cdmlibrary/pom.xml -text
cdmlibrary/src/changes/changes.xml -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationController.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/application/CdmApplicationUtils.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSaveFileSystemXmlApplicationContext.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/application/eclipse/EclipseRcpSavePathMatchingResourcePatternResolver.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/service/AgentServiceImpl.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/service/ServiceBase.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/service/TaxonServiceImpl.java -text
cdmlibrary/src/main/java/eu/etaxonomy/cdm/api/service/TermServiceImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/CdmDataSource.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/DataSourceNotFoundException.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/DatabaseTypeEnum.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/LocalHsqldb.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/AbstractDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/Db2DatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/HSqlDbDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/IDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/MySQLDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/OdbcDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/OracleDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/PostgreSQLDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/SqlServerDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/database/types/SybaseDatabaseType.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/AgentDaoImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/CdmEntityDaoBase.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/CdmGenericDaoImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/DaoBase.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/DefinedTermDaoImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IAgentDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ICdmEntityDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ICdmGenericDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IDefinedTermDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IIdentifiableDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ITermVocabularyDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/ITitledDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/IdentifiableDaoBase.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/common/TermVocabularyDaoImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/name/ITaxonNameDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/name/TaxonNameDaoHibernateImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/reference/IReferenceDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/reference/ReferenceDaoHibernateImpl.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java -text
-cdmlibrary/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/TaxonDaoHibernateImpl.java -text
cdmlibrary/src/main/resources/applicationContext.xml -text
-cdmlibrary/src/main/resources/cdm.datasource.xml -text
cdmlibrary/src/main/resources/log4j.properties -text
-cdmlibrary/src/main/resources/sessionfactory.xml -text
cdmlibrary/src/site/apt/index.apt -text
cdmlibrary/src/site/fml/faq.fml -text
cdmlibrary/src/site/site.xml -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/api/service/TermServiceImplTest.java -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/database/DatabaseEnumTest.java -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/model/DatabaseInitialiser.java -text
-cdmlibrary/src/test/java/eu/etaxonomy/cdm/persistence/dao/common/DefinedTermDaoImplTest.java -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/test/function/Datasource.java -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/test/function/SpringControl.java -text
cdmlibrary/src/test/java/eu/etaxonomy/cdm/test/function/TestDatabase.java -text
</scm>\r
<build>\r
<plugins>
-<!-- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>hibernate3-maven-plugin</artifactId>
- <version>2.0-alpha-2</version>
- <configuration>
- <components>
- <component>
- <name>hbm2cfgxml</name>
- <outputDirectory>src/main/resources</outputDirectory>
- </component>
- </components>
- <componentProperties>
- <drop>true</drop>
- <configurationfile>/src/main/resources/hibernate.cfg.xml</configurationfile>
- </componentProperties>
- </configuration>
- </plugin>-->
<plugin>\r
<artifactId>maven-compiler-plugin</artifactId>\r
<configuration>\r
<target>1.5</target>\r
</configuration>\r
</plugin>\r
- <plugin>\r
- <artifactId>maven-surefire-plugin</artifactId>\r
- <configuration>\r
- <includes>\r
- <include>**/*Test.java</include>\r
- </includes>\r
- <systemProperties>
- <property>
- <name>hibernate.connection.driver_class</name>
- <value>${hibernate.connection.driver_class}</value>
- </property>
- <property>
- <name>hibernate.connection.url</name>
- <value>${hibernate.connection.url}</value>
- </property>
- <property>
- <name>hibernate.connection.username</name>
- <value>${hibernate.connection.username}</value>
- </property>
- <property>
- <name>hibernate.connection.password</name>
- <value>${hibernate.connection.password}</value>
