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
.cdm
.api
.application
;
12 import java
.util
.EnumSet
;
13 import java
.util
.List
;
14 import java
.util
.Properties
;
15 import java
.util
.UUID
;
17 import org
.apache
.log4j
.Logger
;
18 import org
.hibernate
.SessionFactory
;
19 import org
.springframework
.beans
.MutablePropertyValues
;
20 import org
.springframework
.beans
.factory
.config
.BeanDefinition
;
21 import org
.springframework
.beans
.factory
.xml
.XmlBeanDefinitionReader
;
22 import org
.springframework
.context
.ApplicationListener
;
23 import org
.springframework
.context
.support
.AbstractApplicationContext
;
24 import org
.springframework
.core
.io
.ClassPathResource
;
25 import org
.springframework
.core
.io
.Resource
;
26 import org
.springframework
.security
.authentication
.ProviderManager
;
27 import org
.springframework
.security
.authentication
.UsernamePasswordAuthenticationToken
;
28 import org
.springframework
.security
.core
.Authentication
;
29 import org
.springframework
.security
.core
.context
.SecurityContext
;
30 import org
.springframework
.security
.core
.context
.SecurityContextHolder
;
31 import org
.springframework
.transaction
.PlatformTransactionManager
;
32 import org
.springframework
.transaction
.TransactionStatus
;
34 import eu
.etaxonomy
.cdm
.api
.conversation
.ConversationHolder
;
35 import eu
.etaxonomy
.cdm
.api
.service
.IAgentService
;
36 import eu
.etaxonomy
.cdm
.api
.service
.IAnnotationService
;
37 import eu
.etaxonomy
.cdm
.api
.service
.IClassificationService
;
38 import eu
.etaxonomy
.cdm
.api
.service
.ICollectionService
;
39 import eu
.etaxonomy
.cdm
.api
.service
.ICommonService
;
40 import eu
.etaxonomy
.cdm
.api
.service
.IDatabaseService
;
41 import eu
.etaxonomy
.cdm
.api
.service
.IDescriptionService
;
42 import eu
.etaxonomy
.cdm
.api
.service
.IDescriptiveDataSetService
;
43 import eu
.etaxonomy
.cdm
.api
.service
.IEntityConstraintViolationService
;
44 import eu
.etaxonomy
.cdm
.api
.service
.IEntityValidationService
;
45 import eu
.etaxonomy
.cdm
.api
.service
.IEventBaseService
;
46 import eu
.etaxonomy
.cdm
.api
.service
.IFeatureNodeService
;
47 import eu
.etaxonomy
.cdm
.api
.service
.IFeatureTreeService
;
48 import eu
.etaxonomy
.cdm
.api
.service
.IGrantedAuthorityService
;
49 import eu
.etaxonomy
.cdm
.api
.service
.IGroupService
;
50 import eu
.etaxonomy
.cdm
.api
.service
.IIdentificationKeyService
;
51 import eu
.etaxonomy
.cdm
.api
.service
.ILocationService
;
52 import eu
.etaxonomy
.cdm
.api
.service
.IMediaService
;
53 import eu
.etaxonomy
.cdm
.api
.service
.IMetadataService
;
54 import eu
.etaxonomy
.cdm
.api
.service
.INameService
;
55 import eu
.etaxonomy
.cdm
.api
.service
.IOccurrenceService
;
56 import eu
.etaxonomy
.cdm
.api
.service
.IPolytomousKeyNodeService
;
57 import eu
.etaxonomy
.cdm
.api
.service
.IPolytomousKeyService
;
58 import eu
.etaxonomy
.cdm
.api
.service
.IPreferenceService
;
59 import eu
.etaxonomy
.cdm
.api
.service
.IProgressMonitorService
;
60 import eu
.etaxonomy
.cdm
.api
.service
.IReferenceService
;
61 import eu
.etaxonomy
.cdm
.api
.service
.IRegistrationService
;
62 import eu
.etaxonomy
.cdm
.api
.service
.IRightsService
;
63 import eu
.etaxonomy
.cdm
.api
.service
.ITaxonNodeService
;
64 import eu
.etaxonomy
.cdm
.api
.service
.ITaxonService
;
65 import eu
.etaxonomy
.cdm
.api
.service
.ITermService
;
66 import eu
.etaxonomy
.cdm
.api
