Revision 070d8fe4
Added by Niels Hoffmann over 13 years ago
| .gitattributes | ||
|---|---|---|
| 3419 | 3419 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationController.java -text |
| 3420 | 3420 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationDefaultConfiguration.java -text |
| 3421 | 3421 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/ICdmApplicationConfiguration.java -text |
| 3422 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveFileSystemXmlApplicationContext.java -text |
|
| 3423 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveGenericApplicationContext.java -text |
|
| 3424 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSavePathMatchingResourcePatternResolver.java -text |
|
| 3425 | 3422 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/ConversationHolder.java -text |
| 3426 | 3423 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/conversation/IConversationEnabled.java -text |
| 3427 | 3424 |
cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/facade/DerivedUnitFacade.java -text |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationController.java | ||
|---|---|---|
| 16 | 16 |
|
| 17 | 17 |
import org.apache.log4j.Logger; |
| 18 | 18 |
import org.hibernate.SessionFactory; |
| 19 |
import org.springframework.beans.MutablePropertyValues; |
|
| 20 | 19 |
import org.springframework.beans.factory.config.BeanDefinition; |
| 21 | 20 |
import org.springframework.beans.factory.xml.XmlBeanDefinitionReader; |
| 22 | 21 |
import org.springframework.context.support.AbstractApplicationContext; |
| ... | ... | |
| 29 | 28 |
import org.springframework.transaction.TransactionStatus; |
| 30 | 29 |
import org.springframework.transaction.support.DefaultTransactionDefinition; |
| 31 | 30 |
|
| 32 |
import eu.etaxonomy.cdm.api.application.eclipse.EclipseRcpSaveGenericApplicationContext; |
|
| 33 | 31 |
import eu.etaxonomy.cdm.api.conversation.ConversationHolder; |
| 34 | 32 |
import eu.etaxonomy.cdm.api.service.IAgentService; |
| 35 | 33 |
import eu.etaxonomy.cdm.api.service.ICollectionService; |
| ... | ... | |
| 53 | 51 |
import eu.etaxonomy.cdm.common.IProgressMonitor; |
| 54 | 52 |
import eu.etaxonomy.cdm.common.NullProgressMonitor; |
| 55 | 53 |
import eu.etaxonomy.cdm.database.CdmPersistentDataSource; |
| 56 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
|
| 57 | 54 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 58 | 55 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 59 | 56 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
| 60 | 57 |
import eu.etaxonomy.cdm.model.common.CdmMetaData; |
| 61 | 58 |
import eu.etaxonomy.cdm.model.common.DefinedTermBase; |
| 62 | 59 |
import eu.etaxonomy.cdm.model.common.User; |
| 63 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 64 | 60 |
|
| 65 | 61 |
|
| 66 | 62 |
/** |
| ... | ... | |
| 83 | 79 |
|
| 84 | 80 |
|
| 85 | 81 |
/** |
| 86 |
* Constructor, opens an spring 2.5 ApplicationContext by using the default data source
|
|
| 82 |
* Constructor, opens a spring ApplicationContext by using the default data source
|
|
| 87 | 83 |
*/ |
| 88 |
public static CdmApplicationController NewInstance() throws DataSourceNotFoundException, TermNotFoundException {
|
|
| 84 |
public static CdmApplicationController NewInstance() {
|
|
| 89 | 85 |
logger.info("Start CdmApplicationController with default data source");
|
| 90 | 86 |
CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance(); |
| 91 | 87 |
DbSchemaValidation dbSchemaValidation = defaultDbSchemaValidation; |
| ... | ... | |
| 93 | 89 |
} |
| 94 | 90 |
|
| 95 | 91 |
/** |
| 96 |
* Constructor, opens an spring 2.5 ApplicationContext by using the default data source
|
|
| 92 |
* Constructor, opens a spring ApplicationContext by using the default data source
|
|
| 97 | 93 |
* @param dbSchemaValidation validation type for database schema |
| 98 | 94 |
*/ |
| 99 |
public static CdmApplicationController NewInstance(DbSchemaValidation dbSchemaValidation) throws DataSourceNotFoundException, TermNotFoundException {
|
|
| 95 |
public static CdmApplicationController NewInstance(DbSchemaValidation dbSchemaValidation) {
|
|
| 100 | 96 |
logger.info("Start CdmApplicationController with default data source");
|
| 101 | 97 |
CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance(); |
| 102 | 98 |
return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, false); |
| ... | ... | |
| 104 | 100 |
|
| 105 | 101 |
|
| 106 | 102 |
/** |
| 107 |
* Constructor, opens an spring 2.5 ApplicationContext by using the according data source and the
|
|
| 103 |
* Constructor, opens an spring ApplicationContext by using the according data source and the |
|
| 108 | 104 |
* default database schema validation type |
| 109 | 105 |
* @param dataSource |
| 110 | 106 |
*/ |
| 111 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource) |
|
| 112 |
throws DataSourceNotFoundException, TermNotFoundException{
|
|
| 107 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource) {
|
|
| 113 | 108 |
return CdmApplicationController.NewInstance(null, dataSource, defaultDbSchemaValidation, false); |
| 114 | 109 |
} |
| 115 | 110 |
|
| 116 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation) |
|
| 117 |
throws DataSourceNotFoundException, TermNotFoundException{
|
|
| 111 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation) {
|
|
| 118 | 112 |
return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, false); |
| 119 | 113 |
} |
| 120 | 114 |
|
| 121 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) |
|
| 122 |
throws DataSourceNotFoundException, TermNotFoundException{
|
|
| 115 |
public static CdmApplicationController NewInstance(ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {
|
|
| 123 | 116 |
return CdmApplicationController.NewInstance(null, dataSource, dbSchemaValidation, omitTermLoading); |
| 124 | 117 |
} |
| 125 | 118 |
|
| 126 |
public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) |
|
| 127 |
throws DataSourceNotFoundException, TermNotFoundException{
|
|
| 119 |
public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading) {
|
|
| 128 | 120 |
return CdmApplicationController.NewInstance(applicationContextResource, dataSource, dbSchemaValidation, omitTermLoading, null); |
| 129 | 121 |
} |
| 130 | 122 |
|
| 131 |
public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading, IProgressMonitor progressMonitor) |
|
| 132 |
throws DataSourceNotFoundException, TermNotFoundException{
|
|
| 133 |
|
|
| 134 |
|
|
| 123 |
public static CdmApplicationController NewInstance(Resource applicationContextResource, ICdmDataSource dataSource, DbSchemaValidation dbSchemaValidation, boolean omitTermLoading, IProgressMonitor progressMonitor) {
|
|
| 135 | 124 |
return new CdmApplicationController(applicationContextResource, dataSource, dbSchemaValidation, omitTermLoading, progressMonitor); |
| 136 | 125 |
} |
| 137 | 126 |
|
| ... | ... | |
| 164 | 153 |
dbSchemaValidation = defaultDbSchemaValidation; |
| 165 | 154 |
} |
| 166 | 155 |
logger.info("Connecting to '" + dataSource.getName() + "'");
|
| 167 |
progressMonitor.subTask("Connecting to '" + dataSource.getName() + "'");
|
|
| 156 |
progressMonitor.beginTask("Connecting to '" + dataSource.getName() + "'", 6);
|
|
| 168 | 157 |
progressMonitor.worked(1); |
| 169 | 158 |
|
| 170 |
GenericApplicationContext appContext; |
|
| 171 |
appContext = new EclipseRcpSaveGenericApplicationContext(); |
|
| 159 |
GenericApplicationContext applicationContext = new GenericApplicationContext(); |
|
| 172 | 160 |
|
| 173 | 161 |
BeanDefinition datasourceBean = dataSource.getDatasourceBean(); |
| 174 | 162 |
datasourceBean.setAttribute("isLazy", false);
|
| 175 | 163 |
progressMonitor.subTask("Registering datasource.");
|
| 176 | 164 |
progressMonitor.worked(1); |
| 177 |
appContext.registerBeanDefinition("dataSource", datasourceBean);
|
|
| 165 |
applicationContext.registerBeanDefinition("dataSource", datasourceBean);
|
|
| 178 | 166 |
|
| 179 | 167 |
BeanDefinition hibernatePropBean= dataSource.getHibernatePropertiesBean(dbSchemaValidation); |
| 180 |
appContext.registerBeanDefinition("hibernateProperties", hibernatePropBean);
|
|
| 168 |
applicationContext.registerBeanDefinition("hibernateProperties", hibernatePropBean);
|
|
| 181 | 169 |
|
| 182 |
XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(appContext); |
|
| 183 |
progressMonitor.subTask("Registering context resources.");