- </property>
- </systemProperties>
- </configuration>\r
- </plugin>\r
- <plugin>\r
- <artifactId>maven-antrun-plugin</artifactId>\r
- <executions>\r
- <execution>\r
- <phase>generate-resources</phase>\r
- <goals>\r
- <goal>run</goal>\r
- </goals>\r
- <configuration>\r
- <tasks />\r
- </configuration>\r
- </execution>\r
- </executions>\r
- </plugin>\r
- <plugin>\r
- <groupId>org.apache.maven.plugins</groupId>\r
- <artifactId>maven-source-plugin</artifactId>\r
- <executions>\r
- <execution>\r
- <id>attach-sources</id>\r
- <phase>verify</phase>\r
- <goals>\r
- <goal>jar</goal>\r
- </goals>\r
- </execution>\r
- </executions>\r
- </plugin>\r
+<!-- <plugin>-->\r
+<!-- <artifactId>maven-surefire-plugin</artifactId>-->\r
+<!-- <configuration>-->\r
+<!-- <includes>-->\r
+<!-- <include>**/*Test.java</include>-->\r
+<!-- </includes>-->\r
+<!-- <systemProperties>-->
+<!-- <property>-->
+<!-- <name>hibernate.connection.driver_class</name>-->
+<!-- <value>${hibernate.connection.driver_class}</value>-->
+<!-- </property>-->
+<!-- <property>-->
+<!-- <name>hibernate.connection.url</name>-->
+<!-- <value>${hibernate.connection.url}</value>-->
+<!-- </property>-->
+<!-- <property>-->
+<!-- <name>hibernate.connection.username</name>-->
+<!-- <value>${hibernate.connection.username}</value>-->
+<!-- </property>-->
+<!-- <property>-->
+<!-- <name>hibernate.connection.password</name>-->
+<!-- <value>${hibernate.connection.password}</value>-->
+<!-- </property>-->
+<!-- </systemProperties>-->
+<!-- </configuration>-->\r
+<!-- </plugin>-->\r
</plugins>\r
</build>\r
<dependencies>\r
<dependency>\r
<groupId>eu.etaxonomy</groupId>\r
- <artifactId>cdmlib-model</artifactId>\r
+ <artifactId>cdmlib-persistence</artifactId>\r
<version>0.4.5</version>\r
</dependency>\r
- <dependency>\r
- <groupId>com.sun.xml.rpc</groupId>\r
- <artifactId>jaxrpc-impl</artifactId>\r
- <version>1.1.3_01</version>\r
- </dependency>\r
+<!-- <dependency>-->\r
+<!-- <groupId>com.sun.xml.rpc</groupId>-->\r
+<!-- <artifactId>jaxrpc-impl</artifactId>-->\r
+<!-- <version>1.1.3_01</version>-->\r
+<!-- </dependency>-->\r
<dependency>\r
<groupId>javax.persistence</groupId>\r
<artifactId>ejb</artifactId>\r
+++ /dev/null
-package eu.etaxonomy.cdm.api.application;\r
-\r
-import static eu.etaxonomy.cdm.common.XmlHelp.getRoot;\r
-\r
-import java.io.File;\r
-import java.io.FileOutputStream;\r
-import java.io.IOException;\r
-import java.io.InputStream;\r
-import java.net.URL;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.jdom.output.Format;\r
-\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.common.XmlHelp;\r
-import eu.etaxonomy.cdm.database.CdmDataSource;\r
-\r
-public class CdmApplicationUtils {\r
- private static final Logger logger = Logger.getLogger(CdmApplicationUtils.class);\r
- \r
- //directory of the resources (configfiles etc.)\r
- static File fileResourceDir;\r
- static final String MUST_EXIST_FILE = "applicationContext.xml";\r
-\r
- /**\r
- * Returns the directory path to the writable resources. (Resources must be copied to this directory, this is automatically done for\r
- * the cdm.datasource.xml, sessionfactory.xml and applicationContext.xml\r
- * @return \r
- */\r
- public static File getWritableResourceDir(){\r
- //compute only once\r
- if (fileResourceDir == null){\r
- //workaround to find out in which environment the library is executed\r
- URL url = CdmUtils.class.getResource("/"+ MUST_EXIST_FILE);\r
- if (url != null){\r
- File file = new File(url.getPath()); \r
- if (file.exists()){\r
- fileResourceDir= file.getParentFile();\r
- }else{\r
- String subPath = File.separator + "cdmResources" ;\r
- file = new File(System.getProperty("user.home") + File.separator + ".cdmLibrary" + File.separator + "writableResources" );\r
- //file = new File(System.getProperty("user.dir") + subPath ); //does not work in plugin-environmen (uses eclipse installation directory)\r
- \r
- file.mkdirs();\r
- copyResources(file);\r
- fileResourceDir = file;\r
- }\r
- }\r
- logger.debug("Resource directory: " + (fileResourceDir == null?"null":fileResourceDir.getAbsolutePath())); \r
- }\r
- return fileResourceDir;\r
- }\r
- \r
- static private void copyResources(File directory){\r
- copyResource(directory, CdmDataSource.DATASOURCE_FILE_NAME);\r
- copyResource(directory, CdmDataSource.SESSION_FACTORY_FILE);\r
- copyResource(directory, CdmDataSource.APPLICATION_CONTEXT_FILE_NAME);\r
- }\r
- \r
- \r
- /**\r
- * Copies a file from the classpath resource (e.g. jar-File) to the resources directory in the file system (get\r
- * @param directory\r
- * @param resourceFileName\r
- */\r
- static private void copyResource(File directory, String resourceFileName){\r
- try {\r
- File fileToCopy = new File(directory + File.separator + resourceFileName);\r
- if (fileToCopy.createNewFile()){\r
- InputStream isDataSource = CdmUtils.class.getResourceAsStream("/"+ resourceFileName);\r
- XmlHelp.saveToXml(getRoot(isDataSource).getDocument(), new FileOutputStream(fileToCopy), Format.getPrettyFormat());\r
- }\r
- } catch (IOException e) {\r
- logger.error("File " + resourceFileName + " + could not be created");\r
- }\r
- }\r
- \r
- \r
- /**\r
- * Returns the string to the applicationContext.xml to be used.\r
- * @return\r
- */\r
- public static String getApplicationContextString(){\r