.service
.IUserService
;
67 import eu
.etaxonomy
.cdm
.api
.service
.IVocabularyService
;
68 import eu
.etaxonomy
.cdm
.api
.service
.molecular
.IAmplificationService
;
69 import eu
.etaxonomy
.cdm
.api
.service
.molecular
.IPrimerService
;
70 import eu
.etaxonomy
.cdm
.api
.service
.molecular
.ISequenceService
;
71 import eu
.etaxonomy
.cdm
.common
.monitor
.IProgressMonitor
;
72 import eu
.etaxonomy
.cdm
.common
.monitor
.NullProgressMonitor
;
73 import eu
.etaxonomy
.cdm
.common
.monitor
.SubProgressMonitor
;
74 import eu
.etaxonomy
.cdm
.database
.CdmPersistentDataSource
;
75 import eu
.etaxonomy
.cdm
.database
.DataSourceNotFoundException
;
76 import eu
.etaxonomy
.cdm
.database
.DbSchemaValidation
;
77 import eu
.etaxonomy
.cdm
.database
.ICdmDataSource
;
78 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
79 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTermBase
;
80 import eu
.etaxonomy
.cdm
.persistence
.hibernate
.HibernateConfiguration
;
81 import eu
.etaxonomy
.cdm
.persistence
.hibernate
.permission
.CRUD
;
82 import eu
.etaxonomy
.cdm
.persistence
.hibernate
.permission
.ICdmPermissionEvaluator
;
87 public class CdmApplicationController
implements ICdmRepository
{
88 private static final Logger logger
= Logger
.getLogger(CdmApplicationController
.class);
90 public static final String DEFAULT_APPLICATION_CONTEXT_RESOURCE
= "/eu/etaxonomy/cdm/defaultApplicationContext.xml";
92 public AbstractApplicationContext applicationContext
;
93 protected ICdmRepository configuration
;
94 private final Resource applicationContextResource
;
96 private final IProgressMonitor progressMonitor
;
98 final protected static DbSchemaValidation defaultDbSchemaValidation
= DbSchemaValidation
.VALIDATE
;
102 * Constructor, opens a spring ApplicationContext by using the default data source
104 * @throws DataSourceNotFoundException
106 public static CdmApplicationController
NewInstance() throws DataSourceNotFoundException
{
107 logger
.info("Start CdmApplicationController with default data source");
108 CdmPersistentDataSource dataSource
= getDefaultDatasource();
109 DbSchemaValidation dbSchemaValidation
= defaultDbSchemaValidation
;
110 return CdmApplicationController
.NewInstance(null, dataSource
, dbSchemaValidation
, false);
115 * Constructor, opens a spring ApplicationContext by using the default data source
117 * @param dbSchemaValidation
118 * validation type for database schema
119 * @throws DataSourceNotFoundException
121 public static CdmApplicationController
NewInstance(DbSchemaValidation dbSchemaValidation
) throws DataSourceNotFoundException
{
122 logger
.info("Start CdmApplicationController with default data source");
123 CdmPersistentDataSource dataSource
= getDefaultDatasource();
124 return CdmApplicationController
.NewInstance(null, dataSource
, dbSchemaValidation
, false);
129 * Constructor, opens an spring ApplicationContext by using the according data source
130 * and the default database schema validation type
134 public static CdmApplicationController
NewInstance(ICdmDataSource dataSource
){
135 return CdmApplicationController
.NewInstance(null, dataSource
, defaultDbSchemaValidation
, false);
139 public static CdmApplicationController
NewInstance(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
){
140 return CdmApplicationController
.NewInstance(null, dataSource
, dbSchemaValidation
, false);
144 public static CdmApplicationController