|
|
| 170 |
XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(applicationContext);
|
|
| 171 |
progressMonitor.subTask("Registering resources.");
|
|
| 184 | 172 |
progressMonitor.worked(1); |
| 185 |
xmlReader.loadBeanDefinitions(this.applicationContextResource);
|
|
| 173 |
xmlReader.loadBeanDefinitions(applicationContextResource); |
|
| 186 | 174 |
|
| 187 | 175 |
//omitTerms |
| 188 |
String initializerName = "persistentTermInitializer"; |
|
| 189 |
BeanDefinition beanDef = appContext.getBeanDefinition(initializerName); |
|
| 176 |
/*String initializerName = "persistentTermInitializer";
|
|
| 177 |
BeanDefinition beanDef = applicationContext.getBeanDefinition(initializerName);
|
|
| 190 | 178 |
MutablePropertyValues values = beanDef.getPropertyValues(); |
| 191 |
values.addPropertyValue("omit", omitTermLoading);
|
|
| 179 |
values.addPropertyValue("omit", omitTermLoading);*/
|
|
| 192 | 180 |
|
| 193 |
progressMonitor.subTask("Starting context. This might take a while...");
|
|
| 181 |
progressMonitor.subTask("Connecting. This might take a while ...");
|
|
| 194 | 182 |
progressMonitor.worked(1); |
| 195 |
appContext.refresh(); |
|
| 196 |
appContext.start(); |
|
| 183 |
applicationContext.refresh();
|
|
| 184 |
applicationContext.start();
|
|
| 197 | 185 |
|
| 198 |
progressMonitor.subTask("Setting application context.");
|
|
| 186 |
progressMonitor.subTask("Cleaning up.");
|
|
| 199 | 187 |
progressMonitor.worked(1); |
| 200 |
setApplicationContext(appContext); |
|
| 188 |
setApplicationContext(applicationContext);
|
|
| 201 | 189 |
|
| 202 | 190 |
//initialize user and metaData for new databases |
| 203 | 191 |
int userCount = getUserService().count(User.class); |
| ... | ... | |
| 212 | 200 |
progressMonitor.worked(1); |
| 213 | 201 |
createMetadata(); |
| 214 | 202 |
} |
| 215 |
|
|
| 203 |
progressMonitor.done(); |
|
| 216 | 204 |
return true; |
| 217 | 205 |
} |
| 218 | 206 |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveFileSystemXmlApplicationContext.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2007 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
|
|
| 11 |
package eu.etaxonomy.cdm.api.application.eclipse; |
|
| 12 |
|
|
| 13 |
import org.springframework.beans.BeansException; |
|
| 14 |
import org.springframework.context.ApplicationContext; |
|
| 15 |
import org.springframework.context.support.FileSystemXmlApplicationContext; |
|
| 16 |
import org.springframework.core.io.support.ResourcePatternResolver; |
|
| 17 |
|
|
| 18 |
public class EclipseRcpSaveFileSystemXmlApplicationContext extends |
|
| 19 |
FileSystemXmlApplicationContext {
|
|
| 20 |
|
|
| 21 |
|
|
| 22 |
@Override |
|
| 23 |
protected ResourcePatternResolver getResourcePatternResolver() {
|
|
| 24 |
return new EclipseRcpSavePathMatchingResourcePatternResolver(this); |
|
| 25 |
} |
|
| 26 |
|
|
| 27 |
/* all constructors */ |
|
| 28 |
public EclipseRcpSaveFileSystemXmlApplicationContext(String configLocation) |
|
| 29 |
throws BeansException {
|
|
| 30 |
super(configLocation); |
|
| 31 |
} |
|
| 32 |
|
|
| 33 |
public EclipseRcpSaveFileSystemXmlApplicationContext(String[] configLocations, |
|
| 34 |
ApplicationContext parent) throws BeansException {
|
|
| 35 |
super(configLocations, parent); |
|
| 36 |
} |
|
| 37 |
|
|
| 38 |
public EclipseRcpSaveFileSystemXmlApplicationContext(String[] configLocations, |
|
| 39 |
boolean refresh, ApplicationContext parent) throws BeansException {
|
|
| 40 |
super(configLocations, refresh, parent); |
|
| 41 |
} |
|
| 42 |
|
|
| 43 |
public EclipseRcpSaveFileSystemXmlApplicationContext(String[] configLocations, |
|
| 44 |
boolean refresh) throws BeansException {
|
|
| 45 |
super(configLocations, refresh); |
|
| 46 |
} |
|
| 47 |
|
|
| 48 |
public EclipseRcpSaveFileSystemXmlApplicationContext(String[] configLocations) |
|
| 49 |
throws BeansException {
|
|
| 50 |
super(configLocations); |
|
| 51 |
} |
|
| 52 |
|
|
| 53 |
|
|
| 54 |
} |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveGenericApplicationContext.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2007 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
|
|
| 11 |
package eu.etaxonomy.cdm.api.application.eclipse; |
|
| 12 |
|
|
| 13 |
import org.springframework.beans.factory.support.DefaultListableBeanFactory; |
|
| 14 |
import org.springframework.context.ApplicationContext; |
|
| 15 |
import org.springframework.context.support.GenericApplicationContext; |
|
| 16 |
import org.springframework.core.io.support.ResourcePatternResolver; |
|
| 17 |
|
|
| 18 |
/** |
|
| 19 |
* @author a.mueller |
|
| 20 |
* |
|
| 21 |
*/ |
|
| 22 |
public class EclipseRcpSaveGenericApplicationContext extends |
|
| 23 |
GenericApplicationContext {
|
|
| 24 |
|
|
| 25 |
@Override |
|
| 26 |
protected ResourcePatternResolver getResourcePatternResolver() {
|
|
| 27 |
return new EclipseRcpSavePathMatchingResourcePatternResolver(this); |
|
| 28 |
} |
|
| 29 |
|
|
| 30 |
/** |
|
| 31 |
* |
|
| 32 |
*/ |
|
| 33 |
public EclipseRcpSaveGenericApplicationContext() {
|
|
| 34 |
} |
|
| 35 |
|
|
| 36 |
/** |
|
| 37 |
* @param beanFactory |
|
| 38 |
*/ |
|
| 39 |
public EclipseRcpSaveGenericApplicationContext( |
|
| 40 |
DefaultListableBeanFactory beanFactory) {
|
|
| 41 |
super(beanFactory); |
|
| 42 |
} |
|
| 43 |
|
|
| 44 |
/** |
|
| 45 |
* @param parent |
|
| 46 |
*/ |
|
| 47 |
public EclipseRcpSaveGenericApplicationContext(ApplicationContext parent) {
|
|
| 48 |
super(parent); |
|
| 49 |
} |
|
| 50 |
|
|
| 51 |
/** |
|
| 52 |
* @param beanFactory |
|
| 53 |
* @param parent |
|
| 54 |
*/ |
|
| 55 |
public EclipseRcpSaveGenericApplicationContext( |
|
| 56 |
DefaultListableBeanFactory beanFactory, ApplicationContext parent) {
|
|
| 57 |
super(beanFactory, parent); |
|
| 58 |
} |
|
| 59 |
|
|
| 60 |
} |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSavePathMatchingResourcePatternResolver.java | ||
|---|---|---|
| 1 |
// $Id$ |
|
| 2 |
/** |
|
| 3 |
* Copyright (C) 2007 EDIT |
|
| 4 |
* European Distributed Institute of Taxonomy |
|
| 5 |
* http://www.e-taxonomy.eu |
|
| 6 |
* |
|
| 7 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
| 8 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
| 9 |
*/ |
|
| 10 |
|
|
| 11 |
package eu.etaxonomy.cdm.api.application.eclipse; |
|
| 12 |
|
|
| 13 |
import java.io.*; |
|
| 14 |
import java.net.*; |
|
| 15 |
import java.util.*; |
|
| 16 |
|
|
| 17 |
import org.eclipse.osgi.framework.internal.core.*; |
|
| 18 |
import org.springframework.core.*; |
|
| 19 |
import org.springframework.core.io.*; |
|
| 20 |
import org.springframework.core.io.support.*; |
|
| 21 |
|
|
| 22 |
public class EclipseRcpSavePathMatchingResourcePatternResolver extends PathMatchingResourcePatternResolver |
|
| 23 |
{
|
|
| 24 |
public EclipseRcpSavePathMatchingResourcePatternResolver(ResourceLoader resourceLoader) |
|
| 25 |
{
|
|
| 26 |
super(resourceLoader); |
|
| 27 |
} |
|
| 28 |
|
|
| 29 |
protected Resource[] findAllClassPathResources(String location) throws IOException |
|
| 30 |
{
|
|
| 31 |
String path = location; |
|
| 32 |
|
|
| 33 |
if (path.startsWith("/"))
|
|
| 34 |
{
|
|
| 35 |
path = path.substring(1) ; |
|
| 36 |
} |
|
| 37 |
|
|
| 38 |
Enumeration<URL> resourceUrls = getClassLoader().getResources(path); |
|
| 39 |
Set result = CollectionFactory.createLinkedSetIfPossible(16); |
|
| 40 |
while (resourceUrls.hasMoreElements()) |
|
| 41 |
{
|
|
| 42 |
URL url = (URL) resourceUrls.nextElement(); |
|
| 43 |
|
|
| 44 |
if (url.getProtocol().startsWith("bundleresource")){
|
|
| 45 |
//handle eclipse bundleresource: |
|
| 46 |
URLConnection con = url.openConnection(); |
|
| 47 |
BundleURLConnection bundleCon = (BundleURLConnection) con; |
|
| 48 |
// Convert the bundle URL into a file system URL. |
|
| 49 |
result.add(new UrlResource(bundleCon.getFileURL())); |
|
| 50 |
}else{
|
|
| 51 |
result.add(convertClassLoaderURL(url)); |
|
| 52 |
} |
|
| 53 |
} |
|
| 54 |
|
|
| 55 |
return (Resource[]) result.toArray(new Resource[result.size()]); |
|
| 56 |
} |
|
| 57 |
} |
|
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/FeatureTreeServiceImpl.java | ||
|---|---|---|
| 112 | 112 |
public FeatureTree load(UUID uuid, List<String> propertyPaths) {
|
| 113 | 113 |
return super.load(uuid, propertyPaths); |
| 114 | 114 |
} |
| 115 |
|
|
| 116 |
/* (non-Javadoc) |
|
| 117 |
* @see eu.etaxonomy.cdm.api.service.IFeatureTreeService#createTransientDefaultFeatureTree() |
