name.rank.titleCache",
 147             "relationsToThisTaxon.type.$",
 148             "relationsToThisTaxon.relatedFrom.name.rank.titleCache",
 149             "taxonNodes",
 150             "taxonNodes.classification" });
 151
 152     /** Hibernate taxon node initialisation strategy */
 153     private static final List<String> TAXON_NODE_INIT_STRATEGY = Arrays.asList(new String[] {
 154             "taxon.sec",
 155             "taxon.name",
 156             "classification",
 157             "classification.reference.$",
 158             "classification.reference.authorTeam.$" });
 159
 160     /** Hibernate classification vocabulary initialisation strategy */
 161     private static final List<String> VOC_CLASSIFICATION_INIT_STRATEGY = Arrays.asList(new String[] {
 162             "classification",
 163             "classification.reference.$",
 164             "classification.reference.authorTeam.$" });
 165     public NameCatalogueController() {
 166         super();
 167         setInitializationStrategy(Arrays.asList(new String[] { "$" }));
 168     }
 169
 170     /*
 171      * (non-Javadoc)
 172      *
 173      * @see
 174      * eu.etaxonomy.cdm.remote.controller.GenericController#setService(eu
 175      * .etaxonomy.cdm.api.service.IService)
 176      */
 177     @Autowired
 178     @Override
 179     public void setService(INameService service) {
 180         this.service = service;
 181     }
 182
 183     /**
 184      * Returns a documentation page for the Name Search API.
 185      * <p>
 186      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue</b>
 187      *
 188      * @param request
 189      * @param response
 190      * @return Html page describing the Name Search API
 191      * @throws IOException
 192      */
 193     @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {})
 194     public ModelAndView doGetNameSearchDocumentation(
 195             HttpServletRequest request, HttpServletResponse response)
 196             throws IOException {
 197         ModelAndView mv = new ModelAndView();
 198         // Read apt documentation file.
 199         Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-default.apt");
 200         // using input stream as this works for both files in the classes directory
 201         // as well as files inside jars
 202         InputStream aptInputStream = resource.getInputStream();
 203         // Build Html View
 204         Map<String, String> modelMap = new HashMap<String, String>();
 205         // Convert Apt to Html
 206         modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));
 207         mv.addAllObjects(modelMap);
 208
 209         HtmlView hv = new HtmlView();
 210         mv.setView(hv);
 211         return mv;
 212     }
 213
 214     /**
 215      * Returns a list of scientific names matching the <code>{query}</code>
 216      * string pattern. Each of these scientific names is accompanied by a list of
 217      * name uuids, a list of taxon uuids, a list of accepted taxon uuids, etc.
 218      * <p>
 219      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-default.html">here</a>
 220      * <p>
 221      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue</b>
 222      *
 223      * @param queries
 224      *                The base scientific name pattern(s) to query for. The query can
 225      *                contain wildcard characters ('*'). The query can be
 226      *                performed with no wildcard or with the wildcard at the
 227      *                begin and / or end depending on the search pattern.
 228      * @param request Http servlet request.
 229      * @param response Http servlet response.
 230      * @return a list of {@link NameSearch} objects each corresponding to a
 231      *         single query. These are built from {@link TaxonNameBase}
 232      *         entities which are in turn initialized using
 233      *         the {@link #NAME_SEARCH_INIT_STRATEGY}
 234      * @throws IOException
 235      */
 236     @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {"query"})
 237     public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,
 238             HttpServletRequest request, HttpServletResponse response) throws IOException {
 239     return doGetNameSearch(queries, DEFAULT_SEARCH_TYPE, request, response);
 240     }
 241
 242     /**
 243      * Returns a list of scientific names matching the <code>{query}</code>
 244      * string pattern. Each of these scientific names is accompanied by a list of
 245      * name uuids, a list of taxon uuids and a list of accepted taxon uuids.
