2 * Copyright (C) 2007 EDIT
3 * European Distributed Institute of Taxonomy
4 * http://www.e-taxonomy.eu
6 * The contents of this file are subject to the Mozilla Public License Version 1.1
7 * See LICENSE.TXT at the top of this package for the full license terms.
10 package eu
.etaxonomy
.taxeditor
.store
;
12 import java
.util
.ArrayList
;
13 import java
.util
.LinkedHashMap
;
14 import java
.util
.List
;
16 import java
.util
.SortedSet
;
17 import java
.util
.UUID
;
19 import org
.apache
.log4j
.Logger
;
21 import eu
.etaxonomy
.cdm
.api
.application
.CdmApplicationController
;
22 import eu
.etaxonomy
.cdm
.api
.conversation
.ConversationHolder
;
23 import eu
.etaxonomy
.cdm
.api
.service
.ILocationService
;
24 import eu
.etaxonomy
.cdm
.api
.service
.INameService
;
25 import eu
.etaxonomy
.cdm
.api
.service
.IReferenceService
;
26 import eu
.etaxonomy
.cdm
.api
.service
.ITaxonService
;
27 import eu
.etaxonomy
.cdm
.api
.service
.ITermService
;
28 import eu
.etaxonomy
.cdm
.api
.service
.config
.ITaxonServiceConfigurator
;
29 import eu
.etaxonomy
.cdm
.api
.service
.config
.impl
.TaxonServiceConfiguratorImpl
;
30 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
31 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
32 import eu
.etaxonomy
.cdm
.hibernate
.HibernateProxyHelper
;
33 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
34 import eu
.etaxonomy
.cdm
.model
.common
.IdentifiableEntity
;
35 import eu
.etaxonomy
.cdm
.model
.common
.Language
;
36 import eu
.etaxonomy
.cdm
.model
.common
.OrderedTermVocabulary
;
37 import eu
.etaxonomy
.cdm
.model
.common
.TermVocabulary
;
38 import eu
.etaxonomy
.cdm
.model
.common
.VocabularyEnum
;
39 import eu
.etaxonomy
.cdm
.model
.description
.Feature
;
40 import eu
.etaxonomy
.cdm
.model
.name
.NameRelationshipType
;
41 import eu
.etaxonomy
.cdm
.model
.name
.NomenclaturalStatusType
;
42 import eu
.etaxonomy
.cdm
.model
.name
.Rank
;
43 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignationStatus
;
44 import eu
.etaxonomy
.cdm
.model
.name
.TaxonNameBase
;
45 import eu
.etaxonomy
.cdm
.model
.reference
.Article
;
46 import eu
.etaxonomy
.cdm
.model
.reference
.Book
;
47 import eu
.etaxonomy
.cdm
.model
.reference
.BookSection
;
48 import eu
.etaxonomy
.cdm
.model
.reference
.Generic
;
49 import eu
.etaxonomy
.cdm
.model
.reference
.ReferenceBase
;
50 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
51 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationshipType
;
52 import eu
.etaxonomy
.cdm
.persistence
.query
.MatchMode
;
53 import eu
.etaxonomy
.taxeditor
.datasource
.CdmDataSourceRepository
;
54 import eu
.etaxonomy
.taxeditor
.preference
.PreferencesUtil
;
57 * This implementation of ICdmDataRepository depends on hibernate sessions to store the data correctly
58 * for the current session. No state is held in this class.
60 * Only methods that either get or manipulate data are exposed here. So this class acts as a facade
61 * for the methods in cdmlib-service.
68 public class CdmStore
{
69 private static final Logger logger
= Logger
.getLogger(CdmStore
.class);
71 // FIXME change this to ClassPathResources as soon as it is included into the plugin
72 private static String DEFAULT_APPLICATION_CONTEXT
= null;
73 private static DbSchemaValidation DEFAULT_DB_SCHEMA_VALIDATION
= DbSchemaValidation
.UPDATE
;
75 private static CdmStore instance
;
77 private CdmApplicationController applicationController
;
79 private ConversationHolder globalReadOnlyConversation
;
81 private static DbSchemaValidation dbSchemaValidation
;
87 public static CdmStore
getDefault(){
88 return getDefault(DEFAULT_APPLICATION_CONTEXT
);
93 * @param applicationContextBean
96 public static CdmStore
getDefault(String applicationContextBean
){
98 logger
.info("Initializing application context ...");
99 ICdmDataSource cdmDatasource
= CdmDataSourceRepository
.getDefault().