|
| 118 |
*/ |
|
| 119 |
@Override |
|
| 120 |
public FeatureTree createTransientDefaultFeatureTree() {
|
|
| 121 |
return load(IFeatureTreeDao.DefaultFeatureTreeUuid); |
|
| 122 |
} |
|
| 123 |
|
|
| 124 |
|
|
| 115 | 125 |
|
| 116 | 126 |
} |
| cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IFeatureTreeService.java | ||
|---|---|---|
| 36 | 36 |
|
| 37 | 37 |
public Map<UUID, FeatureNode> saveOrUpdateFeatureNodesAll(Collection<FeatureNode> featureNodeCollection); |
| 38 | 38 |
|
| 39 |
public FeatureTree createTransientDefaultFeatureTree(); |
|
| 39 | 40 |
} |
| cdmlib-services/src/main/resources/eu/etaxonomy/cdm/defaultApplicationContext.xml | ||
|---|---|---|
| 16 | 16 |
<context:component-scan base-package="eu/etaxonomy/cdm/api/service"> |
| 17 | 17 |
<!-- <context:exclude-filter type="regex" expression="eu\.etaxonomy\.cdm\.api\.service\.UserService"/> --> |
| 18 | 18 |
</context:component-scan> |
| 19 |
|
|
| 19 | 20 |
<context:component-scan base-package="eu/etaxonomy/cdm/api/application"/> |
| 20 | 21 |
|
| 21 | 22 |
<!-- EditGeoService was moved to ext. Therefore it will not be found by the default component scan. |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/Datasource.java | ||
|---|---|---|
| 26 | 26 |
import eu.etaxonomy.cdm.api.application.CdmApplicationUtils; |
| 27 | 27 |
import eu.etaxonomy.cdm.database.CdmDataSource; |
| 28 | 28 |
import eu.etaxonomy.cdm.database.CdmPersistentDataSource; |
| 29 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
|
| 30 | 29 |
import eu.etaxonomy.cdm.database.DatabaseTypeEnum; |
| 31 | 30 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 32 | 31 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| ... | ... | |
| 42 | 41 |
import eu.etaxonomy.cdm.model.name.NameRelationshipType; |
| 43 | 42 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 44 | 43 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 45 |
import eu.etaxonomy.cdm.model.reference.IGeneric; |
|
| 46 | 44 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
| 47 | 45 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 48 | 46 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| ... | ... | |
| 59 | 57 |
// ICdmDataSource dataSource = CdmDataSource.NewInstance(dbType, "192.168.2.10", "cdm_test_andreas", dbType.getDefaultPort() + "", "edit", "", null, null); |
| 60 | 58 |
CdmPersistentDataSource.save(dataSource.getName(), dataSource); |
| 61 | 59 |
CdmApplicationController appCtr; |
| 62 |
try {
|
|
| 63 |
appCtr = CdmApplicationController.NewInstance(dataSource); |
|
| 64 |
appCtr.close(); |
|
| 65 |
} catch (DataSourceNotFoundException e) {
|
|
| 66 |
logger.error("Unknown datasource");
|
|
| 67 |
} catch (TermNotFoundException e) {
|
|
| 68 |
logger.error("defined terms not found");
|
|
| 69 |
} |
|
| 70 |
|
|
| 60 |
appCtr = CdmApplicationController.NewInstance(dataSource); |
|
| 61 |
appCtr.close(); |
|
| 71 | 62 |
} |
| 72 | 63 |
|
| 73 | 64 |
private void testDatabaseChange(){
|
| 74 | 65 |
CdmApplicationController appCtr; |
| 75 |
try {
|
|
| 76 |
appCtr = CdmApplicationController.NewInstance(); |
|
| 66 |
appCtr = CdmApplicationController.NewInstance(); |
|
| 67 |
|
|
| 68 |
// DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 69 |
// String server = "192.168.2.10"; |
|
| 70 |
// String database = "cdm_test_andreas"; |
|
| 71 |
// String user = "edit"; |
|
| 72 |
// String pwd = "wp5"; |
|
| 73 |
// |
|
| 74 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.SqlServer2005; |
|
| 75 |
String server = "LAPTOPHP"; |
|
| 76 |
String database = "cdmTest"; |
|
| 77 |
String username = "edit"; |
|
| 78 |
String password = ""; |
|
| 77 | 79 |
|
| 78 |
// DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL; |
|
| 79 |
// String server = "192.168.2.10"; |
|
| 80 |
// String database = "cdm_test_andreas"; |
|
| 81 |
// String user = "edit"; |
|
| 82 |
// String pwd = "wp5"; |
|
| 83 |
// |
|
| 84 |
DatabaseTypeEnum dbType = DatabaseTypeEnum.SqlServer2005; |
|
| 85 |
String server = "LAPTOPHP"; |
|
| 86 |
String database = "cdmTest"; |
|
| 87 |
String username = "edit"; |
|
| 88 |
String password = ""; |
|
| 89 |
|
|
| 90 |
ICdmDataSource dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.SqlServer2005, "LAPTOPHP", "cdmTest", DatabaseTypeEnum.SqlServer2005.getDefaultPort(), "edit", ""); |
|
| 91 |
|
|
| 92 |
appCtr.getDatabaseService().saveDataSource("testSqlServer", dataSource);
|
|
| 80 |
ICdmDataSource dataSource = CdmDataSource.NewInstance(DatabaseTypeEnum.SqlServer2005, "LAPTOPHP", "cdmTest", DatabaseTypeEnum.SqlServer2005.getDefaultPort(), "edit", ""); |
|
| 81 |
|
|
| 82 |
appCtr.getDatabaseService().saveDataSource("testSqlServer", dataSource);
|
|
| 83 |
try {
|
|
| 93 | 84 |
appCtr.getDatabaseService().connectToDatabase(dbType, server, database, username, password); |
| 94 |
|
|
| 95 |
appCtr.close(); |
|
| 96 |
} catch (DataSourceNotFoundException e) {
|
|
| 97 |
logger.error("datasource error");
|
|
| 98 | 85 |
} catch (TermNotFoundException e) {
|
| 99 |
logger.error("defined terms not found");
|
|
| 86 |
// TODO Auto-generated catch block |
|
| 87 |
e.printStackTrace(); |
|
| 100 | 88 |
} |
| 89 |
|
|
| 90 |
appCtr.close(); |
|
| 101 | 91 |
} |
| 102 | 92 |
|
| 103 | 93 |
private void testSqlServer(){
|
| ... | ... | |
| 129 | 119 |
TaxonNameBase tn = BotanicalName.NewInstance(null); |
| 130 | 120 |
appCtr.getNameService().save(tn); |
| 131 | 121 |
appCtr.close(); |
| 132 |
} catch (DataSourceNotFoundException e) {
|
|
| 133 |
logger.error("Unknown datasource");
|
|
| 134 |
} catch (TermNotFoundException e) {
|
|
| 135 |
logger.error("defined terms not found");
|
|
| 136 | 122 |
} catch (SQLException e) {
|
| 137 | 123 |
// TODO Auto-generated catch block |
| 138 | 124 |
e.printStackTrace(); |
| ... | ... | |
| 149 | 135 |
ICdmDataSource dataSource = CdmDataSource.NewInstance(databaseTypeEnum, server, database, databaseTypeEnum.getDefaultPort(), username, password); |
| 150 | 136 |
|
| 151 | 137 |
CdmPersistentDataSource ds = CdmPersistentDataSource.save("testSqlServer", dataSource);
|
| 152 |
try {
|
|
| 153 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 154 |
Person agent = Person.NewInstance(); |
|
| 155 |
appCtr.getAgentService().save(agent); |
|
| 156 |
TaxonNameBase tn = BotanicalName.NewInstance(null); |
|
| 157 |
appCtr.getNameService().save(tn); |
|
| 158 |
appCtr.close(); |
|
| 159 |
} catch (DataSourceNotFoundException e) {
|
|
| 160 |
logger.error("Unknown datasource");
|
|
| 161 |
} catch (TermNotFoundException e) {
|
|
| 162 |
logger.error("defined terms not found");
|
|
| 163 |
} |
|
| 138 |
|
|
| 139 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 140 |
Person agent = Person.NewInstance(); |
|
| 141 |
appCtr.getAgentService().save(agent); |
|
| 142 |
TaxonNameBase tn = BotanicalName.NewInstance(null); |
|
| 143 |
appCtr.getNameService().save(tn); |
|
| 144 |
appCtr.close(); |
|
| 145 |
|
|
| 164 | 146 |
} |
| 165 | 147 |
|
| 166 | 148 |
private void testPostgreServer(){
|
| ... | ... | |
| 173 | 155 |
ICdmDataSource dataSource = CdmDataSource.NewInstance(databaseTypeEnum, server, database, databaseTypeEnum.getDefaultPort(), username, password); |
| 174 | 156 |
|
| 175 | 157 |
CdmPersistentDataSource ds = CdmPersistentDataSource.save("PostgreTest", dataSource);
|
| 176 |
try {
|
|
| 177 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 178 |
Person agent = Person.NewInstance(); |
|
| 179 |
appCtr.getAgentService().save(agent); |
|
| 180 |
TaxonNameBase tn = BotanicalName.NewInstance(null); |
|
| 181 |
appCtr.getNameService().save(tn); |
|
| 182 |
appCtr.close(); |
|
| 183 |
} catch (DataSourceNotFoundException e) {
|
|
| 184 |
logger.error("Unknown datasource");
|
|
| 185 |
} catch (TermNotFoundException e) {
|
|
| 186 |
logger.error("defined terms not found");
|
|
| 187 |
} |
|
| 158 |
|
|
| 159 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 160 |
Person agent = Person.NewInstance(); |
|
| 161 |
appCtr.getAgentService().save(agent); |
|
| 162 |
TaxonNameBase tn = BotanicalName.NewInstance(null); |
|
| 163 |
appCtr.getNameService().save(tn); |
|
| 164 |
appCtr.close(); |
|
| 165 |
|
|
| 188 | 166 |
} |
| 189 | 167 |
|
| 190 | 168 |
private void testLocalHsql(){
|
| 169 |
|
|
| 170 |
CdmPersistentDataSource ds = CdmPersistentDataSource.NewLocalHsqlInstance(); |
|
| 171 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 191 | 172 |