 246      * <p>
 247      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-default.html">here</a>
 248      * <p>
 249      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue</b>
 250      *
 251      * @param query
 252      *                The scientific name pattern(s) to query for. The query can
 253      *                contain wildcard characters ('*'). The query can be
 254      *                performed with no wildcard or with the wildcard at the
 255      *                begin and / or end depending on the search pattern.
 256      * @param type
 257      *                The type of name to query. This be either
 258      *                "name" : scientific name corresponding to 'name cache' in CDM or
 259      *                "title" : complete name corresponding to 'title cache' in CDM
 260      * @param request Http servlet request.
 261      * @param response Http servlet response.
 262      * @return a List of {@link NameSearch} objects each corresponding to a
 263      *         single query. These are built from {@link TaxonNameBase} entities
 264      *         which are in turn initialized using the {@link #NAME_SEARCH_INIT_STRATEGY}
 265      * @throws IOException
 266      */
 267     @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {"query", "type"})
 268     public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,
 269             @RequestParam(value = "type", required = false, defaultValue = DEFAULT_SEARCH_TYPE) String searchType,
 270             HttpServletRequest request, HttpServletResponse response) throws IOException {
 271         ModelAndView mv = new ModelAndView();
 272         List<RemoteResponse> nsList = new ArrayList<RemoteResponse>();
 273
 274         // if search type is not known then return error
 275         if (!searchType.equals(NAME_SEARCH) && !searchType.equals(TITLE_SEARCH)) {
 276             ErrorResponse er = new ErrorResponse();
 277             er.setErrorMessage("searchType parameter can only be set as" + NAME_SEARCH + " or "
 278                     + TITLE_SEARCH);
 279             mv.addObject(er);
 280             return mv;
 281         }
 282
 283         // search through each query
 284         for (String query : queries) {
 285
 286             String queryWOWildcards = getQueryWithoutWildCards(query);
 287             MatchMode mm = getMatchModeFromQuery(query);
 288             logger.info("doGetNameSearch()" + request.getServletPath() + " for query \"" + query
 289                     + "\" without wild cards : " + queryWOWildcards + " and match mode : " + mm);
 290             List<NonViralName> nameList = new ArrayList<NonViralName>();
 291
 292             // if "name" search then find by name cache
 293             if (searchType.equals(NAME_SEARCH)) {
 294                 nameList = (List<NonViralName>) service.findNamesByNameCache(queryWOWildcards, mm,
 295                         NAME_SEARCH_INIT_STRATEGY);
 296             }
 297
 298             //if "title" search then find by title cache
 299             if (searchType.equals(TITLE_SEARCH)) {
 300                 nameList = (List<NonViralName>) service.findNamesByTitleCache(queryWOWildcards, mm,
 301                         NAME_SEARCH_INIT_STRATEGY);
 302             }
 303
 304             // if search is successful then get related information , else return error
 305             if (nameList == null || !nameList.isEmpty()) {
 306                 NameSearch ns = new NameSearch();
 307                 ns.setRequest(query);
 308
 309                 for (NonViralName nvn : nameList) {
 310                     // we need to retrieve both taxon uuid of name queried and
 311                     // the corresponding accepted taxa.
 312                     // reason to return accepted taxa also, is to be able to get from
 313                     // scientific name to taxon concept in two web service calls.
 314                     Set<TaxonBase> tbSet = nvn.getTaxonBases();
 315                     Set<TaxonBase> accTbSet = new HashSet<TaxonBase>();
 316                     for (TaxonBase tb : tbSet) {
 317                         // if synonym then get accepted taxa.