100 getCurrentDataSource();
102 instance
= new CdmStore(cdmDatasource
, getDbSchemaValidation(), applicationContextBean
);
104 logger
.info("Application context initialized.");
112 private static DbSchemaValidation
getDbSchemaValidation() {
113 return (dbSchemaValidation
== null) ? DEFAULT_DB_SCHEMA_VALIDATION
: dbSchemaValidation
;
119 private CdmStore(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
, String applicationContextBean
) {
120 // TODO application context bean is not honored by application controller at the moment.
121 // cdmDefaultApplicationController bean gets loaded per default always.
124 CdmStore
.DEFAULT_APPLICATION_CONTEXT
= applicationContextBean
;
125 // applicationController = CdmApplicationController.NewInstance(applicationContextBean, dataSource, dbSchemaValidation, false);
127 // logger.warn("OMITTING TERM LOADING FOR DEBUGGING");
128 // applicationController = CdmApplicationController.NewInstance(dataSource, dbSchemaValidation, true);
129 applicationController
= CdmApplicationController
.NewInstance(dataSource
, dbSchemaValidation
);
130 } catch (Exception e
) {
131 throw new RuntimeException(e
);
135 public Set
<TaxonRelationshipType
> getConceptRelationshipTypes() {
136 Set
<TaxonRelationshipType
> conceptRelationshipTypes
= getTaxonRelationshipTypes().getTerms();
137 // remove these two relations as they are considered standard taxon relations
138 conceptRelationshipTypes
.remove(TaxonRelationshipType
.MISAPPLIED_NAME_FOR());
139 conceptRelationshipTypes
.remove(TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN());
141 return conceptRelationshipTypes
;
144 public ReferenceBase
<?
> getDefaultSec() {
145 // TODO why is this returning null? and of course, replace w the real deal
146 return applicationController
.getReferenceService().getReferenceByUuid(
147 UUID
.fromString("f3593c18-a8d2-4e51-bdad-0befbf8fb2d1"));
150 private TermVocabulary
<Feature
> getFeaturesInternal() {
151 return applicationController
.getTermService().getVocabulary(VocabularyEnum
.Feature
);
154 public static SortedSet
<Feature
> getFeatures() {
155 return getDefault().getFeaturesInternal().getTermsOrderedByLabels(getDefaultLanguage());
158 public SortedSet
<NameRelationshipType
> getNameRelationshipTypes() {
159 return applicationController
.getTermService().getVocabulary(VocabularyEnum
.NameRelationshipType
).getTermsOrderedByLabels(Language
.DEFAULT());
162 public TermVocabulary
<NomenclaturalStatusType
> getNomenclaturalStatusTypesInternal() {
163 return applicationController
.getTermService().getVocabulary(VocabularyEnum
.NomenclaturalStatusType
);
166 public static Set
<NomenclaturalStatusType
> getNomenclaturalStatusTypes(){
168 return getDefault().getNomenclaturalStatusTypesInternal().getTerms();
171 private OrderedTermVocabulary
<Rank
> getRanksInternal(){
172 TermVocabulary
<Rank
> vocabulary
= applicationController
.getTermService().getVocabulary(VocabularyEnum
.Rank
);
173 return HibernateProxyHelper
.deproxy(vocabulary
, OrderedTermVocabulary
.class);
176 public static SortedSet
<Rank
> getRanks(){
177 return getDefault().getRanksInternal().getOrderedTerms(null);
180 public List
<Taxon
> getRootTaxa() {
181 boolean onlyWithChildren
= false;
182 boolean withMisapplications
= true;
184 return applicationController
.getTaxonService().getRootTaxa(
185 getDefaultSec(), onlyWithChildren
, withMisapplications
);
188 public OrderedTermVocabulary
<TaxonRelationshipType
> getTaxonRelationshipTypes() {
189 TermVocabulary vocabulary
= HibernateProxyHelper
.deproxy
190 (applicationController
.getTermService().getVocabulary(VocabularyEnum
.TaxonRelationshipType
), TermVocabulary
.class);
191 return (OrderedTermVocabulary
<TaxonRelationshipType
>) vocabulary
;
194 public TermVocabulary
<SpecimenTypeDesignationStatus
> getSpecimenTypeDesignationStatus() {
195 return applicationController
.getTermService().getVocabulary(VocabularyEnum
.SpecimenTypeDesignationStatus
);
199 public UUID
saveTaxon(Taxon taxon
) {
200 return applicationController
.getTaxonService().save(taxon
);
203 public void setApplicationController(
204 CdmApplicationController applicationController
) {
205 this.applicationController
= applicationController
;
208 public CdmApplicationController
getApplicationController(){
209 return applicationController
;
214 * Create a new conversation and bind resources to it
218 public static ConversationHolder
NewConversation(){
220 CdmStore store
= getDefault();
221 CdmApplicationController controller
= store
.getApplicationController();
223 ConversationHolder conversation
= controller
.NewConversation();
229 * Creates a new conversation, binds resources to the conversation and
230 * start a transaction for this conversation.