try {
|
| 192 |
CdmPersistentDataSource ds = CdmPersistentDataSource.NewLocalHsqlInstance(); |
|
| 193 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds); |
|
| 194 |
try {
|
|
| 195 |
List l = appCtr.getNameService().list(null,5, 1,null,null); |
|
| 196 |
System.out.println(l); |
|
| 197 |
//Agent agent = new Agent(); |
|
| 198 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 199 |
appCtr.close(); |
|
| 200 |
} catch (RuntimeException e) {
|
|
| 201 |
logger.error("Runtime Exception");
|
|
| 202 |
e.printStackTrace(); |
|
| 203 |
appCtr.close(); |
|
| 204 |
|
|
| 205 |
} |
|
| 206 |
} catch (DataSourceNotFoundException e) {
|
|
| 207 |
logger.error("LOCAL HSQL");
|
|
| 208 |
} catch (TermNotFoundException e) {
|
|
| 209 |
logger.error("defined terms not found");
|
|
| 173 |
List l = appCtr.getNameService().list(null,5, 1,null,null); |
|
| 174 |
System.out.println(l); |
|
| 175 |
//Agent agent = new Agent(); |
|
| 176 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 177 |
appCtr.close(); |
|
| 178 |
} catch (RuntimeException e) {
|
|
| 179 |
logger.error("Runtime Exception");
|
|
| 180 |
e.printStackTrace(); |
|
| 181 |
appCtr.close(); |
|
| 182 |
|
|
| 210 | 183 |
} |
| 211 | 184 |
} |
| 212 | 185 |
|
| 213 | 186 |
private void testLocalH2(){
|
| 214 |
try {
|
|
| 215 |
DbSchemaValidation validation = DbSchemaValidation.CREATE;
|
|
| 216 |
ICdmDataSource ds =
|
|
| 217 |
CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
|
|
| 187 |
|
|
| 188 |
DbSchemaValidation validation = DbSchemaValidation.CREATE; |
|
| 189 |
ICdmDataSource ds = |
|
| 190 |
CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
|
|
| 218 | 191 |
// ds = |
| 219 | 192 |
// CdmPersistentDataSource.NewInstance("localH2");
|
| 220 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation); |
|
| 193 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation); |
|
| 194 |
|
|
| 195 |
boolean exists = appCtr.getUserService().userExists("admin");
|
|
| 196 |
try {
|
|
| 197 |
BotanicalName name = BotanicalName.NewInstance(null); |
|
| 198 |
String nameCache = "testName"; |
|
| 199 |
name.setNameCache(nameCache); |
|
| 200 |
name.setTitleCache(nameCache, true); |
|
| 201 |
ReferenceFactory refFactory = ReferenceFactory.newInstance(); |
|
| 202 |
ReferenceBase ref = refFactory.newGeneric(); |
|
| 203 |
ref.setTitleCache("mySec", true);
|
|
| 204 |
Taxon taxon = Taxon.NewInstance(name, ref); |
|
| 205 |
TaxonDescription description = TaxonDescription.NewInstance(); |
|
| 206 |
taxon.addDescription(description); |
|
| 207 |
NamedArea area1 = TdwgArea.getAreaByTdwgAbbreviation("GER");
|
|
| 208 |
Distribution distribution = Distribution.NewInstance(area1, PresenceTerm.PRESENT()); |
|
| 209 |
description.addElement(distribution); |
|
| 221 | 210 |
|
| 222 |
boolean exists = appCtr.getUserService().userExists("admin");
|
|
| 223 |
try {
|
|
| 224 |
BotanicalName name = BotanicalName.NewInstance(null); |
|
| 225 |
String nameCache = "testName"; |
|
| 226 |
name.setNameCache(nameCache); |
|
| 227 |
name.setTitleCache(nameCache, true); |
|
| 228 |
ReferenceFactory refFactory = ReferenceFactory.newInstance(); |
|
| 229 |
ReferenceBase ref = refFactory.newGeneric(); |
|
| 230 |
ref.setTitleCache("mySec", true);
|
|
| 231 |
Taxon taxon = Taxon.NewInstance(name, ref); |
|
| 232 |
TaxonDescription description = TaxonDescription.NewInstance(); |
|
| 233 |
taxon.addDescription(description); |
|
| 234 |
NamedArea area1 = TdwgArea.getAreaByTdwgAbbreviation("GER");
|
|
| 235 |
Distribution distribution = Distribution.NewInstance(area1, PresenceTerm.PRESENT()); |
|
| 236 |
description.addElement(distribution); |
|
| 237 |
|
|
| 238 |
List<Distribution> distrList = new ArrayList<Distribution>(); |
|
| 239 |
distrList.add(distribution); |
|
| 240 |
List<NamedArea> areaList = new ArrayList<NamedArea>(); |
|
| 241 |
areaList.add(area1); |
|
| 242 |
|
|
| 243 |
// distribution.getInDescription().get |
|
| 244 |
appCtr.getTaxonService().save(taxon); |
|
| 211 |
List<Distribution> distrList = new ArrayList<Distribution>(); |
|
| 212 |
distrList.add(distribution); |
|
| 213 |
List<NamedArea> areaList = new ArrayList<NamedArea>(); |
|
| 214 |
areaList.add(area1); |
|
| 215 |
|
|
| 216 |
// distribution.getInDescription().get |
|
| 217 |
appCtr.getTaxonService().save(taxon); |
|
| 245 | 218 |
|
| 246 |
System.out.println(taxon.getDescriptions().size());
|
|
| 247 |
|
|
| 248 |
TransactionStatus txStatus = appCtr.startTransaction();
|
|
| 249 |
|
|
| 250 |
Session session = appCtr.getSessionFactory().getCurrentSession();
|
|
| 251 |
|
|
| 252 |
//String hqlQuery = "from DescriptionBase d join d.elements as e "
|
|
| 219 |
System.out.println(taxon.getDescriptions().size()); |
|
| 220 |
|
|
| 221 |
TransactionStatus txStatus = appCtr.startTransaction(); |
|
| 222 |
|
|
| 223 |
Session session = appCtr.getSessionFactory().getCurrentSession(); |
|
| 224 |
|
|
| 225 |
//String hqlQuery = "from DescriptionBase d join d.elements as e " |
|
| 253 | 226 |
// String hqlQuery = "from Taxon t join t.descriptions as d "+ |
| 254 | 227 |
// " inner join d.elements e on e member of d " |
| 255 | 228 |
// + |
| 256 | 229 |
// "";//" where e.area = :namedArea " ; |
| 257 |
String hqlQuery = "Select t from Distribution e join e.inDescription d join d.taxon t join t.name n "+ |
|
| 258 |
" WHERE e.area in (:namedArea) AND n.nameCache = :nameCache "; |
|
| 259 |
Query query = session.createQuery(hqlQuery); |
|
| 260 |
|
|
| 261 |
//query.setEntity("namedArea", area1);
|
|
| 262 |
query.setParameter("nameCache", nameCache);
|
|
| 263 |
query.setParameterList("namedArea", areaList);
|
|
| 264 |
List resultList = query.list(); |
|
| 265 |
//List list = appCtr.getCommonService().getHqlResult(hqlQuery); |
|
| 266 |
|
|
| 267 |
for (Object o:resultList){
|
|
| 268 |
System.out.println(o); |
|
| 269 |
} |
|
| 270 |
appCtr.commitTransaction(txStatus); |
|
| 271 |
|
|
| 272 |
//System.out.println(l); |
|
| 273 |
//Agent agent = new Agent(); |
|
| 274 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 275 |
appCtr.close(); |
|
| 276 |
} catch (RuntimeException e) {
|
|
| 277 |
logger.error("Runtime Exception");
|
|
| 278 |
e.printStackTrace(); |
|
| 279 |
appCtr.close(); |
|
| 280 |
|
|
| 230 |
String hqlQuery = "Select t from Distribution e join e.inDescription d join d.taxon t join t.name n "+ |
|
| 231 |
" WHERE e.area in (:namedArea) AND n.nameCache = :nameCache "; |
|
| 232 |
Query query = session.createQuery(hqlQuery); |
|
| 233 |
|
|
| 234 |
//query.setEntity("namedArea", area1);
|
|
| 235 |
query.setParameter("nameCache", nameCache);
|
|
| 236 |
query.setParameterList("namedArea", areaList);
|
|
| 237 |
List resultList = query.list(); |
|
| 238 |
//List list = appCtr.getCommonService().getHqlResult(hqlQuery); |
|
| 239 |
|
|
| 240 |
for (Object o:resultList){
|
|
| 241 |
System.out.println(o); |
|
| 281 | 242 |
} |
| 282 |
} catch (DataSourceNotFoundException e) {
|
|
| 283 |
logger.error("Error in LOCAL HSQL");
|
|
| 284 |
} catch (TermNotFoundException e) {
|
|
| 285 |
logger.error("defined terms not found");
|
|
| 243 |
appCtr.commitTransaction(txStatus); |
|
| 244 |
|
|
| 245 |
//System.out.println(l); |
|
| 246 |
//Agent agent = new Agent(); |
|
| 247 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 248 |
appCtr.close(); |
|
| 249 |
} catch (RuntimeException e) {
|
|
| 250 |
logger.error("Runtime Exception");
|
|
| 251 |
e.printStackTrace(); |
|
| 252 |
appCtr.close(); |
|
| 253 |
|
|
| 286 | 254 |
} |
| 287 | 255 |
} |
| 288 | 256 |
|
| ... | ... | |
| 294 | 262 |
private boolean testH2(){
|
| 295 | 263 |
// testLocalH2(); |
| 296 | 264 |
// if (true)return true; |
| 297 |
try{
|
|
| 298 |
DbSchemaValidation validation = DbSchemaValidation.CREATE; |
|
| 299 |
ICdmDataSource ds = |
|
| 300 |
CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
|
|
| 301 |
//CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
|
|
| 302 |
// ds = |
|
| 303 |
// CdmPersistentDataSource.NewInstance("localH2");
|
|
| 304 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation); |
|
| 265 |
|
|
| 266 |
DbSchemaValidation validation = DbSchemaValidation.CREATE; |
|
| 267 |
ICdmDataSource ds = |
|
| 268 |
CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "", null);
|
|
| 269 |
//CdmDataSource.NewH2EmbeddedInstance("cdm", "sa", "");
|
|
| 270 |
// ds = |
|
| 271 |