 318                         if (tb instanceof Synonym) {
 319                             Synonym synonym = (Synonym) tb;
 320                             Set<SynonymRelationship> synRelationships = synonym.getSynonymRelations();
 321                             for (SynonymRelationship sr : synRelationships) {
 322                                 Taxon accTaxon = sr.getAcceptedTaxon();
 323                                 accTbSet.add(accTaxon);
 324                             }
 325                         } else {
 326                             accTbSet.add(tb);
 327                         }
 328                     }
 329                     // update name search object
 330                     ns.addToResponseList(nvn.getTitleCache(), nvn.getNameCache(), nvn.getUuid()
 331                             .toString(), tbSet, accTbSet);
 332                 }
 333                 nsList.add(ns);
 334
 335             } else {
 336                 ErrorResponse er = new ErrorResponse();
 337                 er.setErrorMessage("No Taxon Name for given query : " + query);
 338                 nsList.add(er);
 339             }
 340         }
 341         mv.addObject(nsList);
 342         return mv;
 343     }
 344
 345
 346     /**
 347      * Returns a documentation page for the Name Information API.
 348      * <p>
 349      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/name</b>
 350      *
 351      * @param request Http servlet request.
 352      * @param response Http servlet response.
 353      * @return Html page describing the Name Information API
 354      * @throws IOException
 355      */
 356     @RequestMapping(value = { "name" }, method = RequestMethod.GET, params = {})
 357     public ModelAndView doGetNameInformationDocumentation(
 358             HttpServletRequest request, HttpServletResponse response)
 359             throws IOException {
 360         ModelAndView mv = new ModelAndView();
 361         // Read apt documentation file.
 362         Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-name-info.apt");
 363         // using input stream as this works for both files in the classes directory
 364         // as well as files inside jars
 365         InputStream aptInputStream = resource.getInputStream();
 366         // Build Html View
 367         Map<String, String> modelMap = new HashMap<String, String>();
 368         // Convert Apt to Html
 369         modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));
 370         mv.addAllObjects(modelMap);
 371
 372         HtmlView hv = new HtmlView();
 373         mv.setView(hv);
 374         return mv;
 375     }
 376
 377     /**
 378      * Returns information related to the scientific name matching the given
 379      * <code>{nameUuid}</code>. The information includes the name string,
 380      * relationships, rank, list of related lsids / taxon uuids, etc.
 381      * <p>
 382      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-name-info.html">here</a>
 383      * <p>
 384      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/name</b>
 385      *
 386      * @param nameUuids uuid(s) of the scientific name to search for.
 387      * @param request Http servlet request.
 388      * @param response Http servlet response.
 389      * @return a List of {@link NameInformation} objects each corresponding to a
 390      *         single name uuid. These are built from {@link TaxonNameBase} entities
 391      *         which are in turn initialized using the {@link #NAME_INFORMATION_INIT_STRATEGY}
 392      * @throws IOException
 393      */
 394     @RequestMapping(value = { "name" }, method = RequestMethod.GET, params = {"nameUuid"})
 395     public ModelAndView doGetNameInformation(@RequestParam(value = "nameUuid", required = true) String[] nameUuids,
 396             HttpServletRequest request, HttpServletResponse response) throws IOException {
 397         ModelAndView mv = new ModelAndView();
 398         List<RemoteResponse> niList = new ArrayList<RemoteResponse>();
 399         // loop through each name uuid
 400         for (String nameUuid : nameUuids) {
 401             logger.info("doGetNameInformation()" + request.getServletPath() + " for name uuid \""
 402                     + nameUuid + "\"");
 403             // find name by uuid
 404             NonViralName nvn = (NonViralName) service.findNameByUuid(UUID.fromString(nameUuid),
 405                         NAME_INFORMATION_INIT_STRATEGY);
 406
 407             // if search is successful then get related information, else return error
 408             if (nvn != null) {
 409                 NameInformation ni = new NameInformation();
 410                 ni.setRequest(nameUuid);
 411                 Reference ref = (Reference) nvn.getNomenclaturalReference();
 412                 String citation = "";
 413                 String citation_details = "";
 414                 if (ref != null) {
 415                     citation = ref.getTitleCache();
 416                 }
 417                 // update name information object
 418                 ni.setResponse(nvn.getTitleCache(), nvn.getNameCache(), nvn.getRank().getTitleCache(),
 419                         nvn.getStatus(), citation, nvn.getRelationsFromThisName(),
 420                         nvn.getRelationsToThisName(), nvn.getTaxonBases());
 421                 niList.add(ni);
 422             } else {
 423                 ErrorResponse re = new ErrorResponse();
 424
 425                 if(isValid(nameUuid)) {
 426                     re.setErrorMessage("No Name for given UUID : " + nameUuid);
 427                 } else {
 428                     re.setErrorMessage(nameUuid + " not a valid UUID");
 429                 }
 430                 niList.add(re);
 431             }
 432         }
 433         mv.addObject(niList);
 434         return mv;
 435     }
 436
 437     /**
 438      * Returns a documentation page for the Taxon Information API.