NewInstance(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
, boolean omitTermLoading
){
145 return CdmApplicationController
.NewInstance(null, dataSource
, dbSchemaValidation
, omitTermLoading
);
148 public static CdmApplicationController
NewInstance(Resource applicationContextResource
, ICdmDataSource dataSource
,
149 DbSchemaValidation dbSchemaValidation
, boolean omitTermLoading
){
150 return CdmApplicationController
.NewInstance(applicationContextResource
, dataSource
, dbSchemaValidation
,
151 null, omitTermLoading
, null);
153 public static CdmApplicationController
NewInstance(Resource applicationContextResource
, ICdmDataSource dataSource
,
154 DbSchemaValidation dbSchemaValidation
, boolean omitTermLoading
, IProgressMonitor progressMonitor
){
155 return new CdmApplicationController(applicationContextResource
, dataSource
, dbSchemaValidation
,
156 null, omitTermLoading
, progressMonitor
, null);
158 public static CdmApplicationController
NewInstance(Resource applicationContextResource
, ICdmDataSource dataSource
,
159 DbSchemaValidation dbSchemaValidation
, HibernateConfiguration hibernateConfig
,
160 boolean omitTermLoading
, IProgressMonitor progressMonitor
){
161 return new CdmApplicationController(applicationContextResource
, dataSource
, dbSchemaValidation
,
162 hibernateConfig
, omitTermLoading
, progressMonitor
, null);
166 //TODO discuss need for listeners before commit to trunk
167 // public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading, IProgressMonitor progressMonitor, List<ApplicationListener> listeners) {
168 // return new CdmApplicationController(applicationContextResource, dataSource, dbSchemaValidation, omitTermLoading, progressMonitor,listeners);
174 protected static ClassPathResource
getClasspathResource(){
175 return new ClassPathResource(DEFAULT_APPLICATION_CONTEXT_RESOURCE
);
181 * @throws DataSourceNotFoundException
183 protected static CdmPersistentDataSource
getDefaultDatasource() throws DataSourceNotFoundException
{
184 CdmPersistentDataSource dataSource
= CdmPersistentDataSource
.NewDefaultInstance();
191 * FIXME:Remoting this constructor is added only to allow extension of this cntroller
192 * class. and should be removed after refactoring
194 protected CdmApplicationController(){
195 applicationContextResource
= null;
196 progressMonitor
= null;
201 * Constructor, opens an spring 2.5 ApplicationContext by using the according data
205 * @param dbSchemaValidation
206 * @param omitTermLoading
208 protected CdmApplicationController(Resource applicationContextResource
, ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
,
209 HibernateConfiguration hibernateConfig
,
210 boolean omitTermLoading
, IProgressMonitor progressMonitor
, List
<ApplicationListener
> listeners
){
211 logger
.info("Start CdmApplicationController with datasource: " + dataSource
.getName());
213 if (dbSchemaValidation
== null) {
214 dbSchemaValidation
= defaultDbSchemaValidation
;
216 this.applicationContextResource
= applicationContextResource
!= null ? applicationContextResource
: getClasspathResource();
217 this.progressMonitor
= progressMonitor
!= null ? progressMonitor
: new NullProgressMonitor();
219 setNewDataSource(dataSource
, dbSchemaValidation
, hibernateConfig
, omitTermLoading
, listeners
);
224 * Sets the application context to a new spring ApplicationContext by using the
225 * according data source and initializes the Controller.