// CdmPersistentDataSource.NewInstance("localH2");
|
|
| 272 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(ds, validation); |
|
| 273 |
try {
|
|
| 274 |
BotanicalName botName1 = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 275 |
BotanicalName botName2 = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 276 |
BotanicalName hybridName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 277 |
botName1.addRelationshipToName(botName2, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), null); |
|
| 278 |
UUID uuid1 = botName1.getUuid(); |
|
| 279 |
UUID uuid2 = botName2.getUuid(); |
|
| 305 | 280 |
try {
|
| 306 |
BotanicalName botName1 = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 307 |
BotanicalName botName2 = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 308 |
BotanicalName hybridName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 309 |
botName1.addRelationshipToName(botName2, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), null); |
|
| 310 |
UUID uuid1 = botName1.getUuid(); |
|
| 311 |
UUID uuid2 = botName2.getUuid(); |
|
| 312 |
try {
|
|
| 313 |
Logger loggerTrace = logger.getLogger("org.hibernate.type");
|
|
| 314 |
loggerTrace.setLevel(Level.TRACE); |
|
| 315 |
System.out.println(logger.getName()); |
|
| 316 |
|
|
| 317 |
appCtr.getNameService().save(botName1); |
|
| 318 |
ResultSet rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 319 |
rs.next(); |
|
| 320 |
int c = rs.getInt("n");
|
|
| 321 |
System.out.println("Begin :" + c);
|
|
| 322 |
|
|
| 323 |
botName1.removeRelationToTaxonName(botName2); |
|
| 324 |
botName1.setSpecificEpithet("DELETED");
|
|
| 325 |
botName2.addHybridParent(hybridName, HybridRelationshipType.FIRST_PARENT(), null); |
|
| 326 |
|
|
| 327 |
TransactionStatus tx = appCtr.startTransaction(); |
|
| 328 |
appCtr.getNameService().saveOrUpdate(botName2); |
|
| 329 |
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 330 |
rs.next(); |
|
| 331 |
c = rs.getInt("n");
|
|
| 332 |
System.out.println("End: " + c);
|
|
| 333 |
|
|
| 334 |
appCtr.commitTransaction(tx); |
|
| 335 |
|
|
| 336 |
appCtr.getNameService().saveOrUpdate(botName1); |
|
| 337 |
|
|
| 338 |
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 339 |
rs.next(); |
|
| 340 |
c = rs.getInt("n");
|
|
| 341 |
System.out.println("End: " + c);
|
|
| 342 |
|
|
| 343 |
} catch (SQLException e) {
|
|
| 344 |
// TODO Auto-generated catch block |
|
| 345 |
e.printStackTrace(); |
|
| 346 |
} |
|
| 281 |
Logger loggerTrace = logger.getLogger("org.hibernate.type");
|
|
| 282 |
loggerTrace.setLevel(Level.TRACE); |
|
| 283 |
System.out.println(logger.getName()); |
|
| 347 | 284 |
|
| 285 |
appCtr.getNameService().save(botName1); |
|
| 286 |
ResultSet rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 287 |
rs.next(); |
|
| 288 |
int c = rs.getInt("n");
|
|
| 289 |
System.out.println("Begin :" + c);
|
|
| 348 | 290 |
|
| 349 |
//Agent agent = new Agent(); |
|
| 350 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 351 |
appCtr.close(); |
|
| 352 |
return true; |
|
| 353 |
} catch (RuntimeException e) {
|
|
| 354 |
logger.error("Runtime Exception");
|
|
| 355 |
e.printStackTrace(); |
|
| 356 |
appCtr.close(); |
|
| 291 |
botName1.removeRelationToTaxonName(botName2); |
|
| 292 |
botName1.setSpecificEpithet("DELETED");
|
|
| 293 |
botName2.addHybridParent(hybridName, HybridRelationshipType.FIRST_PARENT(), null); |
|
| 357 | 294 |
|
| 295 |
TransactionStatus tx = appCtr.startTransaction(); |
|
| 296 |
appCtr.getNameService().saveOrUpdate(botName2); |
|
| 297 |
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 298 |
rs.next(); |
|
| 299 |
c = rs.getInt("n");
|
|
| 300 |
System.out.println("End: " + c);
|
|
| 301 |
|
|
| 302 |
appCtr.commitTransaction(tx); |
|
| 303 |
|
|
| 304 |
appCtr.getNameService().saveOrUpdate(botName1); |
|
| 305 |
|
|
| 306 |
rs = ds.executeQuery("Select count(*) as n FROM NameRelationship");
|
|
| 307 |
rs.next(); |
|
| 308 |
c = rs.getInt("n");
|
|
| 309 |
System.out.println("End: " + c);
|
|
| 310 |
|
|
| 311 |
} catch (SQLException e) {
|
|
| 312 |
// TODO Auto-generated catch block |
|
| 313 |
e.printStackTrace(); |
|
| 358 | 314 |
} |
| 359 |
} catch (DataSourceNotFoundException e) {
|
|
| 360 |
logger.error("Error in LOCAL HSQL");
|
|
| 361 |
} catch (TermNotFoundException e) {
|
|
| 362 |
logger.error("defined terms not found");
|
|
| 315 |
|
|
| 316 |
|
|
| 317 |
//Agent agent = new Agent(); |
|
| 318 |
//appCtr.getAgentService().saveAgent(agent); |
|
| 319 |
appCtr.close(); |
|
| 320 |
return true; |
|
| 321 |
} catch (RuntimeException e) {
|
|
| 322 |
logger.error("Runtime Exception");
|
|
| 323 |
e.printStackTrace(); |
|
| 324 |
appCtr.close(); |
|
| 325 |
|
|
| 363 | 326 |
} |
| 364 | 327 |
return false; |
| 365 | 328 |
} |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestDatabase.java | ||
|---|---|---|
| 21 | 21 |
|
| 22 | 22 |
import org.apache.log4j.Logger; |
| 23 | 23 |
import org.hibernate.mapping.Column; |
| 24 |
import org.junit.Test; |
|
| 25 | 24 |
import org.springframework.core.io.ClassPathResource; |
| 26 | 25 |
import org.springframework.core.io.Resource; |
| 27 | 26 |
|
| ... | ... | |
| 39 | 38 |
import eu.etaxonomy.cdm.model.agent.Contact; |
| 40 | 39 |
import eu.etaxonomy.cdm.model.agent.Person; |
| 41 | 40 |
import eu.etaxonomy.cdm.model.common.Annotation; |
| 42 |
import eu.etaxonomy.cdm.model.common.AnnotationType; |
|
| 43 | 41 |
import eu.etaxonomy.cdm.model.common.Language; |
| 44 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 45 | 42 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 46 | 43 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
| 47 | 44 |
import eu.etaxonomy.cdm.model.description.Feature; |
| ... | ... | |
| 56 | 53 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
| 57 | 54 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 58 | 55 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 59 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 60 | 56 |
|
| 61 | 57 |
|
| 62 | 58 |
public class TestDatabase {
|
| ... | ... | |
| 74 | 70 |
} |
| 75 | 71 |
|
| 76 | 72 |
public void testNewDatabaseConnection(){
|
| 77 |
try {
|
|
| 78 |
|
|
| 79 |
Column coL; |
|
| 80 |
boolean omitTermLoading = false; |
|
| 81 |
Resource applicationContextResource = new ClassPathResource(CdmApplicationController.DEFAULT_APPLICATION_CONTEXT_RESOURCE); |
|
| 82 |
CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance(); |
|
| 83 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(applicationContextResource, dataSource, DbSchemaValidation.CREATE, omitTermLoading); |
|
| 84 |
appCtr.NewConversation(); |
|
| 85 |
appCtr.NewConversation(); |
|
| 86 |
|
|
| 87 |
//CdmApplicationController appCtr = CdmApplicationController.NewInstance(DbSchemaValidation.CREATE); |
|
| 88 |
appCtr.close(); |
|
| 89 |
} catch (DataSourceNotFoundException e) {
|
|
| 90 |
logger.error("datasource error");
|
|
| 91 |
} catch (TermNotFoundException e) {
|
|
| 92 |
logger.error("defined terms not found");
|
|
| 93 |
} |
|
| 73 |
|
|
| 74 |
Column coL; |
|
| 75 |
boolean omitTermLoading = false; |
|
| 76 |
Resource applicationContextResource = new ClassPathResource(CdmApplicationController.DEFAULT_APPLICATION_CONTEXT_RESOURCE); |
|
| 77 |
CdmPersistentDataSource dataSource = CdmPersistentDataSource.NewDefaultInstance(); |
|
| 78 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(applicationContextResource, dataSource, DbSchemaValidation.CREATE, omitTermLoading); |
|
| 79 |
appCtr.NewConversation(); |
|
| 80 |
appCtr.NewConversation(); |
|
| 81 |
|
|
| 82 |
//CdmApplicationController appCtr = CdmApplicationController.NewInstance(DbSchemaValidation.CREATE); |
|
| 83 |
appCtr.close(); |
|
| 94 | 84 |
} |
| 95 | 85 |
|
| 96 | 86 |
public void testNewDatasourceClass(){
|
| 97 |
try {
|
|
| 98 | 87 |
// String server = "192.168.2.10"; |
| 99 | 88 |
// String database = "cdm_test_andreasM"; |
| 100 | 89 |
// String username = "edit"; |
| 101 | 90 |
// String password = CdmUtils.readInputLine("Password: ");
|
| 102 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
|
|
| 91 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 103 | 92 |
|
| 104 | 93 |
// ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
| 105 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
|
|
| 106 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 107 |
|
|
| 108 |
Rank genus = Rank.GENUS(); |
|