 439      * <p>
 440      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/taxon</b>
 441      *
 442      * @param request Http servlet request.
 443      * @param response Http servlet response.
 444      * @return Html page describing the Taxon Information API
 445      * @throws IOException
 446      */
 447     @RequestMapping(value = { "taxon" }, method = RequestMethod.GET, params = {})
 448     public ModelAndView doGetTaxonInformation(
 449             HttpServletRequest request, HttpServletResponse response)
 450             throws IOException {
 451         ModelAndView mv = new ModelAndView();
 452         // Read apt documentation file.
 453         Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-taxon-info.apt");
 454         // using input stream as this works for both files in the classes directory
 455         // as well as files inside jars
 456         InputStream aptInputStream = resource.getInputStream();
 457         // Build Html View
 458         Map<String, String> modelMap = new HashMap<String, String>();
 459         // Convert Apt to Html
 460         modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));
 461         mv.addAllObjects(modelMap);
 462
 463         HtmlView hv = new HtmlView();
 464         mv.setView(hv);
 465         return mv;
 466     }
 467
 468     /**
 469      * Returns information related to the taxon matching the given
 470      * <code>{taxonUuid}</code>. The information includes the name cache, title cache
 471      * relationship type, taxonomic status, information , etc.
 472      * <p>
 473      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-taxon-info.html">here</a>
 474      * <p>
 475      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue</b>
 476      *
 477      * @param taxonUuid
 478      *                 The taxon uuid to query for. The classification returned corresponds
 479      *                 to the first in the alphabetically sorted list of classifications
 480      *                 currently available in the database.
 481      *
 482      * @param request Http servlet request.
 483      * @param response Http servlet response.
 484      * @return a List of {@link TaxonInformation} objects each corresponding to a
 485      *         single query. These are built from {@TaxonBase} entities which are
 486      *         in turn initialized using the {@link #TAXON_INFORMATION_INIT_STRATEGY}
 487      * @throws IOException
 488      */
 489     @RequestMapping(value = { "taxon" }, method = RequestMethod.GET,params = {"taxonUuid"})
 490     public ModelAndView doGetTaxonInformation(
 491             @RequestParam(value = "taxonUuid", required = true) String[] taxonUuids,
 492             HttpServletRequest request, HttpServletResponse response) throws IOException {
 493         return doGetTaxonInformation(taxonUuids,CLASSIFICATION_DEFAULT, request, response);
 494     }
 495
 496     /**
 497      * Returns information related to the taxon matching the given
 498      * <code>{taxonUuid}</code>. The information includes the name cache, title cache
 499      * relationship type, taxonomic status, information , etc.
 500      * <p>
 501      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-taxon-info.html">here</a>
 502      * <p>
 503      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/taxon</b>
 504      *
 505      * @param taxonUuid
 506      *                 The taxon uuid to query for.
 507      * @param classification
 508      *                 [Optional] String representing the taxonomic classification to use for
 509      *                 building the classification tree. Defaults to the first in the alphabetically
 510      *                 sorted list of classifications currently available in the database.
