/ - Diff - EDIT - EDIT Project Management

« Previous | Next »

Revision 16495c16

Added by Cherian Mathew about 11 years ago

ID 16495c1687767e4fdb660fa36a4aa540e123dade
Parent ed07b709
Child 2f50e942

NameCatalogueController : updated controller to improve exact and fuzzy name search to use lucene document only searches
NameSearch : updated dto to accomodate lucene documents

     import java.util.List;
     import java.util.Map;
     import java.util.Set;
     import java.util.StringTokenizer;
     import java.util.TreeMap;
     import java.util.UUID;
-...
     import java.util.Hashtable;
     import org.apache.log4j.Level;
     import org.apache.lucene.document.Document;
     import org.apache.lucene.queryParser.ParseException;
     import org.joda.time.DateTime;
     import org.joda.time.format.DateTimeFormat;
-...
     import eu.etaxonomy.cdm.api.service.INameService;
     import eu.etaxonomy.cdm.api.service.ITaxonService;
     import eu.etaxonomy.cdm.api.service.ITermService;
     import eu.etaxonomy.cdm.api.service.search.DocumentSearchResult;
     import eu.etaxonomy.cdm.api.service.search.SearchResult;
     import eu.etaxonomy.cdm.common.DocUtils;
     import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
     import eu.etaxonomy.cdm.hibernate.search.AcceptedTaxonBridge;
     import eu.etaxonomy.cdm.remote.controller.BaseController;
     import eu.etaxonomy.cdm.remote.dto.common.ErrorResponse;
-...
         /** Default name search type */
         public static final String DEFAULT_SEARCH_TYPE = NAME_SEARCH;
         /** Default max number of hits for the exact name search  */
         public static final String DEFAULT_MAX_NB_FOR_EXACT_SEARCH = "100";
         /** Classifcation 'default' key */
         public static final String CLASSIFICATION_DEFAULT = "default";
-...
         @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {"query"})
         public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,
                 HttpServletRequest request, HttpServletResponse response) throws IOException {
         return doGetNameSearch(queries, DEFAULT_SEARCH_TYPE, request, response);
         return doGetNameSearch(queries, DEFAULT_SEARCH_TYPE, DEFAULT_MAX_NB_FOR_EXACT_SEARCH, request, response);
+        }
         /**
-...
          * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue</b>
+         *
          * @param query
          *                The scientific name pattern(s) to query for. The query can
          *                contain wildcard characters ('*'). The query can be
          *                performed with no wildcard or with the wildcard at the
          *                begin and / or end depending on the search pattern.
          *             	The scientific name pattern(s) to query for. The query can
          *             	contain wildcard characters ('*'). The query can be
          *              performed with no wildcard or with the wildcard at the
          *              begin and / or end depending on the search pattern.
          * @param type
          *                The type of name to query. This be either
          *                "name" : scientific name corresponding to 'name cache' in CDM or
          *                "title" : complete name corresponding to 'title cache' in CDM
          *              The type of name to query. This be either
          *              "name" : scientific name corresponding to 'name cache' in CDM or
          *              "title" : complete name corresponding to 'title cache' in CDM
          * @param hits
          *            	Maximum number of responses to be returned.
          * @param request Http servlet request.
          * @param response Http servlet response.
          * @return a List of {@link NameSearch} objects each corresponding to a
-...
         @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {"query", "type"})
         public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,
                 @RequestParam(value = "type", required = false, defaultValue = DEFAULT_SEARCH_TYPE) String searchType,
                 @RequestParam(value = "hits", required = false, defaultValue = DEFAULT_MAX_NB_FOR_EXACT_SEARCH) String hits,
                 HttpServletRequest request, HttpServletResponse response) throws IOException {
             ModelAndView mv = new ModelAndView();
             List<RemoteResponse> nsList = new ArrayList<RemoteResponse>();
             // if search type is not known then return error
             if (!searchType.equals(NAME_SEARCH) && !searchType.equals(TITLE_SEARCH)) {