229 private boolean setNewDataSource(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
,
230 HibernateConfiguration hibernateConfig
,
231 boolean omitTermLoading
, List
<ApplicationListener
> listeners
){
233 if (dbSchemaValidation
== null) {
234 dbSchemaValidation
= defaultDbSchemaValidation
;
236 logger
.info("Connecting to '" + dataSource
.getName() + "'");
238 MonitoredGenericApplicationContext applicationContext
= new MonitoredGenericApplicationContext();
239 int refreshTasks
= 45;
240 int nTasks
= 5 + refreshTasks
;
241 // nTasks += applicationContext.countTasks();
242 progressMonitor
.beginTask("Connecting to '" + dataSource
.getName() + "'", nTasks
);
244 // progressMonitor.worked(1);
246 BeanDefinition datasourceBean
= dataSource
.getDatasourceBean();
247 datasourceBean
.setAttribute("isLazy", false);
248 progressMonitor
.subTask("Registering datasource.");
249 applicationContext
.registerBeanDefinition("dataSource", datasourceBean
);
250 progressMonitor
.worked(1);
252 BeanDefinition hibernatePropBean
= dataSource
.getHibernatePropertiesBean(dbSchemaValidation
, hibernateConfig
);
253 applicationContext
.registerBeanDefinition("hibernateProperties", hibernatePropBean
);
255 XmlBeanDefinitionReader xmlReader
= new XmlBeanDefinitionReader(applicationContext
);
256 progressMonitor
.subTask("Registering resources.");
257 xmlReader
.loadBeanDefinitions(applicationContextResource
);
258 progressMonitor
.worked(1);
261 if (omitTermLoading
== true) {
262 String initializerName
= "persistentTermInitializer";
263 BeanDefinition beanDef
= applicationContext
.getBeanDefinition(initializerName
);
264 MutablePropertyValues values
= beanDef
.getPropertyValues();
265 values
.addPropertyValue("omit", omitTermLoading
);
268 if (listeners
!= null) {
269 for (ApplicationListener
<?
> listener
: listeners
) {
270 applicationContext
.addApplicationListener(listener
);
274 // String message = "Start application context. This might take a while ...";
275 //// progressMonitor.subTask(message);
276 // SubProgressMonitor subMonitor= new SubProgressMonitor(progressMonitor, 10);
277 // subMonitor.beginTask(message, 2);
278 // applicationContext.setProgressMonitor(subMonitor);
280 applicationContext
.refresh(new SubProgressMonitor(progressMonitor
, refreshTasks
));
281 applicationContext
.start();
282 // progressMonitor.worked(1);
284 progressMonitor
.subTask("Cleaning up.");
285 setApplicationContext(applicationContext
);
286 progressMonitor
.worked(1);
288 progressMonitor
.done();
293 * Overrides all default with values in hibernate config, if defined
294 * @param hibernatePropBean
295 * @param hibernateConfig
297 private void registerHibernateConfig(BeanDefinition hibernatePropBean
, HibernateConfiguration hibernateConfig
) {
298 setHibernateProperty(hibernatePropBean
, HibernateConfiguration
.REGISTER_ENVERS
,
299 hibernateConfig
.getRegisterEnvers());
300 setHibernateProperty(hibernatePropBean
, HibernateConfiguration
.REGISTER_SEARCH
,
301 hibernateConfig
.getRegisterSearch());
302 setHibernateProperty(hibernatePropBean
, HibernateConfiguration
.SHOW_SQL
,
303 hibernateConfig
.getShowSql());
304 setHibernateProperty(hibernatePropBean
, HibernateConfiguration
.FORMAT_SQL
,
305 hibernateConfig
.getFormatSql());
309 private void setHibernateProperty(BeanDefinition hibernatePropBean
, String key
, Boolean value
) {
311 setHibernateProperty(hibernatePropBean
, key
, String
.valueOf(value
));
314 private void setHibernateProperty(BeanDefinition hibernatePropBean
, String key
, String value
) {
316 Properties props
= (Properties
)hibernatePropBean
.getPropertyValues().get("properties");
317 props
.setProperty(key
, value
);
323 * Tests if some DefinedTermsAreMissing.
325 * @return true, if at least one is missing, else false
327 public boolean testDefinedTermsAreMissing(){
328 UUID englishUuid
= UUID
.fromString("e9f8cdb7-6819-44e8-95d3-e2d0690c3523");
329 DefinedTermBase
<?