 511      *
 512      * @param request Http servlet request.
 513      * @param response Http servlet response.
 514      * @return a List of {@link TaxonInformation} objects each corresponding to a
 515      *         single query. These are built from {@TaxonBase} entities which are
 516      *         in turn initialized using the {@link #TAXON_INFORMATION_INIT_STRATEGY}
 517      * @throws IOException
 518      */
 519     @RequestMapping(value = { "taxon" }, method = RequestMethod.GET, params = {"taxonUuid", "classification"})
 520     public ModelAndView doGetTaxonInformation(
 521             @RequestParam(value = "taxonUuid", required = true) String[] taxonUuids,
 522             @RequestParam(value = "classification", required = false, defaultValue = CLASSIFICATION_DEFAULT) String classificationType,
 523             HttpServletRequest request, HttpServletResponse response) throws IOException {
 524         ModelAndView mv = new ModelAndView();
 525         List<RemoteResponse> tiList = new ArrayList<RemoteResponse>();
 526         // loop through each name uuid
 527         for (String taxonUuid : taxonUuids) {
 528             logger.info("doGetTaxonInformation()" + request.getServletPath() + " for taxon uuid \""
 529                     + taxonUuid);
 530             // find name by uuid
 531             TaxonBase tb = taxonService.findTaxonByUuid(UUID.fromString(taxonUuid),
 532                     TAXON_INFORMATION_INIT_STRATEGY);
 533             // if search is successful then get related information, else return error
 534             if (tb != null) {
 535                 TaxonInformation ti = new TaxonInformation();
 536                 ti.setRequest(taxonUuid);
 537                 // check if result (taxon base) is a taxon or synonym
 538                 if (tb.isInstanceOf(Taxon.class)) {
 539                     Taxon taxon = (Taxon) tb;
 540                     // build classification map
 541                     Map classificationMap = getClassification(taxon, classificationType);
 542
 543                     logger.info("taxon uuid " + taxon.getUuid().toString() + " original hash code : " + System.identityHashCode(taxon) + ", name class " + taxon.getName().getClass().getName());
 544                     // update taxon information object with taxon related data
 545                     NonViralName nvn = (NonViralName) taxon.getName();
 546                     ti.setResponseTaxon(tb.getTitleCache(),
 547                             nvn.getTitleCache(),
 548                             nvn.getRank().getTitleCache(),
 549                             ACCEPTED_NAME_STATUS,
 550                             buildFlagMap(tb),
 551                             classificationMap);
 552
 553                     Set<SynonymRelationship> synRelationships = taxon.getSynonymRelations();
 554                     // add synonyms (if exists) to taxon information object
 555                     for (SynonymRelationship sr : synRelationships) {
 556                         Synonym syn = sr.getSynonym();
 557                         String uuid = syn.getUuid().toString();
 558                         String title = syn.getTitleCache();
 559                         NonViralName synnvn = (NonViralName) syn.getName();
 560                         String name = synnvn.getTitleCache();
 561                         String rank = synnvn.getRank().getTitleCache();
 562                         String status = SYNONYM_STATUS;
 563                         String relLabel = sr.getType()
 564                                 .getInverseRepresentation(Language.DEFAULT())
 565                                 .getLabel();
 566                         ti.addToResponseRelatedTaxa(uuid, title, name, rank, status, "", relLabel);
 567                     }
 568
 569                     // build relationship information as,
 570                     // - relationships from the requested taxon
 571                     Set<TaxonRelationship> trFromSet = taxon.getRelationsFromThisTaxon();
 572                     for (TaxonRelationship tr : trFromSet) {
 573                         String titleTo = tr.getToTaxon().getTitleCache();
 574                         NonViralName tonvn = (NonViralName) tr.getToTaxon().getName();
 575                         String name = tonvn.getTitleCache();
 576                         String rank = tonvn.getRank().getTitleCache();