                 ErrorResponse er = new ErrorResponse();
                 er.setErrorMessage("searchType parameter can only be set as" + NAME_SEARCH + " or "
                         + TITLE_SEARCH);
                 mv.addObject(er);
             int h = 100;
             try {
             	h = Integer.parseInt(hits);
             } catch(NumberFormatException nfe) {
             	ErrorResponse er = new ErrorResponse();
             	er.setErrorMessage("hits parameter is not a number");
             	mv.addObject(er);
                 return mv;
+            }
             // search through each query
             for (String query : queries) {
             	if(query.equals("")) {
     				ErrorResponse er = new ErrorResponse();
                     er.setErrorMessage("Empty query field");
                     nsList.add(er);
                     continue;
+            	}
             	// remove wildcards if any
                 String queryWOWildcards = getQueryWithoutWildCards(query);
                 MatchMode mm = getMatchModeFromQuery(query);
                 logger.info("doGetNameSearch()" + request.getRequestURI() + " for query \"" + query
                         + "\" without wild cards : " + queryWOWildcards + " and match mode : " + mm);
                 List<NonViralName> nameList = new ArrayList<NonViralName>();
                 // if "name" search then find by name cache
                 if (searchType.equals(NAME_SEARCH)) {
                     nameList = (List<NonViralName>) service.findNamesByNameCache(queryWOWildcards, mm,
                             NAME_SEARCH_INIT_STRATEGY);
+                }
                 //if "title" search then find by title cache
                 if (searchType.equals(TITLE_SEARCH)) {
                     nameList = (List<NonViralName>) service.findNamesByTitleCache(queryWOWildcards, mm,
                             NAME_SEARCH_INIT_STRATEGY);
                 // convert first char to upper case
                 char[] stringArray = queryWOWildcards.toCharArray();
                 stringArray[0] = Character.toUpperCase(stringArray[0]);
                 queryWOWildcards = new String(stringArray);
                 boolean wc = false;
                 if(getMatchModeFromQuery(query) == MatchMode.BEGINNING) {
                 	wc = true;
+                }
                 logger.info("doGetNameSearch()" + request.getRequestURI() + " for query \"" + query);
                 List<DocumentSearchResult> nameSearchList = new ArrayList<DocumentSearchResult>();
                 try {
     				nameSearchList = service.findByNameExactSearch(
     				        queryWOWildcards,
     				        wc,
     				        null,
     				        false,
     				        h);
     			} catch (ParseException e) {
     				// TODO Auto-generated catch block
     				//e.printStackTrace();
     				ErrorResponse er = new ErrorResponse();
                     er.setErrorMessage("Could not parse name : " + query);
                     nsList.add(er);
                     continue;
+    			}
                 // if search is successful then get related information , else return error
                 if (nameList == null || !nameList.isEmpty()) {
                 if (nameSearchList == null || !nameSearchList.isEmpty()) {
                     NameSearch ns = new NameSearch();
                     ns.setRequest(query);
                     for (NonViralName nvn : nameList) {
                     for (DocumentSearchResult searchResult : nameSearchList) {
                     	for(Document doc : searchResult.getDocs()) {
                         // we need to retrieve both taxon uuid of name queried and
                         // the corresponding accepted taxa.
                         // reason to return accepted taxa also, is to be able to get from
                         // scientific name to taxon concept in two web service calls.
                         Set<TaxonBase> tbSet = nvn.getTaxonBases();
                         Set<TaxonBase> accTbSet = new HashSet<TaxonBase>();
                         for (TaxonBase tb : tbSet) {
                             // if synonym then get accepted taxa.
                             if (tb instanceof Synonym) {
                                 Synonym synonym = (Synonym) tb;
                                 Set<SynonymRelationship> synRelationships = synonym.getSynonymRelations();
                                 for (SynonymRelationship sr : synRelationships) {
                                     Taxon accTaxon = sr.getAcceptedTaxon();