- String result = "file:" + CdmApplicationUtils.getWritableResourceDir() + File.separator + CdmDataSource.APPLICATION_CONTEXT_FILE_NAME;\r
- return result;\r
- }\r
- \r
-\r
-}\r
*/\r
package eu.etaxonomy.cdm.api.service;\r
\r
-import java.util.Iterator;\r
-import java.util.Properties;\r
-\r
-import javax.naming.NamingException;\r
-\r
import org.apache.log4j.Logger;\r
-import org.hibernate.Session;\r
import org.hibernate.SessionFactory;\r
-import org.hibernate.cfg.AnnotationConfiguration;\r
-import org.hibernate.cfg.Configuration;\r
-import org.hibernate.impl.SessionFactoryImpl;\r
import org.springframework.beans.factory.annotation.Autowired;\r
import org.springframework.context.ApplicationContext;\r
import org.springframework.context.ApplicationContextAware;\r
-import org.springframework.dao.DataAccessResourceFailureException;\r
import org.springframework.jdbc.datasource.DriverManagerDataSource;\r
-import org.springframework.orm.hibernate3.HibernateTemplate;\r
-import org.springframework.orm.hibernate3.LocalSessionFactoryBean;\r
import org.springframework.orm.hibernate3.SessionFactoryUtils;\r
-import org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean;\r
-import org.springframework.orm.hibernate3.support.HibernateDaoSupport;\r
import org.springframework.stereotype.Service;\r
import org.springframework.transaction.annotation.Transactional;\r
\r
import eu.etaxonomy.cdm.api.application.CdmApplicationController;\r
import eu.etaxonomy.cdm.database.CdmDataSource;\r
import eu.etaxonomy.cdm.database.DatabaseTypeEnum;\r
-import eu.etaxonomy.cdm.database.LocalHsqldb;\r
-import eu.etaxonomy.cdm.database.types.MySQLDatabaseType;\r
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
-import eu.etaxonomy.cdm.model.common.Language;\r
-import eu.etaxonomy.cdm.model.location.Continent;\r
-import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;\r
-import eu.etaxonomy.cdm.model.name.HybridRelationshipType;\r
-import eu.etaxonomy.cdm.model.name.NameRelationshipType;\r
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;\r
-import eu.etaxonomy.cdm.model.name.Rank;\r
-import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;\r
-import eu.etaxonomy.cdm.model.taxon.ConceptRelationshipType;\r
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;\r
+\r
+\r
\r
/**\r
* @author a.mueller\r
+++ /dev/null
-package eu.etaxonomy.cdm.database;\r
-\r
-import java.io.File;\r
-import java.io.FileInputStream;\r
-import java.io.FileNotFoundException;\r
-import java.io.FileOutputStream;\r
-import java.io.FilenameFilter;\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.jdom.Attribute;\r
-import org.jdom.Document;\r
-import org.jdom.Element;\r
-import org.jdom.output.Format;\r
-import org.springframework.jdbc.datasource.DriverManagerDataSource;\r
-\r
-import eu.etaxonomy.cdm.api.application.CdmApplicationUtils;\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-import eu.etaxonomy.cdm.common.XmlHelp;\r
-\r
-import static eu.etaxonomy.cdm.common.XmlHelp.getFirstAttributedChild;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.getOrAddChild;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.getRoot;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.insertXmlBean;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.insertXmlRefProperty;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.insertXmlValueProperty;\r
-import static eu.etaxonomy.cdm.common.XmlHelp.saveToXml;\r
-\r
-\r
-/**\r
- * class to access an CdmDataSource\r
- */\r
-public class CdmDataSource {\r
- private static final Logger logger = Logger.getLogger(CdmDataSource.class);\r
- \r
- public static final String DATASOURCE_BEAN_POSTFIX = "DataSource";\r
- public static final String SESSION_FACTORY_FILE = "sessionfactory.xml";\r
- public final static String DATASOURCE_FILE_NAME = "cdm.datasource.xml";\r
- public final static String APPLICATION_CONTEXT_FILE_NAME = "applicationContext.xml";\r
- private final static Format format = Format.getPrettyFormat(); \r
- \r
- //name\r
- protected String dataSourceName;\r
-\r
- \r
- /**\r
- * Returns the default CdmDataSource\r
- * @return the default CdmDataSource\r
- */\r
- public final static CdmDataSource NewDefaultInstance(){\r
- try {\r
- return NewInstance("default");\r
- } catch (DataSourceNotFoundException e) {\r
- logger.error("Default datasource does not exist in config file");\r
- return null;\r
- }\r
- }\r
- \r
- \r
- /**\r
- * Returns the default CdmDataSource\r
- * @return the default CdmDataSource\r
- */\r
- public final static CdmDataSource NewLocalHsqlInstance(){\r
- try {\r
- return NewInstance("localDefaultHsql");\r
- } catch (DataSourceNotFoundException e) {\r
- logger.error("Local datasource does not exist in config file");\r
- return null;\r
- }\r
- }\r
- \r
- /**\r
- * Returns the CdmDataSource named by strDataSource\r
- * @param strDataSource\r
- * @return\r
- */\r
- public final static CdmDataSource NewInstance(String dataSourceName) \r
- throws DataSourceNotFoundException{\r
- if (exists(dataSourceName)){\r
- return new CdmDataSource(dataSourceName);\r
- }else{\r
- throw new DataSourceNotFoundException("Datasource not found: " + dataSourceName);\r
- }\r
- }\r
-\r
- /**\r
- * Private Constructor. Use NewXXX factory methods for creating a new instance of CdmDataSource!\r