 577                         String uuid = tr.getToTaxon().getUuid().toString();
 578                         String status = ACCEPTED_NAME_STATUS;
 579                         String relLabel = tr.getType().getRepresentation(Language.DEFAULT())
 580                                 .getLabel();
 581                         ti.addToResponseRelatedTaxa(uuid, titleTo, name, rank, status, "", relLabel);
 582                     }
 583
 584                     // - relationships from the requested taxon
 585                     Set<TaxonRelationship> trToSet = taxon.getRelationsToThisTaxon();
 586                     for (TaxonRelationship tr : trToSet) {
 587                         String titleFrom = tr.getFromTaxon().getTitleCache();
 588                         NonViralName fromnvn = (NonViralName) tr.getToTaxon().getName();
 589                         String name = fromnvn.getTitleCache();
 590                         String rank = fromnvn.getRank().getTitleCache();
 591                         String uuid = tr.getFromTaxon().getUuid().toString();
 592                         String status = ACCEPTED_NAME_STATUS;
 593                         String relLabel = tr.getType()
 594                                 .getInverseRepresentation(Language.DEFAULT())
 595                                 .getLabel();
 596                         ti.addToResponseRelatedTaxa(uuid, titleFrom, name, rank, status, "", relLabel);
 597                     }
 598                 } else if (tb instanceof Synonym) {
 599                     Synonym synonym = (Synonym) tb;
 600                     NonViralName nvn = (NonViralName) synonym.getName();
 601                  // update taxon information object with synonym related data
 602                     ti.setResponseTaxon(synonym.getTitleCache(),
 603                             nvn.getTitleCache(),
 604                             nvn.getRank().getTitleCache(),
 605                             SYNONYM_STATUS,
 606                             buildFlagMap(synonym),
 607                             new TreeMap<String,Map>());
 608                     // add accepted taxa (if exists) to taxon information object
 609
 610                     //FIXME commenting out below line in order to allow fixing the bug #3064 (portal synonymy service produces massive response for Crepis tectorum)
 611                     Set<SynonymRelationship> synRelationships = synonym.getSynonymRelations();
 612                     for (SynonymRelationship sr : synRelationships) {
 613                         Taxon accTaxon = sr.getAcceptedTaxon();
 614                         String uuid = accTaxon.getUuid().toString();
 615                         logger.info("acc taxon uuid " + accTaxon.getUuid().toString() + " original hash code : " + System.identityHashCode(accTaxon) + ", name class " + accTaxon.getName().getClass().getName());
 616                         String title = accTaxon.getTitleCache();
 617                         logger.info("taxon title cache : " + accTaxon.getTitleCache());
 618                         //NonViralName accnvn = CdmBase.deproxy(accTaxon.getName(), NonViralName.class);
 619                         NonViralName accnvn = (NonViralName)accTaxon.getName();
 620                         String name = accnvn.getTitleCache();
 621                         String rank = accnvn.getRank().getTitleCache();
 622                         String status = ACCEPTED_NAME_STATUS;
 623                         String relLabel = sr.getType().getRepresentation(Language.DEFAULT())
 624                                 .getLabel();
 625                         ti.addToResponseRelatedTaxa(uuid, title, name, rank, status, "", relLabel);
 626                     }
 627
 628                 }
 629                 tiList.add(ti);
 630             } else {
 631                 ErrorResponse re = new ErrorResponse();
 632                 if(isValid(taxonUuid)) {
 633                     re.setErrorMessage("No Taxon for given UUID : " + taxonUuid);
 634                 } else {
 635                     re.setErrorMessage(taxonUuid + " not a valid UUID");
 636                 }
 637                 tiList.add(re);
 638             }
 639         }
 640         mv.addObject(tiList);
 641         return mv;
 642     }
 643
 644     /**
 645      * Returns a list of all available classifications (with associated referenc information) and the default classification.