234 public static ConversationHolder
NewTransactionalConversation() {
235 ConversationHolder conversation
= NewConversation();
237 conversation
.startTransaction();
242 private ConversationHolder
getGlobalReadOnlyConversation() {
243 ConversationHolder conversation
= globalReadOnlyConversation
== null
245 : globalReadOnlyConversation
;
250 public static ConversationHolder
getGlobalConversation(){
251 return getDefault().getGlobalReadOnlyConversation();
254 public static ITaxonService
getTaxonService(){
255 return getDefault().getApplicationController().getTaxonService();
258 public static INameService
getNameService(){
259 return getDefault().getApplicationController().getNameService();
262 public static IReferenceService
getReferenceService(){
263 return getDefault().getApplicationController().getReferenceService();
266 public static ILocationService
getLocationService(){
267 return getDefault().getApplicationController().getLocationService();
274 @SuppressWarnings("unchecked")
275 public static List
<TaxonNameBase
> searchNameString(String searchText
) {
276 List
<TaxonNameBase
> resultSet
= new ArrayList
<TaxonNameBase
>();
277 resultSet
.addAll(getNameService()
278 .getNamesByName(searchText
.replace("*", "%")));
282 private List
<IdentifiableEntity
> findTaxaByName(String queryString
, boolean restrictToTaxonObjs
) {
284 ITaxonServiceConfigurator configurator
= new TaxonServiceConfiguratorImpl();
286 configurator
.setSearchString(queryString
);
287 configurator
.setDoTaxa(true);
288 configurator
.setMatchMode(MatchMode
.BEGINNING
);
289 if (restrictToTaxonObjs
) {
290 configurator
.setDoNamesWithoutTaxa(false);
291 configurator
.setDoSynonyms(false);
293 configurator
.setDoNamesWithoutTaxa(true);
294 configurator
.setDoSynonyms(true);
296 configurator
.setReferenceBase(null);
297 configurator
.setPageNumber(0);
298 // TODO currently limit results to 1000
299 configurator
.setPageSize(1000);
301 List
<IdentifiableEntity
> result
= getTaxonService().findTaxaAndNames(configurator
).getRecords();
306 public static List
<IdentifiableEntity
> searchTaxaByName(String queryString
){
307 return getDefault().findTaxaByName(queryString
, false);
310 public static List
<IdentifiableEntity
> searchTaxaByName(String queryString
, boolean restrictToTaxonObjs
){
311 return getDefault().findTaxaByName(queryString
, restrictToTaxonObjs
);
315 * Searches for references by string. "%" is used as a wildcard.
320 public static List
<ReferenceBase
> getReferencesByTitle(String reference
) {
322 reference
= reference
.replace("*", "%");
323 List
<ReferenceBase
> resultsList
= null;
325 resultsList
= getReferenceService().getReferencesByTitle(reference
);
326 } catch (RuntimeException e
) {
327 // MessageDialog.openError(GlobalController.getShell(), "Search reference error",
328 // "Reference search returned an error. This could be a Hibernate concurrency problem. " +
329 // "Please try saving your work, then searching again.");
336 public static List
<Language
> getLanguages() {
337 ITermService termService
= getDefault().getApplicationController().getTermService();
338 ArrayList
<Language
> languages
= new ArrayList
<Language
>();
339 for (Language language
: termService
.getLanguageVocabulary()) {
340 languages
.add(language
);
343 // TODO sort languages
345 // languages.add(Language.ENGLISH());
346 // languages.add(Language.GERMAN());
355 public static Language
getDefaultLanguage(){
356 return Language
.ENGLISH();
362 private static String
getApplicationContextBean() {
363 return DEFAULT_APPLICATION_CONTEXT
;
369 public static LinkedHashMap
<Class
<?
>, String
> getReferenceTypes() {
370 LinkedHashMap
<Class
<?
>, String
> nomReferenceTypeMap
= new LinkedHashMap
<Class
<?
>, String
>();
372 // referenceTypeMap.put(BibtexReference.class, "BibTeX Reference");
373 nomReferenceTypeMap
.put(Article
.class, "Article");
374 nomReferenceTypeMap
.put(Generic
.class, "Generic");
375 nomReferenceTypeMap
.put(Book
.class, "Book");
376 nomReferenceTypeMap
.put(BookSection
.class, "Book Section");
378 return nomReferenceTypeMap
;