- * @param strDataSource\r
- */\r
- private CdmDataSource(String strDataSource){\r
- dataSourceName = strDataSource;\r
- }\r
- \r
- /**\r
- * Returns the name of the bean.\r
- * @return\r
- */\r
- public String getName(){\r
- return dataSourceName;\r
- }\r
- \r
- \r
- /**\r
- * Returns the name of the bean Element in the xml config file.\r
- * @return bean name\r
- */\r
- private static String getBeanName(String name){\r
- return name == null? null : name + DATASOURCE_BEAN_POSTFIX;\r
- }\r
-\r
-\r
- \r
- /**\r
- * Updates the session factory config file for using this database.\r
- * Writes the datasource property and the dialect property into the session factory.\r
- * @param hibernateHbm2ddlAuto value for the hibernate property hibernate.hbm2dll.auto . If null the properties is not changed. Possible values are 'validate', 'create', 'update' and 'create-drop'.\r
- * @return true if successful.\r
- */\r
- public boolean updateSessionFactory(String hibernateHbm2ddlAuto){\r
- Element root = getRoot(getSessionFactoryInputStream());\r
- if (root == null){\r
- return false;\r
- }\r
- //get sessionFactory bean\r
- Element sessionFactoryBean = getFirstAttributedChild(root, "bean", "id", "sessionFactory");\r
- //sessionFactory must exist \r
- if (sessionFactoryBean == null){\r
- return false;\r
- }\r
- \r
- //set dataSource property\r
- Element dataSourceProperty = getFirstAttributedChild(sessionFactoryBean, "property", "name", "dataSource");\r
- if (dataSourceProperty == null){\r
- dataSourceProperty = insertXmlRefProperty(sessionFactoryBean, "dataSource", getBeanName(this.dataSourceName));\r
- }\r
- Attribute attrRef = dataSourceProperty.getAttribute("ref");\r
- if (attrRef == null){\r
- dataSourceProperty.setAttribute("ref", getBeanName(this.dataSourceName));\r
- }else{\r
- attrRef.setValue(getBeanName(this.dataSourceName));\r
- }\r
- \r
- //set dialect\r
- Element elHibernateProperties = getOrAddChild(sessionFactoryBean, "property", "name", "hibernateProperties");\r
- Element props = getOrAddChild(elHibernateProperties, "props", null, null);\r
- Element elDialectProp = getOrAddChild(props, "prop", "key", "hibernate.dialect");\r
- elDialectProp.setText(this.getDatabaseType().getHibernateDialect());\r
- \r
- //set hibernateHbm2ddlAuto\r
- if (hibernateHbm2ddlAuto != null){\r
- if (hibernateHbm2ddlAuto != "validate" && hibernateHbm2ddlAuto != "create" && hibernateHbm2ddlAuto != "update " && hibernateHbm2ddlAuto != "create-drop" ){\r
- logger.warn("Invalid value " + hibernateHbm2ddlAuto + " for property hibernate.hbm2ddl.auto");\r
- }\r
- Element elHbm2ddlAutoProp = getOrAddChild(props, "prop", "key", "hibernate.hbm2ddl.auto");\r
- elHbm2ddlAutoProp.setText(hibernateHbm2ddlAuto);\r
- }\r
- \r
- //save\r
- saveToXml(root.getDocument(), getSessionFactoryOutputStream() , format );\r
- return true;\r
- }\r
-\r
- \r
- /**\r
- * Returns the database type of the data source. \r
- * @return the database type of the data source. Null if the bean or the driver class property does not exist or the driver class is unknown.\r
- */\r
- public DatabaseTypeEnum getDatabaseType(){\r
- Element bean = getDatasourceBeanXml(this.dataSourceName);\r
- if (bean == null){\r
- return null;\r
- }else{\r
- Element driverProp = XmlHelp.getFirstAttributedChild(bean, "property", "name", "driverClassName");\r
- if (driverProp == null){\r
- logger.warn("Unknown property driverClass");\r
- return null;\r
- }else{\r
- String strDriverClass = driverProp.getAttributeValue("value");\r
- DatabaseTypeEnum dbType = DatabaseTypeEnum.getDatabaseEnumByDriverClass(strDriverClass);\r
- return dbType;\r
- }\r
- }\r
- }\r
- \r
- /**\r
- * Tests existing of the datsource in the according config file.\r
- * @return true if a datasource with the given name exists in the according datasource config file.\r
- */\r
- public static boolean exists(String strDataSourceName){\r
- Element bean = getDatasourceBeanXml(strDataSourceName);\r
- return (bean != null);\r
- }\r
-\r
- \r
- /**\r
- * Saves or updates the datasource to the datasource config file.\r
- * Uses default port.\r
- * @param strDataSourceName name of the datasource (without postfix DataSource)\r
- * @param databaseTypeEnum\r
- * @param server\r
- * @param database\r
- * @param username\r
- * @param password\r
- * @return the CdmDataSource, null if not successful.\r
- */\r
- public static CdmDataSource save(String strDataSourceName, DatabaseTypeEnum databaseTypeEnum, String server, String database, \r
- String username, String password){\r
- return save(strDataSourceName, databaseTypeEnum, server, database, \r
- databaseTypeEnum.getDefaultPort(), username, password);\r
- }\r
- \r
- /**\r
- * Saves or updates the datasource to the datasource config file.\r
- * @param strDataSourceName name of the datasource (without postfix DataSource)\r
- * @param databaseTypeEnum\r
- * @param server\r
- * @param database\r
- * @param port\r
- * @param username\r
- * @param password\r
- * @return the CdmDataSource, null if not successful.\r
- */\r
- public static CdmDataSource save(String strDataSourceName, DatabaseTypeEnum databaseTypeEnum, String server, String database, \r
- int port, String username, String password){\r
- Class<? extends DriverManagerDataSource> driverManagerDataSource = DriverManagerDataSource.class;\r