> english
= this.getTermService().load(englishUuid
);
330 if (english
== null || !english
.getUuid().equals(englishUuid
)) {
340 * Changes the ApplicationContext to the new dataSource
344 public boolean changeDataSource(ICdmDataSource dataSource
){
345 //logger.info("Change datasource to : " + dataSource);
346 return setNewDataSource(dataSource
, DbSchemaValidation
.VALIDATE
, null, false, null);
351 * Changes the ApplicationContext to the new dataSource
354 * @param dbSchemaValidation
356 public boolean changeDataSource(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
){
357 //logger.info("Change datasource to : " + dataSource);
358 return setNewDataSource(dataSource
, dbSchemaValidation
, null, false, null);
363 * Changes the ApplicationContext to the new dataSource
366 * @param dbSchemaValidation
367 * @param omitTermLoading
369 public boolean changeDataSource(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
, boolean omitTermLoading
){
370 logger
.info("Change datasource to : " + dataSource
);
371 return setNewDataSource(dataSource
, dbSchemaValidation
, null, omitTermLoading
, null);
376 * Changes the ApplicationContext to the new dataSource
379 * @param dbSchemaValidation
380 * @param omitTermLoading
382 public boolean changeDataSource(ICdmDataSource dataSource
, DbSchemaValidation dbSchemaValidation
, boolean omitTermLoading
,
383 List
<ApplicationListener
> listeners
){
384 logger
.info("Change datasource to : " + dataSource
);
385 return setNewDataSource(dataSource
, dbSchemaValidation
, null, omitTermLoading
, listeners
);
390 * Sets a new application Context.
394 public void setApplicationContext(AbstractApplicationContext ac
){
395 closeApplicationContext(); //closes old application context if necessary
396 applicationContext
= ac
;
397 applicationContext
.registerShutdownHook();
402 public void finalize(){
407 * closes the application
410 closeApplicationContext();
415 * closes the application context
417 protected void closeApplicationContext(){
418 if (applicationContext
!= null) {
419 logger
.info("Close ApplicationContext");
420 applicationContext
.close();
425 protected void init(){
426 logger
.debug("Init " + this.getClass().getName() + " ... ");
427 if (logger
.isDebugEnabled()) {
428 for (String beanName
: applicationContext
.getBeanDefinitionNames()) {
429 logger
.debug(beanName
);
432 //TODO delete next row (was just for testing)
433 if (logger
.isInfoEnabled()) {
434 logger
.info("Registered Beans: ");
435 String
[] beanNames
= applicationContext
.getBeanDefinitionNames();
436 for (String beanName
: beanNames
) {
437 logger
.info(beanName
);
440 configuration
= (ICdmRepository
) applicationContext
.getBean("cdmRepository");
442 //FIXME:Remoting catching exection to allow for remoting
443 getDatabaseService().setApplicationController(this);
445 catch (UnsupportedOperationException uoe
) {
446 logger
.warn("getDatabaseService() is not implmented for current application context");
451 /* ****** Services ******** */
453 public final IAnnotationService
getAnnotationService(){
454 return configuration
.getAnnotationService();
458 public final INameService
getNameService(){
459 return configuration
.getNameService();
464 public final ITaxonService
getTaxonService(){
465 return configuration
.getTaxonService();
470 public final IClassificationService
getClassificationService(){
471 return configuration
.getClassificationService();
476 public final ITaxonNodeService
getTaxonNodeService(){
478 return configuration
.getTaxonNodeService();
479 } catch (Exception e
){
487 public final IReferenceService
getReferenceService(){
488 return configuration
.getReferenceService();
493 public final IAgentService
getAgentService(){
494 return configuration
.getAgentService();
499 public final IDatabaseService
getDatabaseService(){
500 return configuration
.getDatabaseService();
505 public final ITermService
getTermService(){
506 return configuration
.getTermService();
511 public final IDescriptionService
getDescriptionService(){
512 return configuration
.getDescriptionService();
517 public final IOccurrenceService
getOccurrenceService(){
518 return configuration
.getOccurrenceService();
522 public IAmplificationService
getAmplificationService(){
523 return configuration
.getAmplificationService();
527 public ISequenceService
getSequenceService(){
528 return configuration
.getSequenceService();
532 public IEventBaseService
getEventBaseService() {
533 return configuration
.getEventBaseService();
539 public final IPrimerService
getPrimerService(){
540 return configuration
.getPrimerService();
545 public final IMediaService