| 109 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 110 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 94 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
|
|
| 95 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 111 | 96 |
|
| 112 |
IJournal journal = refFactory.newJournal(); |
|
| 113 |
journal.setTitleCache("Afro+Doc", true);
|
|
| 114 |
|
|
| 115 |
// Taxon taxon = Taxon.NewInstance(botanicalName, journal); |
|
| 97 |
Rank genus = Rank.GENUS(); |
|
| 98 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 99 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 100 |
|
|
| 101 |
IJournal journal = refFactory.newJournal(); |
|
| 102 |
journal.setTitleCache("Afro+Doc", true);
|
|
| 103 |
|
|
| 104 |
// Taxon taxon = Taxon.NewInstance(botanicalName, journal); |
|
| 116 | 105 |
// Taxon taxon2 = Taxon.NewInstance(botanicalName2, null); |
| 117 |
// botanicalName.getTitleCache();
|
|
| 118 |
|
|
| 119 |
Taxon taxon1 = Taxon.NewInstance(botanicalName,(ReferenceBase)journal);
|
|
| 120 |
appCtr.getTaxonService().save(taxon1);
|
|
| 121 |
BotanicalName homotypName = BotanicalName.NewInstance(Rank.SUBGENUS(), botanicalName.getHomotypicalGroup());
|
|
| 122 |
homotypName.setGenusOrUninomial("Subgenus");
|
|
| 123 |
homotypName.setInfraGenericEpithet("homotyp");
|
|
| 124 |
|
|
| 125 |
//Synonym synonym = Synonym.NewInstance(homotypName, journal);
|
|
| 126 |
|
|
| 127 |
System.out.println("Taxa of " + botanicalName + ": " + botanicalName.getTaxonBases());
|
|
| 128 |
System.out.println("Synonyms of " + homotypName + ": " + homotypName.getSynonyms());
|
|
| 129 |
|
|
| 130 |
HomotypicalGroup homotypicalGroup = taxon1.getHomotypicGroup();
|
|
| 131 |
System.out.println("HomotypicNames of " + botanicalName + ":" + homotypicalGroup.getTypifiedNames());
|
|
| 132 |
System.out.println("HomotypicSynonymsByGroup of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicGroup());
|
|
| 133 |
System.out.println("HomotypicSynonymsBySynonymy of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicRelationship());
|
|
| 134 |
|
|
| 106 |
// botanicalName.getTitleCache(); |
|
| 107 |
|
|
| 108 |
Taxon taxon1 = Taxon.NewInstance(botanicalName,(ReferenceBase)journal); |
|
| 109 |
appCtr.getTaxonService().save(taxon1); |
|
| 110 |
BotanicalName homotypName = BotanicalName.NewInstance(Rank.SUBGENUS(), botanicalName.getHomotypicalGroup()); |
|
| 111 |
homotypName.setGenusOrUninomial("Subgenus");
|
|
| 112 |
homotypName.setInfraGenericEpithet("homotyp");
|
|
| 113 |
|
|
| 114 |
//Synonym synonym = Synonym.NewInstance(homotypName, journal); |
|
| 115 |
|
|
| 116 |
System.out.println("Taxa of " + botanicalName + ": " + botanicalName.getTaxonBases());
|
|
| 117 |
System.out.println("Synonyms of " + homotypName + ": " + homotypName.getSynonyms());
|
|
| 118 |
|
|
| 119 |
HomotypicalGroup homotypicalGroup = taxon1.getHomotypicGroup(); |
|
| 120 |
System.out.println("HomotypicNames of " + botanicalName + ":" + homotypicalGroup.getTypifiedNames());
|
|
| 121 |
System.out.println("HomotypicSynonymsByGroup of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicGroup());
|
|
| 122 |
System.out.println("HomotypicSynonymsBySynonymy of " + taxon1 + ":" + taxon1.getHomotypicSynonymsByHomotypicRelationship());
|
|
| 123 |
|
|
| 135 | 124 |
// appCtr.getTaxonService().saveTaxon(taxon2); |
| 136 | 125 |
// appCtr.getTaxonService().saveTaxon(taxon); |
| 137 |
|
|
| 138 |
appCtr.close(); |
|
| 139 |
|
|
| 140 |
} catch (DataSourceNotFoundException e) {
|
|
| 141 |
logger.error("datasource error");
|
|
| 142 |
} catch (TermNotFoundException e) {
|
|
| 143 |
logger.error("defined terms not found");
|
|
| 144 |
} |
|
| 126 |
|
|
| 127 |
appCtr.close(); |
|
| 145 | 128 |
} |
| 146 | 129 |
|
| 147 | 130 |
|
| 148 | 131 |
public void testFacts(){
|
| 149 |
try {
|
|
| 150 |
String server = "192.168.2.10"; |
|
| 151 |
String database = "cdm_test_andreasM"; |
|
| 152 |
String username = "edit"; |
|
| 153 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 154 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE; |
|
| 155 |
ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
|
| 156 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 157 |
|
|
| 158 |
Rank genus = Rank.GENUS(); |
|
| 159 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 160 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 161 |
|
|
| 162 |
IJournal journal = refFactory.newJournal(); |
|
| 163 |
journal.setTitleCache("Afro+Doc", true);
|
|
| 164 |
|
|
| 165 |
Taxon taxon = Taxon.NewInstance(botanicalName,(ReferenceBase)journal); |
|
| 166 |
appCtr.getTaxonService().save(taxon); |
|
| 167 |
|
|
| 168 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
|
| 169 |
taxon.addDescription(taxonDescription); |
|
| 170 |
|
|
| 171 |
//textData |
|
| 172 |
TextData textData = TextData.NewInstance(); |
|
| 173 |
textData.putText("XXX", Language.DEFAULT());
|
|
| 174 |
taxonDescription.addElement(textData); |
|
| 175 |
|
|
| 176 |
//commonNames |
|
| 177 |
String commonNameString; |
|
| 178 |
if (taxon.getName() != null){
|
|
| 179 |
commonNameString = "Common " + taxon.getName().getTitleCache(); |
|
| 180 |
}else{
|
|
| 181 |
commonNameString = "Common (null)"; |
|
| 182 |
} |
|
| 183 |
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, Language.DEFAULT()); |
|
| 184 |
taxonDescription.addElement(commonName); |
|
| 185 |
|
|
| 186 |
//save |
|
| 187 |
appCtr.getTaxonService().save(taxon); |
|
| 188 | 132 |
|
| 189 |
|
|
| 190 |
appCtr.close(); |
|
| 191 |
|
|
| 192 |
} catch (DataSourceNotFoundException e) {
|
|
| 193 |
logger.error("datasource error");
|
|
| 194 |
} catch (TermNotFoundException e) {
|
|
| 195 |
logger.error("defined terms not found");
|
|
| 133 |
String server = "192.168.2.10"; |
|
| 134 |
String database = "cdm_test_andreasM"; |
|
| 135 |
String username = "edit"; |
|
| 136 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 137 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE; |
|
| 138 |
ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
|
| 139 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 140 |
|
|
| 141 |
Rank genus = Rank.GENUS(); |
|
| 142 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 143 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 144 |
|
|
| 145 |
IJournal journal = refFactory.newJournal(); |
|
| 146 |
journal.setTitleCache("Afro+Doc", true);
|
|
| 147 |
|
|
| 148 |
Taxon taxon = Taxon.NewInstance(botanicalName,(ReferenceBase)journal); |
|
| 149 |
appCtr.getTaxonService().save(taxon); |
|
| 150 |
|
|
| 151 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
|
| 152 |
taxon.addDescription(taxonDescription); |
|
| 153 |
|
|
| 154 |
//textData |
|
| 155 |
TextData textData = TextData.NewInstance(); |
|
| 156 |
textData.putText("XXX", Language.DEFAULT());
|
|
| 157 |
taxonDescription.addElement(textData); |
|
| 158 |
|
|
| 159 |
//commonNames |
|
| 160 |
String commonNameString; |
|
| 161 |
if (taxon.getName() != null){
|
|
| 162 |
commonNameString = "Common " + taxon.getName().getTitleCache(); |
|
| 163 |
}else{
|
|
| 164 |
commonNameString = "Common (null)"; |
|
| 196 | 165 |
} |
| 166 |
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, Language.DEFAULT()); |
|
| 167 |
taxonDescription.addElement(commonName); |
|
| 168 |
|
|
| 169 |
//save |
|
| 170 |
appCtr.getTaxonService().save(taxon); |
|
| 171 |
|
|
| 172 |
|
|
| 173 |
appCtr.close(); |
|
| 197 | 174 |
} |
| 198 | 175 |
|
| 199 | 176 |
|
| 200 | 177 |
public void testHybridRelationships(){
|
| 201 |
try {
|
|
| 178 |
|
|
| 202 | 179 |
// String database = "cdm"; |
| 203 | 180 |
// String username = "sa"; |
| 204 | 181 |
|
| 205 |
String server = "192.168.2.10"; |
|
| 206 |
String database = "cdm_test_andreasM"; |
|
| 207 |
String username = "edit"; |
|
| 208 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 209 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 210 |
ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
|
| 211 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 212 |
|
|
| 213 |
Rank genus = Rank.GENUS(); |
|
| 214 |
BotanicalName parentName = BotanicalName.NewInstance(genus); |
|
| 215 |
parentName.setGenusOrUninomial("parent");
|
|
| 182 |
String server = "192.168.2.10"; |
|
| 183 |
String database = "cdm_test_andreasM"; |
|
| 184 |
String username = "edit"; |
|
| 185 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 186 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 187 |
ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
|
| 188 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 216 | 189 |
|
| 217 |
BotanicalName childName = BotanicalName.NewInstance(genus); |
|
| 218 |
childName.setGenusOrUninomial("child");
|
|
| 219 |
parentName.addHybridChild(childName, HybridRelationshipType.FIRST_PARENT(), null); |
|
| 220 |
|
|
| 221 |
//save |
|
| 222 |
appCtr.getNameService().save(parentName); |
|
| 223 |
|
|
| 224 |
|
|
| 225 |
appCtr.close(); |
|
| 190 |
Rank genus = Rank.GENUS(); |
|
| 191 |
BotanicalName parentName = BotanicalName.NewInstance(genus); |
|
| 192 |
parentName.setGenusOrUninomial("parent");
|
|
| 193 |
|
|
| 194 |
BotanicalName childName = BotanicalName.NewInstance(genus); |
|
| 195 |
childName.setGenusOrUninomial("child");
|
|
| 196 |
parentName.addHybridChild(childName, HybridRelationshipType.FIRST_PARENT(), null); |
|
| 197 |
|
|
| 198 |
//save |
|
| 199 |
appCtr.getNameService().save(parentName); |
|
| 226 | 200 |
|
| 227 |
} catch (DataSourceNotFoundException e) {
|
|
| 228 |
logger.error("datasource error");
|
|
| 229 |
} catch (TermNotFoundException e) {
|
|
| 230 |
logger.error("defined terms not found");
|
|
| 231 |
} |
|
| 201 |
|
|
| 202 |
appCtr.close(); |
|
| 232 | 203 |
} |
| 233 | 204 |
|
| 234 | 205 |
public void testPaddie(){
|
| 206 |
String server = "PADDIE"; |
|
| 207 |
String database = "edit_test"; |
|
| 208 |
String username = "andreas"; |
|
| 209 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 210 |
DbSchemaValidation validation = DbSchemaValidation.VALIDATE; |
|
| 211 |
ICdmDataSource datasource = CdmDataSource.NewSqlServer2005Instance(server, database, -1, username, password, null); |
|
| 212 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, validation); |
|
| 235 | 213 |
|
| 236 |
|
|
| 237 |
try {
|
|
| 238 |
String server = "PADDIE"; |
|
| 239 |
String database = "edit_test"; |
|
| 240 |
String username = "andreas"; |
|
| 241 |
String password = CdmUtils.readInputLine("Password: ");
|
|
| 242 |
DbSchemaValidation validation = DbSchemaValidation.VALIDATE; |
|
| 243 |
ICdmDataSource datasource = CdmDataSource.NewSqlServer2005Instance(server, database, -1, username, password, null); |
|
| 244 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, validation); |
|
| 245 |
|
|
| 246 |
Rank genus = Rank.GENUS(); |
|
| 247 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 248 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 214 |
Rank genus = Rank.GENUS(); |
|
| 215 |
BotanicalName botanicalName = BotanicalName.NewInstance(genus); |
|
| 216 |
botanicalName.setGenusOrUninomial("GenusName");
|
|
| 217 |
|
|
| 218 |
IJournal journal = refFactory.newJournal(); |
|
| 219 |
journal.setTitle("JournalTitel");
|
|
| 249 | 220 |
|
| 250 |
IJournal journal = refFactory.newJournal(); |
|
| 251 |
journal.setTitle("JournalTitel");
|
|
| 252 |
|
|
| 253 |
// Taxon taxon = Taxon.NewInstance(botanicalName, journal); |
|
| 221 |
// Taxon taxon = Taxon.NewInstance(botanicalName, journal); |
|
| 254 | 222 |
// Taxon taxon2 = Taxon.NewInstance(botanicalName2, null); |
| 255 |
// botanicalName.getTitleCache();
|
|
| 256 |
Rank.SPECIES();
|
|
| 257 |
appCtr.getNameService().save(botanicalName);
|
|
| 223 |
// botanicalName.getTitleCache(); |
|
| 224 |
Rank.SPECIES(); |
|
| 225 |
appCtr.getNameService().save(botanicalName); |
|
| 258 | 226 |
|
| 259 | 227 |
// appCtr.getTaxonService().saveTaxon(taxon2); |
| 260 | 228 |
// appCtr.getTaxonService().saveTaxon(taxon); |
| 261 |
|
|
| 262 |
appCtr.close(); |
|
| 263 |
} catch (DataSourceNotFoundException e) {
|
|
| 264 |
logger.error("datasource error");
|
|
| 265 |
} catch (TermNotFoundException e) {
|
|
| 266 |
logger.error("defined terms not found");
|
|
| 267 |
} |
|
| 229 |
|
|
| 230 |
appCtr.close(); |
|
| 268 | 231 |
} |
| 269 | 232 |
|
| 270 | 233 |
|
| 271 | 234 |
public void testContact(){
|
| 272 |
try {
|
|
| 273 | 235 |
// String server = "192.168.2.10"; |
| 274 | 236 |
// String database = "cdm_test_andreasM"; |
| 275 | 237 |
// String username = "edit"; |
| 276 | 238 |
// String password = CdmUtils.readInputLine("Password: ");
|
| 277 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
|
|
| 239 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 278 | 240 |
|
| 279 | 241 |
// ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
| 280 |
//ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "");
|
|
| 281 |
ICdmDataSource datasource = cdm_test_anahit2();
|
|
| 282 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
|
|
| 283 |
AgentBase person = Person.NewTitledInstance("TestPerson");
|
|
| 284 |
Contact contact1 = new Contact();
|
|
| 285 |
Set<String> set = new HashSet<String>();
|
|
| 286 |
set.add("email1");
|
|
| 287 |
set.add("c@d.org");
|
|
| 242 |
//ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "");
|
|
| 243 |
ICdmDataSource datasource = cdm_test_anahit2(); |
|
| 244 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 245 |
AgentBase person = Person.NewTitledInstance("TestPerson");
|
|
| 246 |
Contact contact1 = new Contact(); |
|
| 247 |
Set<String> set = new HashSet<String>(); |
|
| 248 |
set.add("email1");
|
|
| 249 |
set.add("c@d.org");
|
|
| 288 | 250 |
// contact1.setEmail(set); |
| 289 | 251 |
// person.setContact(contact1); |
| 290 |
appCtr.getAgentService().save(person); |
|
| 291 |
appCtr.close(); |
|
| 292 |
System.out.println("End");
|
|
| 293 |
} catch (DataSourceNotFoundException e) {
|
|
| 294 |
logger.error("datasource error");
|
|
| 295 |
} catch (TermNotFoundException e) {
|
|
| 296 |
logger.error("defined terms not found");
|
|
| 297 |
} |
|
| 252 |
appCtr.getAgentService().save(person); |
|
| 253 |
appCtr.close(); |
|
| 254 |
System.out.println("End");
|
|
| 298 | 255 |
} |
| 299 | 256 |
|
| 300 | 257 |
|
| 301 | 258 |
public void testNewVersion(){
|
| 302 |
try {
|
|
| 303 |
System.out.println("Start");
|
|
| 304 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 259 |
System.out.println("Start");
|
|
| 260 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 305 | 261 |
|
| 306 | 262 |
// ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
| 307 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
|
|
| 308 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation);
|
|
| 309 |
BotanicalName botName = BotanicalName.NewInstance(Rank.SPECIES());
|
|
| 310 |
botName.setGenusOrUninomial("Genus");
|
|
| 311 |
botName.setSpecificEpithet("species");
|
|
| 312 |
appCtr.getNameService().save(botName);
|
|
| 313 |
List<?> names = appCtr.getNameService().findNamesByTitle("Genus species");
|
|
| 263 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("CDM", "sa", "", null);
|
|
| 264 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 265 |
BotanicalName botName = BotanicalName.NewInstance(Rank.SPECIES()); |
|
| 266 |
botName.setGenusOrUninomial("Genus");
|
|
| 267 |
botName.setSpecificEpithet("species");
|
|
| 268 |
appCtr.getNameService().save(botName); |
|
| 269 |
List<?> names = appCtr.getNameService().findNamesByTitle("Genus species");
|
|
| 314 | 270 |
|
| 315 |
names.size();
|
|
| 271 |
names.size(); |
|
| 316 | 272 |
// AgentBase person = Person.NewTitledInstance("TestPerson");
|
| 317 | 273 |
// Contact contact1 = new Contact(); |
| 318 | 274 |
// Set<String> set = new HashSet<String>(); |
| ... | ... | |
| 321 | 277 |
//// contact1.setEmail(set); |
| 322 | 278 |
// person.setContact(contact1); |
| 323 | 279 |
// appCtr.getAgentService().save(person); |
| 324 |
appCtr.close(); |
|
| 325 |
System.out.println("End");
|
|
| 326 |
} catch (DataSourceNotFoundException e) {
|
|
| 327 |
logger.error("datasource error");
|
|
| 328 |
} catch (TermNotFoundException e) {
|
|
| 329 |
logger.error("defined terms not found");
|
|
| 330 |
} |
|
| 280 |
appCtr.close(); |
|
| 281 |
System.out.println("End");
|
|
| 331 | 282 |
} |
| 332 | 283 |
|
| 333 | 284 |
public void testDataSourceWithNomenclaturalCode(){
|
| ... | ... | |
| 358 | 309 |
public void testLoadedAnnotationGetAnnotatedObjectCall(){
|
| 359 | 310 |
String password = CdmUtils.readInputLine("Password: ");
|
| 360 | 311 |
ICdmDataSource dataSource = CdmDataSource.NewMySqlInstance("192.168.2.10", "cdm_test_niels2", 3306, "edit", password, NomenclaturalCode.ICBN);
|
| 361 |
try {
|
|
| 362 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.UPDATE); |
|
| 363 |
|
|
| 364 |