- return save(strDataSourceName, databaseTypeEnum, server, database, port, username, password, driverManagerDataSource, null, null, null, null, null);\r
- }\r
- \r
- \r
- public static CdmDataSource saveLocalHsqlDb(String strDataSourceName, String databasePath, String databaseName, String username, String password){\r
- DatabaseTypeEnum databaseTypeEnum = DatabaseTypeEnum.HSqlDb;\r
- Class<? extends DriverManagerDataSource> driverManagerDataSource = LocalHsqldb.class;\r
- String server = "localhost";\r
- int port = databaseTypeEnum.getDefaultPort();\r
- return save(strDataSourceName, databaseTypeEnum, server, databaseName, port, username, password, driverManagerDataSource, "init", "destroy", true, true, databasePath);\r
- }\r
- \r
- //\r
- private static CdmDataSource save(String strDataSourceName, \r
- DatabaseTypeEnum databaseTypeEnum, \r
- String server, \r
- String database, \r
- int port, \r
- String username, \r
- String password, \r
- Class<? extends DriverManagerDataSource> driverManagerDataSource,\r
- String initMethod,\r
- String destroyMethod,\r
- Boolean startSilent,\r
- Boolean startServer, \r
- String databasePath\r
- ){\r
- //root\r
- Element root = getRoot(getDataSourceInputStream());\r
- if (root == null){\r
- return null;\r
- }\r
- //bean\r
- Element bean = XmlHelp.getFirstAttributedChild(root, "bean", "id", getBeanName(strDataSourceName));\r
- if (bean != null){\r
- bean.detach(); //delete old version if necessary\r
- }\r
- bean = insertXmlBean(root, getBeanName(strDataSourceName), driverManagerDataSource.getName());\r
- //attributes\r
- bean.setAttribute("lazy-init", "true");\r
- if (initMethod != null) {bean.setAttribute("init-method", initMethod);}\r
- if (destroyMethod != null) {bean.setAttribute("destroy-method", destroyMethod);}\r
- \r
- //set properties\r
- insertXmlValueProperty(bean, "driverClassName", databaseTypeEnum.getDriverClassName());\r
- insertXmlValueProperty(bean, "url", databaseTypeEnum.getConnectionString(server, database, port));\r
- if (username != null) {insertXmlValueProperty(bean, "username", username );}\r
- if (startSilent != null) {insertXmlValueProperty(bean, "startSilent", startSilent.toString() );}\r
- if (startServer != null) {insertXmlValueProperty(bean, "startServer", startServer.toString() );}\r
- if (startServer != null) {insertXmlValueProperty(bean, "databasePath", databasePath );}\r
- \r
- //save\r
- saveToXml(root.getDocument(), getResourceDirectory(), DATASOURCE_FILE_NAME, format );\r
- try {\r
- return NewInstance(strDataSourceName) ;\r
- } catch (DataSourceNotFoundException e) {\r
- logger.error("Error when saving datasource");\r
- return null;\r
- }\r
- }\r
- \r
- \r
- /**\r
- * Deletes a dataSource\r
- * @param dataSource\r
- */\r
- public static void delete (CdmDataSource dataSource){\r
- Element bean = getDatasourceBeanXml(dataSource.getName());\r
- if (bean != null){\r
- Document doc = bean.getDocument();\r
- bean.detach();\r
- saveToXml(doc, getDataSourceOutputStream(), format );\r
- }\r
- }\r
- \r
- \r
- /**\r
- * Returns a list of all datasources stored in the datasource config file\r
- * @return all existing data sources\r
- */\r
- static public List<CdmDataSource> getAllDataSources(){\r
- List<CdmDataSource> dataSources = new ArrayList<CdmDataSource>();\r
- \r
- Element root = getRoot(getDataSourceInputStream());\r
- if (root == null){\r
- return null;\r
- }else{\r
- List<Element> lsChildren = root.getChildren("bean", root.getNamespace());\r
- \r
- for (Element elBean : lsChildren){\r
- String strId = elBean.getAttributeValue("id");\r
- if (strId != null && strId.endsWith(DATASOURCE_BEAN_POSTFIX)){\r
- strId = strId.replace(DATASOURCE_BEAN_POSTFIX, "");\r
- dataSources.add(new CdmDataSource(strId));\r
- }\r
- }\r
- }\r
- return dataSources;\r
- }\r
- \r
- \r
- /* (non-Javadoc)\r
- * @see java.lang.Object#toString()\r
- */\r
- public String toString(){\r
- if (this.dataSourceName != null){\r
- return dataSourceName;\r
- }else{\r
- return null;\r
- }\r
- }\r
-\r
-\r
- \r
- /**\r
- * Returns the datasource config file input stream.\r
- * @return data source config file input stream\r
- */\r
- static protected FileInputStream getDataSourceInputStream(){\r
- String dir = getResourceDirectory();\r
- File file = new File(dir + File.separator + DATASOURCE_FILE_NAME);\r
- return fileInputStream(file);\r
- }\r
- \r
- \r
- /**\r
- * Returns the datasource config file outputStream.\r
- * @return data source config file outputStream\r
- */\r
- static protected FileOutputStream getDataSourceOutputStream(){\r
- String dir = getResourceDirectory();\r
- File file = new File(dir + File.separator + DATASOURCE_FILE_NAME);\r
- return fileOutputStream(file);\r
- }\r
-\r
- /**\r
- * Returns the jdom Element representing the data source bean in the config file.\r
- * @return\r
- */\r
- private static Element getDatasourceBeanXml(String strDataSourceName){\r
- Element root = getRoot(getDataSourceInputStream());\r
- if (root == null){\r
- return null;\r
- }else{\r
- Element xmlBean = XmlHelp.getFirstAttributedChild(root, "bean", "id", getBeanName(strDataSourceName));\r
- if (xmlBean == null){logger.warn("Unknown Element 'bean' ");};\r
- return xmlBean;\r
- }\r
- }\r
- \r
- // returns the directory containing the resources \r