getMediaService(){
546 return configuration
.getMediaService();
551 public final IMetadataService
getMetadataService(){
552 return configuration
.getMetadataService();
557 public final ICommonService
getCommonService(){
558 return configuration
.getCommonService();
563 public final ILocationService
getLocationService(){
564 return configuration
.getLocationService();
569 public final IUserService
getUserService(){
570 return configuration
.getUserService();
575 public final IGrantedAuthorityService
getGrantedAuthorityService(){
576 return configuration
.getGrantedAuthorityService();
581 public IGroupService
getGroupService(){
582 return configuration
.getGroupService();
587 public final ICollectionService
getCollectionService(){
588 return configuration
.getCollectionService();
593 public final IFeatureTreeService
getFeatureTreeService(){
594 return configuration
.getFeatureTreeService();
598 public final IPreferenceService
getPreferenceService(){
599 return configuration
.getPreferenceService();
604 public final IFeatureNodeService
getFeatureNodeService(){
605 return configuration
.getFeatureNodeService();
610 public final IVocabularyService
getVocabularyService(){
611 return configuration
.getVocabularyService();
616 public final IIdentificationKeyService
getIdentificationKeyService(){
617 return configuration
.getIdentificationKeyService();
622 public final IPolytomousKeyService
getPolytomousKeyService(){
623 return configuration
.getPolytomousKeyService();
628 public final IPolytomousKeyNodeService
getPolytomousKeyNodeService(){
629 return configuration
.getPolytomousKeyNodeService();
637 public IProgressMonitorService
getProgressMonitorService() {
638 return configuration
.getProgressMonitorService();
643 public IEntityValidationService
getEntityValidationService(){
644 return configuration
.getEntityValidationService();
649 public IEntityConstraintViolationService
getEntityConstraintViolationService(){
650 return configuration
.getEntityConstraintViolationService();
654 public final IDescriptiveDataSetService
getDescriptiveDataSetService(){
655 return configuration
.getDescriptiveDataSetService();
660 public final ConversationHolder
NewConversation(){
661 //return (ConversationHolder)applicationContext.getBean("conversationHolder");
662 return configuration
.NewConversation();
666 /* **** Security ***** */
669 public void authenticate(String username
, String password
){
670 UsernamePasswordAuthenticationToken tokenForUser
= new UsernamePasswordAuthenticationToken(username
, password
);
671 Authentication authentication
= this.getAuthenticationManager().authenticate(tokenForUser
);
672 SecurityContext context
= SecurityContextHolder
.getContext();
673 context
.setAuthentication(authentication
);
677 public final ProviderManager
getAuthenticationManager(){
678 return configuration
.getAuthenticationManager();
683 public ICdmPermissionEvaluator
getPermissionEvaluator(){
684 return configuration
.getPermissionEvaluator();
688 * @see org.springframework.security.access.PermissionEvaluator#hasPermission(org.springframework.security.core.Authentication,
689 * java.lang.Object, java.lang.Object)
691 * @param targetDomainObject
695 public boolean currentAuthentiationHasPermissions(CdmBase targetDomainObject
, EnumSet
<CRUD
> permission
){
696 SecurityContext context
= SecurityContextHolder
.getContext();
697 return getPermissionEvaluator().hasPermission(context
.getAuthentication(), targetDomainObject
, permission
);
702 public final PlatformTransactionManager
getTransactionManager(){
703 return configuration
.getTransactionManager();
708 public final Object
getBean(String name
){
709 return this.applicationContext
.getBean(name
);
714 * OLD TRANSACTION STUFF
717 /* **** flush ********** */
719 SessionFactory sf
= (SessionFactory
) applicationContext
.getBean("sessionFactory");
720 sf
.getCurrentSession().flush();
724 public SessionFactory
getSessionFactory(){
725 return (SessionFactory
) applicationContext
.getBean("sessionFactory");
730 public TransactionStatus
startTransaction(){
731 return startTransaction(false);
736 public TransactionStatus
startTransaction(Boolean readOnly
){
737 return configuration
.startTransaction(readOnly
);
741 public void commitTransaction(TransactionStatus txStatus
){
742 PlatformTransactionManager txManager
= configuration
.getTransactionManager();
743 txManager
.commit(txStatus
);
752 public IRightsService
getRightsService() {
753 return configuration
.getRightsService();
761 public IRegistrationService
getRegistrationService() {
762 return configuration
.getRegistrationService();