                                     accTbSet.add(accTaxon);
+                                }
                             } else {
                                 accTbSet.add(tb);
+                            }
                         List<String> tbUuidList = new ArrayList<String>();//nvn.getTaxonBases();
                         List<String> accTbUuidList = new ArrayList<String>();
                         String[] tbUuids = doc.getValues("taxonBases.uuid");
                         String[] tbClassNames = doc.getValues("taxonBases.classInfo.name");
                         for(int i=0;i<tbUuids.length;i++) {
                         	if(tbClassNames[i].equals("eu.etaxonomy.cdm.model.taxon.Taxon")) {
                         		accTbUuidList.add(tbUuids[i]);
+                        	}
+                        }
                         // update name search object
                         ns.addToResponseList(nvn.getTitleCache(), nvn.getNameCache(), 0, nvn.getUuid()
                                 .toString(), tbSet, accTbSet);
                         ns.addToResponseList(doc.getValues("titleCache")[0],
                         		doc.getValues("nameCache")[0],
                         		searchResult.getMaxScore(),
                         		doc.getValues("uuid")[0].toString(),
                         		doc.getValues("taxonBases.uuid"),
                         		mergeSynAccTaxonUuids(doc.getValues("taxonBases.accTaxon.uuids")));
+                    	}
+                    }
                     nsList.add(ns);
                 } else {
                     ErrorResponse er = new ErrorResponse();
                     er.setErrorMessage("No Taxon Name for given query : " + query);
                     er.setErrorMessage("No Taxon Name matches : " + query + ", for given accuracy");
                     nsList.add(er);
+                }
+            }
-...
          */
         @RequestMapping(value = { "fuzzy" }, method = RequestMethod.GET, params = {"query"})
         public ModelAndView doGetNameFuzzySearch(@RequestParam(value = "query", required = true) String[] queries,
         		@RequestParam(value = "accuracy", required = false, defaultValue = "0.5") String accuracy,
         		@RequestParam(value = "accuracy", required = false, defaultValue = "0.6") String accuracy,
         		@RequestParam(value = "hits", required = false, defaultValue = "10") String hits,
                 HttpServletRequest request, HttpServletResponse response) throws IOException {
             ModelAndView mv = new ModelAndView();
-...
                 queryWOWildcards = new String(stringArray);
                 logger.info("doGetNameSearch()" + request.getRequestURI() + " for query \"" + queryWOWildcards + " with accuracy " + accuracy);
                 //List<NonViralName> nameList = new ArrayList<NonViralName>();
                 List<SearchResult<TaxonNameBase>> nameSearchList = new ArrayList<SearchResult<TaxonNameBase>>();
                 List<DocumentSearchResult> nameSearchList = new ArrayList<DocumentSearchResult>();
                 try {
     				nameSearchList = service.findByNameFuzzySearch(
     				        queryWOWildcards,
     				        acc,
     				        null,
     				        false,
     				        NAME_SEARCH_INIT_STRATEGY,
     				        h);
     			} catch (ParseException e) {
     				// TODO Auto-generated catch block
-...
                     NameSearch ns = new NameSearch();
                     ns.setRequest(query);
                     for (SearchResult searchResult : nameSearchList) {
                     	NonViralName nvn = HibernateProxyHelper.deproxy(searchResult.getEntity(), NonViralName.class);
                     for (DocumentSearchResult searchResult : nameSearchList) {
                     	for(Document doc : searchResult.getDocs()) {
                         // we need to retrieve both taxon uuid of name queried and
                         // the corresponding accepted taxa.
                         // reason to return accepted taxa also, is to be able to get from
                         // scientific name to taxon concept in two web service calls.
                         Set<TaxonBase> tbSet = nvn.getTaxonBases();
                         Set<TaxonBase> accTbSet = new HashSet<TaxonBase>();
                         for (TaxonBase tb : tbSet) {
                             // if synonym then get accepted taxa.
                             if (tb instanceof Synonym) {
                                 Synonym synonym = (Synonym) tb;