- private static String getResourceDirectory(){\r
- File f = CdmApplicationUtils.getWritableResourceDir();\r
- return f.getPath();\r
- }\r
- \r
- /**\r
- * Returns the session factory config file input stream.\r
- * @return session factory config file\r
- */\r
- private FileInputStream getSessionFactoryInputStream(){\r
- String dir = getResourceDirectory();\r
- File file = new File(dir + File.separator + SESSION_FACTORY_FILE);\r
- return fileInputStream(file);\r
- }\r
- \r
- /**\r
- * Returns the session factory output stream.\r
- * @return \r
- */\r
- private FileOutputStream getSessionFactoryOutputStream(){\r
- String dir = getResourceDirectory();\r
- File file = new File(dir + File.separator + SESSION_FACTORY_FILE);\r
- return fileOutputStream(file);\r
- }\r
- \r
- \r
- static private FileInputStream fileInputStream(File file){\r
- try {\r
- FileInputStream fis = new FileInputStream(file);\r
- return fis;\r
- } catch (FileNotFoundException e) {\r
- logger.warn("File " + file == null?"null":file.getAbsolutePath() + " does not exist in the file system");\r
- return null;\r
- }\r
- }\r
- \r
- static private FileOutputStream fileOutputStream(File file){\r
- try {\r
- FileOutputStream fos = new FileOutputStream(file);\r
- return fos;\r
- } catch (FileNotFoundException e) {\r
- logger.warn("File " + (file == null?"null":file.getAbsolutePath()) + " does not exist in the file system");\r
- return null;\r
- }\r
- }\r
- \r
- \r
- /**\r
- * Filter class to define datasource file format\r
- */\r
- private static class DataSourceFileNameFilter implements FilenameFilter{\r
- public boolean accept(File dir, String name) {\r
- return (name.endsWith(DATASOURCE_FILE_NAME));\r
- }\r
- }\r
-}
\ No newline at end of file
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class DataSourceNotFoundException extends Exception {\r
-\r
-\r
- /**\r
- * @param message\r
- */\r
- public DataSourceNotFoundException() {\r
- super();\r
- }\r
- \r
- /**\r
- * @param message\r
- */\r
- public DataSourceNotFoundException(String message) {\r
- super(message);\r
- }\r
-\r
- /**\r
- * @param cause\r
- */\r
- public DataSourceNotFoundException(Throwable cause) {\r
- super(cause);\r
- }\r
-\r
- /**\r
- * @param message\r
- * @param cause\r
- */\r
- public DataSourceNotFoundException(String message, Throwable cause) {\r
- super(message, cause);\r
- }\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database;\r
-\r
-import java.util.ArrayList;\r
-import java.util.List;\r
-\r
-import org.apache.log4j.Logger;\r
-\r
-import eu.etaxonomy.cdm.database.types.HSqlDbDatabaseType;\r
-import eu.etaxonomy.cdm.database.types.IDatabaseType;\r
-import eu.etaxonomy.cdm.database.types.MySQLDatabaseType;\r
-import eu.etaxonomy.cdm.database.types.OdbcDatabaseType;\r
-import eu.etaxonomy.cdm.database.types.PostgreSQLDatabaseType;\r
-import eu.etaxonomy.cdm.database.types.SqlServerDatabaseType;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public enum DatabaseTypeEnum {\r
- HSqlDb(1),\r
- MySQL(2),\r
- ODBC(3),\r
- PostgreSQL(4),\r
- SqlServer(5)\r
- ;\r
-\r
- /**\r
- * Constructor\r
- * @param i\r
- */\r
- private DatabaseTypeEnum(int i) {\r
- switch(i)\r
- {\r
- case 1:\r
- this.dbType = new HSqlDbDatabaseType(); break;\r
- case 2:\r
- this.dbType = new MySQLDatabaseType(); break;\r
- case 3:\r
- this.dbType = new OdbcDatabaseType(); break;\r
- case 4:\r
- this.dbType = new PostgreSQLDatabaseType(); break;\r
- case 5:\r
- this.dbType = new SqlServerDatabaseType(); break;\r
- default:\r
- //TODO Exception\r
- }\r
- }\r
- \r
- //Logger\r
- private static final Logger logger = Logger.getLogger(DatabaseTypeEnum.class);\r
- protected IDatabaseType dbType;\r
- \r
- \r
- /**\r
- * @return\r
- */\r
- public String getName(){\r
- return dbType.getName();\r
- }\r
- \r
- /**\r
- * @return\r
- */\r
- public String getDriverClassName(){\r
- return dbType.getClassString();\r
- }\r
- \r
- /**\r
- * @return\r
- */\r
- public String getUrl(){\r
- return dbType.getUrlString();\r
- }\r
- \r
- /**\r
- * @return\r
- */\r
- public String getHibernateDialect(){\r
- return dbType.getHibernateDialect();\r
- }\r
- \r
- /**\r
- * @return\r
- */\r
- public int getDefaultPort(){\r
- return dbType.getDefaultPort();\r
- }\r
-\r
- /**\r
- * returns the connection string \r
- * @param server the server, e.g. IP-Address\r
- * @param database the database name on the server (e.g. "testDB")\r
- * @param port the port number\r
- * @return the connection string\r
- */\r
- public String getConnectionString(String server, String database, int port){\r
- String result = dbType.getConnectionString(server, database, port);\r
- logger.debug("Connection String: " + result); \r
- return result;\r
- }\r
- \r
-\r
- /**\r
- * returns the connection string (using the default port)\r
- * @param server the server, e.g. IP-Address\r
- * @param database the database name on the server (e.g. "testDB")\r
- * @return the connection string\r
- */\r
- public String getConnectionString(String server, String database){\r
- String result = dbType.getConnectionString(server, database);\r
- logger.debug("Connection String: " + result); \r
- return result;\r
- }\r
- \r
- /**\r
- * Returns a List of all available DatabaseEnums.\r
- * @return List of DatabaseEnums\r
- */\r