 646      * <p>
 647      * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-classification-info.html">here</a>
 648      * <p>
 649      * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/voc/classification</b>
 650      *
 651      * @param request Http servlet request.
 652      * @param response Http servlet response.
 653      * @return a List of {@link Classification} objects represebted as strings.
 654      *         These are initialized using the {@link #VOC_CLASSIFICATION_INIT_STRATEGY}
 655      * @throws IOException
 656      */
 657     @RequestMapping(value = { "voc/classification" }, method = RequestMethod.GET, params = {})
 658     public ModelAndView doGetClassificationMap(HttpServletRequest request, HttpServletResponse response) throws IOException {
 659         List<Map> cmapList = new ArrayList<Map>();
 660         Map<String, String> classifications = new HashMap<String, String>();
 661         ModelAndView mv = new ModelAndView();
 662         List<Classification> clist = getClassificationList(100);
 663         boolean isFirst = true;
 664         Iterator itr = clist.iterator();
 665         // loop through all classifications and populate map with
 666         // (classificationKey, reference) elements
 667         while(itr.hasNext()) {
 668             Classification c = (Classification) itr.next();
 669             String refTitleCache = "";
 670             String classificationKey = removeInternalWhitespace(c.getTitleCache());
 671             if(c.getReference() != null) {
 672                 refTitleCache = c.getReference().getTitleCache();
 673             }
 674             // default is the first element of the list
 675             // always created with the same sorting (DESCENDING)
 676             if(isFirst) {
 677                 Map<String, String> defaultMap = new HashMap<String, String>();
 678                 defaultMap.put("default", classificationKey);
 679                 cmapList.add(defaultMap);
 680                 isFirst = false;
 681             }
 682             classifications.put(classificationKey, refTitleCache);
 683
 684         }
 685         Map<String, Map> cmap = new HashMap<String, Map>();
 686         cmap.put("classification",classifications);
 687         cmapList.add(cmap);
 688         mv.addObject(cmapList);
 689         return mv;
 690     }
 691
 692     /**
 693      * Returns the match mode by parsing the input string of wildcards.
 694      *
 695      * @param query
 696      *             String to parse.
 697      *
 698      * @return {@link MatchMode} depending on the the position of the wildcard (*)
 699      */
 700     private MatchMode getMatchModeFromQuery(String query) {
 701         if (query.startsWith("*") && query.endsWith("*")) {
 702             return MatchMode.ANYWHERE;
 703         } else if (query.startsWith("*")) {
 704             return MatchMode.END;
 705         } else if (query.endsWith("*")) {
 706             return MatchMode.BEGINNING;
 707         } else {
 708             return MatchMode.EXACT;
 709         }
 710     }
 711
 712     /**
 713      * Removes wildcards from the input string.
 714      *
 715      * @param query
 716      *             String to parse.
 717      *
 718      * @return input string with wildcards removed
 719      */
 720     private String getQueryWithoutWildCards(String query) {
 721
 722         String newQuery = query;
 723
 724         if (query.startsWith("*")) {
 725             newQuery = newQuery.substring(1, newQuery.length());
 726         }
 727
 728         if (query.endsWith("*")) {
 729             newQuery = newQuery.substring(0, newQuery.length() - 1);
 730         }
 731
 732         return newQuery.trim();
 733     }
 734
 735     /**
 736      * Build map with taxon flag key-value pairs.
 737      */
 738     private Map<String, String> buildFlagMap(TaxonBase tb) {
 739         Map<String, String> flags = new Hashtable<String, String>();
 740         flags.put(DOUBTFUL_FLAG, Boolean.toString(tb.isDoubtful()));
 741         return flags;
 742     }
 743
 744     /**
 745      * Build classification map.
 746      */
 747     private Map<String, Map> getClassification(Taxon taxon, String classificationType) {
 748         // Using TreeMap is important, because we need the sorting of the classification keys
 749         // in the map to be stable.