                                 Set<SynonymRelationship> synRelationships = synonym.getSynonymRelations();
                                 for (SynonymRelationship sr : synRelationships) {
                                     Taxon accTaxon = sr.getAcceptedTaxon();
                                     accTbSet.add(accTaxon);
+                                }
                             } else {
                                 accTbSet.add(tb);
+                            }
                         List<String> tbUuidList = new ArrayList<String>();//nvn.getTaxonBases();
                         List<String> accTbUuidList = new ArrayList<String>();
                         String[] tbUuids = doc.getValues("taxonBases.uuid");
                         String[] tbClassNames = doc.getValues("taxonBases.classInfo.name");
                         for(int i=0;i<tbUuids.length;i++) {
                         	if(tbClassNames[i].equals("eu.etaxonomy.cdm.model.taxon.Taxon")) {
                         		accTbUuidList.add(tbUuids[i]);
+                        	}
+                        }
                         // update name search object
                         ns.addToResponseList(nvn.getTitleCache(), nvn.getNameCache(), searchResult.getMaxScore(), nvn.getUuid()
                                 .toString(), tbSet, accTbSet);
                         ns.addToResponseList(doc.getValues("titleCache")[0],
                         		doc.getValues("nameCache")[0],
                         		searchResult.getMaxScore(),
                         		doc.getValues("uuid")[0].toString(),
                         		doc.getValues("taxonBases.uuid"),
                         		mergeSynAccTaxonUuids(doc.getValues("taxonBases.accTaxon.uuids")));
+                    	}
+                    }
                     nsList.add(ns);
-...
             mv.addObject(nsList);
             return mv;
+        }
         private String[] mergeSynAccTaxonUuids(String[] accTaxonUuids) {
         	List<String> accTaxonUuidList = new ArrayList<String>();
         	for(String accTaxonUuid : accTaxonUuids) {
         		for(String uuidListAsString : accTaxonUuid.split(AcceptedTaxonBridge.ACCEPTED_TAXON_UUID_LIST_SEP)) {
         			accTaxonUuidList.add(uuidListAsString);
+        		}
+        	}
         	return accTaxonUuidList.toArray(new String[0]);
+        }
         /**
          * Returns a documentation page for the Name Information API.
          * <p>
-...
                             String title = syn.getTitleCache();
                             TaxonNameBase synnvn = (TaxonNameBase) syn.getName();
                             String name = synnvn.getTitleCache();
                             String rank = synnvn.getRank().getTitleCache();
                             String rank = (synnvn.getRank() == null)? "" : synnvn.getRank().getTitleCache();
                             String status = SYNONYM_STATUS;
                             String relLabel = sr.getType()
                                     .getInverseRepresentation(Language.DEFAULT())
-...
             ModelAndView mv = new ModelAndView();
             List<RemoteResponse> ansList = new ArrayList<RemoteResponse>();
             logger.info("doGetAcceptedNameSearch()");
             // if search type is not known then return error
             if (!searchType.equals(NAME_SEARCH) && !searchType.equals(TITLE_SEARCH)) {
                 ErrorResponse er = new ErrorResponse();

                 res.addToAcceptedTaxontUuids(acctb.getUuid().toString());
+            }
+        }
         public void addToResponseList(String title,
         		String name,
         		float score,
         		String nameUuid,
         		String[] taxonBaseUuids,
         		String[] accTaxonUuids) {
             NameSearch.NameSearchResponse res = responseWithtitle(title);
             if (res == null) {
                 res = new NameSearch.NameSearchResponse();
                 res.setTitle(title);
                 res.setName(name);
                 res.setScore(score);
                 response.add(res);
+            }
             res.addToNameUuids(nameUuid);
             for (String tbuuid : taxonBaseUuids) {
                 res.addToTaxonConceptUuids(tbuuid);
+            }
             for (String acctbuuid : accTaxonUuids) {
                 res.addToAcceptedTaxontUuids(acctbuuid);
+            }
+        }
         public List<NameSearch.NameSearchResponse> getResponse() {
             return this.response;

Also available in: Unified diff

Project

General

Profile

EDIT

Revision 16495c16

Added by Cherian Mathew about 11 years ago