- public static List<DatabaseTypeEnum> getAllTypes(){\r
- List<DatabaseTypeEnum> result = new ArrayList<DatabaseTypeEnum>();\r
- for (DatabaseTypeEnum dbEnum : DatabaseTypeEnum.values()){\r
- result.add(dbEnum);\r
- }\r
- return result;\r
- }\r
-\r
- /**\r
- * Returns the DatabaseTypeEnum to a given DriverClass\r
- * @param strDriverClass\r
- * @return the according DatabaseTypeEnum. Null if the driver class does not exist.\r
- */\r
- public static DatabaseTypeEnum getDatabaseEnumByDriverClass(String strDriverClass){\r
- for (DatabaseTypeEnum dbEnum : DatabaseTypeEnum.values()){\r
- if (dbEnum.getDriverClassName().equals(strDriverClass)){\r
- return dbEnum;\r
- }\r
- }\r
- logger.warn("Unknown driver class " + strDriverClass==null ? "null" : strDriverClass);\r
- return null;\r
- }\r
- \r
-}\r
-\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database;\r
-\r
-import java.io.File;\r
-import java.sql.Connection;\r
-import java.sql.Driver;\r
-import java.sql.DriverManager;\r
-import java.sql.SQLException;\r
-import java.util.Properties;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.hsqldb.Server;\r
-import org.springframework.jdbc.CannotGetJdbcConnectionException;\r
-import org.springframework.jdbc.datasource.DriverManagerDataSource;\r
-\r
-import eu.etaxonomy.cdm.api.application.CdmApplicationUtils;\r
-import eu.etaxonomy.cdm.common.CdmUtils;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-\r
-public class LocalHsqldb extends DriverManagerDataSource {\r
- private static final Logger logger = Logger.getLogger(LocalHsqldb.class);\r
- \r
- private String sep = System.getProperty("file.separator");\r
- \r
- /** url without database name */\r
- protected String pureUrl = "jdbc:hsqldb:hsql://localhost/";\r
- /** database name */\r
- protected String dbName = "cdm";\r
- /** path, where database should be stored in the file system */\r
- protected String databasePath = getDefaultPath();\r
- /** Server instance */\r
- protected Server hsqldbServer;\r
- /** if true starts server on init() */\r
- protected boolean isStartServer = true;\r
- /** makes the Server silent (no messages) */\r
- protected boolean isSilent = true;\r
- /** default driver class name */\r
- protected String DEFAULT_DRIVER_CLASS_NAME = "org.hsqldb.jdbcDriver";\r
- \r
- \r
- /**\r
- * \r
- */\r
- public LocalHsqldb() {\r
- setDriverClassName(DEFAULT_DRIVER_CLASS_NAME);\r
- setComposedUrl();\r
- }\r
-\r
- /**\r
- * @param url\r
- * @throws CannotGetJdbcConnectionException\r
- */\r
- public LocalHsqldb(String url) throws CannotGetJdbcConnectionException {\r
- super(url);\r
- setDriverClassName(DEFAULT_DRIVER_CLASS_NAME);\r
- }\r
-\r
- /**\r
- * @param url\r
- * @param username\r
- * @param password\r
- * @throws CannotGetJdbcConnectionException\r
- */\r
- public LocalHsqldb(String url, String username, String password)\r
- throws CannotGetJdbcConnectionException {\r
- super(url, username, password);\r
- this.setDriverClassName(DEFAULT_DRIVER_CLASS_NAME);\r
- }\r
-\r
- /**\r
- * @param driverClassName\r
- * @param url\r
- * @param username\r
- * @param password\r
- * @throws CannotGetJdbcConnectionException\r
- */\r
- public LocalHsqldb(String driverClassName, String url, String username,\r
- String password) throws CannotGetJdbcConnectionException {\r
- super(driverClassName, url, username, password);\r
- }\r
-\r
- public void init(){\r
- if (isStartServer){\r
- this.startHsqldbServer();\r
- }\r
- }\r
- \r
- public void destroy(){\r
- this.stopHsqldbServer();\r
- }\r
- \r
-\r
- /* (non-Javadoc)\r
- * @see org.springframework.jdbc.datasource.DriverManagerDataSource#getUrl()\r
- */\r
- @Override\r
- public String getUrl() {\r
- return super.getUrl();\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see org.springframework.jdbc.datasource.DriverManagerDataSource#setUrl(java.lang.String)\r
- */\r
- @Override\r
- public void setUrl(String url) {\r
- super.setUrl(url);\r
- }\r
-\r
- /**\r
- * @return the pureUrl\r
- */\r
- public String getPureUrl() {\r
- return pureUrl;\r
- }\r
-\r
- /**\r
- * @param pureUrl the pureUrl to set\r
- */\r
- public void setPureUrl(String pureUrl) {\r
- this.pureUrl = pureUrl;\r
- if (dbName != null){\r
- setComposedUrl();\r
- }\r
- }\r
-\r
- /**\r
- * @return the dbName\r
- */\r
- public String getDbName() {\r
- return dbName;\r
- }\r
-\r
- /**\r
- * @param dbName the dbName to set\r
- */\r
- public void setDbName(String dbName) {\r
- this.dbName = dbName;\r
- if (pureUrl != null){\r
- setComposedUrl();\r
- }\r
- }\r
- \r
- private void setComposedUrl(){\r
- setUrl(getPureUrl() + getDbName());\r
- }\r
- \r
- //checks if hsqldb-server is started, if not it will be started \r
- private void startHsqldbServer(){\r
- try {\r
- Driver driver = DriverManager.getDriver(getUrl());\r
- Properties prop = new Properties();\r
- prop.setProperty("user", this.getUsername());\r
- prop.setProperty("password", this.getPassword());\r
- Connection con = driver.connect(getUrl(), prop);\r
- if (con == null) {\r
- logger.warn("Connection to URL " + getUrl() + " could not be established");\r
- throw new SQLException();\r
- }\r
- } catch (SQLException e) {\r
- try {\r
- //server is probably not runing on the url (or login is wrong !!)\r
- logger.warn("Start HsqldbServer"); //TODO make it .info\r
- hsqldbServer = new Server();\r