 750         TreeMap<String, Map> sourceClassificationMap = buildClassificationMap(taxon, classificationType);
 751
 752         // if classification key is 'default' then return the default element of the map
 753         if(classificationType.equals(CLASSIFICATION_DEFAULT) && !sourceClassificationMap.isEmpty()) {
 754             List<Classification> clist = getClassificationList(1);
 755             String defaultKey = removeInternalWhitespace(clist.get(0).getTitleCache());
 756             return sourceClassificationMap.get(defaultKey);
 757             // if classification key is provided then return the classification corresponding to the key
 758         } else if(sourceClassificationMap.containsKey(classificationType)) {
 759             return sourceClassificationMap.get(classificationType);
 760             // if classification key is 'all' then return the entire map
 761         } else if(classificationType.equals(CLASSIFICATION_ALL)) {
 762             return sourceClassificationMap;
 763         } else {
 764             return new TreeMap<String,Map>();
 765         }
 766     }
 767
 768     /**
 769      * Build classification map.
 770      */
 771     private TreeMap<String, Map> buildClassificationMap(Taxon taxon, String classificationType) {
 772         // Using TreeMap is important, because we need the sorting of the classification keys
 773         // in the map to be stable.
 774         TreeMap<String, Map> sourceClassificationMap = new TreeMap<String, Map>();
 775         Set<TaxonNode> taxonNodes = taxon.getTaxonNodes();
 776         //loop through taxon nodes and build classification map for each classification key
 777         for (TaxonNode tn : taxonNodes) {
 778             Map<String, String> classificationMap = new LinkedHashMap<String, String>();
 779             List<TaxonNode> tnList = classificationService.loadTreeBranchToTaxon(taxon,
 780                     tn.getClassification(), null, TAXON_NODE_INIT_STRATEGY);
 781             for (TaxonNode classificationtn : tnList) {
 782                 classificationMap.put(classificationtn.getTaxon().getName().getRank().getTitleCache(),
 783                         classificationtn.getTaxon().getName().getTitleCache());
 784             }
 785             String cname = removeInternalWhitespace(tn.getClassification().getTitleCache());
 786             logger.info("Building classification map " + cname);
 787             sourceClassificationMap.put(cname, classificationMap);
 788         }
 789         return sourceClassificationMap;
 790     }
 791
 792     private String removeInternalWhitespace(String withWSpace) {
 793         String[] words = withWSpace.split("\\s+");
 794         // "\\s+" in regular expression language meaning one or
 795         // more spaces
 796         StringBuilder builder = new StringBuilder();
 797         for (String word : words) {
 798             builder.append(word);
 799         }
 800         return builder.toString();
 801     }
 802
 803     private List<Classification> getClassificationList(int limit) {
 804         List<OrderHint> orderHints = new ArrayList<OrderHint>();
 805         orderHints.add(new OrderHint("titleCache", SortOrder.DESCENDING));
 806         List<Classification> clist = classificationService.listClassifications(limit, 0, orderHints, VOC_CLASSIFICATION_INIT_STRATEGY);
 807         return clist;
 808     }
 809
 810     private boolean isValid(String uuid){
 811         if( uuid == null) return false;
 812         try {
 813             // we have to convert to object and back to string because the built in fromString does not have
 814             // good validation logic.
 815
 816             UUID fromStringUUID = UUID.fromString(uuid);
 817             String toStringUUID = fromStringUUID.toString();
 818
 819             System.out.println("input uuid : " + uuid + " , parsed uuid : " + toStringUUID);
 820             return toStringUUID.equals(uuid);
 821         } catch(IllegalArgumentException e) {
 822             return false;
 823         }
 824     }
 825     @Override
 826     public void setResourceLoader(ResourceLoader resourceLoader) {
 827         this.resourceLoader = resourceLoader;
 828
 829     }
 830 }