ConversationHolder conversation = appCtr.NewConversation(); |
|
| 365 |
|
|
| 366 |
// make the taxon and description elements |
|
| 367 |
Taxon taxon = Taxon.NewInstance(null, null); |
|
| 368 | 312 |
|
| 369 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon); |
|
| 370 |
|
|
| 371 |
UUID taxonDescriptionUuid = taxonDescription.getUuid(); |
|
| 372 |
|
|
| 373 |
Feature featureAnatomy = Feature.ANATOMY(); |
|
| 374 |
|
|
| 375 |
TextData textData = TextData.NewInstance(); |
|
| 376 |
textData.addAnnotation(Annotation.NewInstance(null, null)); |
|
| 377 |
|
|
| 378 |
assertNotNull(textData.getAnnotations().iterator().next().getAnnotatedObj()); |
|
| 379 |
|
|
| 380 |
textData.setFeature(featureAnatomy); |
|
| 381 |
|
|
| 382 |
taxonDescription.addElement(textData); |
|
| 313 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.UPDATE); |
|
| 314 |
|
|
| 315 |
ConversationHolder conversation = appCtr.NewConversation(); |
|
| 316 |
|
|
| 317 |
// make the taxon and description elements |
|
| 318 |
Taxon taxon = Taxon.NewInstance(null, null); |
|
| 383 | 319 |
|
| 384 |
appCtr.getTaxonService().save(taxon); |
|
| 385 |
|
|
| 386 |
conversation.commit(false); |
|
| 387 |
// end of creation phase |
|
| 388 |
|
|
| 389 |
|
|
| 390 |
// load the new taxon in a new conversation to assure that it was loaded into a new session |
|
| 391 |
// if you are willing to blame it on conversations, please rewrite into two methods |
|
| 392 |
// the result will be the same |
|
| 393 |
ConversationHolder newConversation = appCtr.NewConversation(); |
|
| 394 |
DescriptionBase loadedDescription = appCtr.getDescriptionService().load(taxonDescriptionUuid); |
|
| 395 |
|
|
| 396 |
TextData descriptionElement = (TextData) loadedDescription.getElements().iterator().next(); |
|
| 320 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon); |
|
| 397 | 321 |
|
| 398 |
Annotation annotation = descriptionElement.getAnnotations().iterator().next(); |
|
| 399 |
|
|
| 400 |
// this should not be null |
|
| 401 |
assertNotNull(annotation.getAnnotatedObj()); |
|
| 402 |
|
|
| 403 |
|
|
| 404 |
} catch (DataSourceNotFoundException e) {
|
|
| 405 |
// TODO Auto-generated catch block |
|
| 406 |
e.printStackTrace(); |
|
| 407 |
} catch (TermNotFoundException e) {
|
|
| 408 |
// TODO Auto-generated catch block |
|
| 409 |
e.printStackTrace(); |
|
| 410 |
} |
|
| 322 |
UUID taxonDescriptionUuid = taxonDescription.getUuid(); |
|
| 323 |
|
|
| 324 |
Feature featureAnatomy = Feature.ANATOMY(); |
|
| 325 |
|
|
| 326 |
TextData textData = TextData.NewInstance(); |
|
| 327 |
textData.addAnnotation(Annotation.NewInstance(null, null)); |
|
| 328 |
|
|
| 329 |
assertNotNull(textData.getAnnotations().iterator().next().getAnnotatedObj()); |
|
| 330 |
|
|
| 331 |
textData.setFeature(featureAnatomy); |
|
| 332 |
|
|
| 333 |
taxonDescription.addElement(textData); |
|
| 334 |
|
|
| 335 |
appCtr.getTaxonService().save(taxon); |
|
| 336 |
|
|
| 337 |
conversation.commit(false); |
|
| 338 |
// end of creation phase |
|
| 339 |
|
|
| 340 |
|
|
| 341 |
// load the new taxon in a new conversation to assure that it was loaded into a new session |
|
| 342 |
// if you are willing to blame it on conversations, please rewrite into two methods |
|
| 343 |
// the result will be the same |
|
| 344 |
ConversationHolder newConversation = appCtr.NewConversation(); |
|
| 345 |
DescriptionBase loadedDescription = appCtr.getDescriptionService().load(taxonDescriptionUuid); |
|
| 346 |
|
|
| 347 |
TextData descriptionElement = (TextData) loadedDescription.getElements().iterator().next(); |
|
| 348 |
|
|
| 349 |
Annotation annotation = descriptionElement.getAnnotations().iterator().next(); |
|
| 350 |
|
|
| 351 |
// this should not be null |
|
| 352 |
assertNotNull(annotation.getAnnotatedObj()); |
|
| 411 | 353 |
|
| 412 | 354 |
} |
| 413 | 355 |
|
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestLocationServiceImpl.java | ||
|---|---|---|
| 21 | 21 |
import eu.etaxonomy.cdm.api.service.ILocationService; |
| 22 | 22 |
import eu.etaxonomy.cdm.api.service.ILocationService.NamedAreaVocabularyType; |
| 23 | 23 |
import eu.etaxonomy.cdm.database.CdmDataSource; |
| 24 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
|
| 25 | 24 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 26 | 25 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 27 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 28 |
|
|
| 29 | 26 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 30 | 27 |
import eu.etaxonomy.cdm.test.integration.CdmIntegrationTest; |
| 31 | 28 |
|
| ... | ... | |
| 59 | 56 |
} |
| 60 | 57 |
|
| 61 | 58 |
public void testNewDatasourceClass(){
|
| 62 |
try {
|
|
| 63 | 59 |
// String server = "192.168.2.10"; |
| 64 | 60 |
// String database = "cdm_test_andreasM"; |
| 65 | 61 |
// String username = "edit"; |
| 66 | 62 |
// String password = CdmUtils.readInputLine("Password: ");
|
| 67 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE;
|
|
| 63 |
DbSchemaValidation dbSchemaValidation = DbSchemaValidation.CREATE; |
|
| 68 | 64 |
|
| 69 | 65 |
// ICdmDataSource datasource = CdmDataSource.NewMySqlInstance(server, database, username, password); |
| 70 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("test", "sa", "", null);
|
|
| 71 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 72 |
|
|
| 73 |
ConversationHolder conversation = appCtr.NewConversation(); |
|
| 74 |
conversation.bind(); |
|
| 75 |
|
|
| 76 |
Taxon taxon = Taxon.NewInstance(null, null); |
|
| 77 |
|
|
| 66 |
ICdmDataSource datasource = CdmDataSource.NewH2EmbeddedInstance("test", "sa", "", null);
|
|
| 67 |
CdmApplicationController appCtr = CdmApplicationController.NewInstance(datasource, dbSchemaValidation); |
|
| 68 |
|
|
| 69 |
ConversationHolder conversation = appCtr.NewConversation(); |
|
| 70 |
conversation.bind(); |
|
| 71 |
|
|
| 72 |
Taxon taxon = Taxon.NewInstance(null, null); |
|
| 78 | 73 |
|
| 79 |
} catch (DataSourceNotFoundException e) {
|
|
| 80 |
logger.error("datasource error");
|
|
| 81 |
} catch (TermNotFoundException e) {
|
|
| 82 |
logger.error("defined terms not found");
|
|
| 83 |
} |
|
| 84 | 74 |
} |
| 85 | 75 |
} |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/function/TestTaxonFunction.java | ||
|---|---|---|
| 18 | 18 |
import eu.etaxonomy.cdm.database.CdmPersistentDataSource; |
| 19 | 19 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
| 20 | 20 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 21 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 22 | 21 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 23 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
|
| 24 | 22 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 25 | 23 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 26 |
import eu.etaxonomy.cdm.model.reference.IBook; |
|
| 27 | 24 |
import eu.etaxonomy.cdm.model.reference.ReferenceBase; |
| 28 | 25 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
| 29 | 26 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
| ... | ... | |
| 43 | 40 |
cdmApp = CdmApplicationController.NewInstance(dataSource, hbm2dll); |
| 44 | 41 |
} catch (DataSourceNotFoundException e) {
|
| 45 | 42 |
e.printStackTrace(); |
| 46 |
} catch (TermNotFoundException e) {
|
|
| 47 |
logger.error("defined terms not found");
|
|
| 48 |
} |
|
| 43 |
} |
|
| 49 | 44 |
return cdmApp; |
| 50 | 45 |
|
| 51 | 46 |
} |
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/test/integration/CreateDataTestNoUnit.java | ||
|---|---|---|
| 19 | 19 |
import org.apache.log4j.Logger; |
| 20 | 20 |
|
| 21 | 21 |
import eu.etaxonomy.cdm.api.application.CdmApplicationController; |
| 22 |
import eu.etaxonomy.cdm.database.DataSourceNotFoundException; |
|
| 23 | 22 |
import eu.etaxonomy.cdm.database.DbSchemaValidation; |
| 24 | 23 |
import eu.etaxonomy.cdm.database.ICdmDataSource; |
| 25 | 24 |
import eu.etaxonomy.cdm.model.common.Language; |
| 26 |
import eu.etaxonomy.cdm.model.common.init.TermNotFoundException; |
|
| 27 | 25 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 28 | 26 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 29 | 27 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| ... | ... | |
| 51 | 49 |
dbSchemaValidation = DbSchemaValidation.CREATE; |
| 52 | 50 |
} |
| 53 | 51 |
ICdmDataSource dataSource = CreateDataTest.cdm_test(); |
| 54 |
try {
|
|
Also available in: Unified diff
Changed exception handling