- hsqldbServer.setSilent(this.isSilent);\r
- for (int i = 0; i < 10; i++){\r
- logger.info("DatabaseName " + i + ": " + hsqldbServer.getDatabaseName(i, true));\r
- logger.info("DatabaseName " + i + ": " + hsqldbServer.getDatabaseName(i, false));\r
- logger.info("DatabasePath " + i + ": " + hsqldbServer.getDatabasePath(i, true));\r
- logger.info("DatabasePath " + i + ": " + hsqldbServer.getDatabasePath(i, false));\r
- logger.info("DatabaseType " + i + ": " + hsqldbServer.getDatabaseType(i));\r
- }\r
- hsqldbServer.setDatabaseName(0, getDbName());\r
- hsqldbServer.setDatabasePath(0, getDatabasePath());\r
- hsqldbServer.start();\r
- hsqldbServer.checkRunning(true);\r
- } catch (RuntimeException e1) {\r
- logger.error("Local hsqlServer could not be started or connection to existing server could not be established.");\r
- }\r
- }\r
- }\r
- \r
- \r
- /**\r
- * stops the Hsqldb Server\r
- */\r
- private void stopHsqldbServer(){\r
- if (hsqldbServer != null){\r
- logger.info("stop HsqldbServer");\r
- hsqldbServer.stop();\r
- }\r
- }\r
- \r
- private static final String getDefaultPath(){\r
- //String path = System.getProperty("user.dir");\r
- File path = CdmApplicationUtils.getWritableResourceDir();\r
- String supPath = File.separator + "db" + File.separator + "LocalHsqldb"; \r
- return path + supPath;\r
- }\r
-\r
- /**\r
- * @return the dbPath\r
- */\r
- public String getDatabasePath() {\r
- return databasePath;\r
- }\r
-\r
- /**\r
- * @param dbPath the dbPath to set\r
- */\r
- public void setDatabasePath(String databasePath) {\r
- if (databasePath.endsWith(sep)){\r
- databasePath = databasePath + "localCdm";\r
- }\r
- this.databasePath = databasePath;\r
- }\r
-\r
- /**\r
- * @return the isStartServer\r
- */\r
- public boolean isStartServer() {\r
- return isStartServer;\r
- }\r
-\r
- /**\r
- * @param isStartServer the isStartServer to set\r
- */\r
- public void setStartServer(boolean isStartServer) {\r
- this.isStartServer = isStartServer;\r
- }\r
-\r
- /**\r
- * @return the isSilent\r
- */\r
- public boolean isSilent() {\r
- return isSilent;\r
- }\r
-\r
- /**\r
- * @param isSilent the isSilent to set\r
- */\r
- public void setSilent(boolean isSilent) {\r
- if (this.hsqldbServer != null){\r
- this.hsqldbServer.setSilent(isSilent);\r
- }\r
- this.isSilent = isSilent;\r
- }\r
- \r
- \r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-abstract class AbstractDatabaseType implements IDatabaseType {\r
- //typeName\r
- private String typeName;\r
- //String for DriverClass\r
- private String classString;\r
- //url\r
- private String urlString;\r
- //defaultPort\r
- private int defaultPort;\r
- //hibernate dialect\r
- private String hibernateDialect;\r
- \r
- //init\r
- protected void init(String typeName, String classString,\r
- String urlString, int defaultPort, String hibernateDialect) {\r
- this.typeName = typeName;\r
- this.classString = classString;\r
- this.urlString = urlString;\r
- this.defaultPort = defaultPort;\r
- this.hibernateDialect = hibernateDialect;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getName()\r
- */\r
- public String getName(){\r
- return typeName;\r
- }\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getClassString()\r
- */\r
- public String getClassString(){\r
- return classString;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getUrlString()\r
- */\r
- public String getUrlString(){\r
- return urlString;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getDefaultPort()\r
- */\r
- public int getDefaultPort(){\r
- return defaultPort;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getHibernateDialect()\r
- */\r
- public String getHibernateDialect(){\r
- return "org.hibernate.dialect." + hibernateDialect;\r
- }\r
- \r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.database.IDatabaseType#getConnectionString(java.lang.String, java.lang.String)\r
- */\r
- public String getConnectionString(String server, String database){\r
- return getConnectionString(server, database, defaultPort);\r
- } \r
- \r
- \r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * !! UNTESTED !!\r
- * Db2 in use with Universal Driver (db2jcc.jar)\r
- * \r
- * @author a.mueller\r
- *\r
- */\r
-public class Db2DatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "DB2 Universal";\r
- //class\r
- protected String classString = "com.ibm.db2.jcc.DB2Driver"; \r
- //protected String classString = "COM.ibm.db2.jdbc.app.DB2Driver";\r
- //protected String classString = "COM.ibm.db2.jdbc.net.DB2Driver";\r
- \r
- //url\r
- protected String urlString = "jdbc:db2://";\r
- //port\r
- private int defaultPort = 50000;\r
- //hibernate dialect\r
- private String hibernateDialect = "DB2Dialect";\r
-\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + database;\r
- } \r
- \r
- public Db2DatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class HSqlDbDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- private String typeName = "Hypersonic SQL DB (HSqlDb)";\r
- \r
- //class\r
- private String classString = "org.hsqldb.jdbcDriver";\r
- \r
- //url\r
- private String urlString = "jdbc:hsqldb:hsql://";\r
- \r
- //port\r
- private int defaultPort = 9001;\r
- \r
- //hibernate dialect\r
- private String hibernateDialect = "HSQLDialect";\r
- \r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + "/" + database;\r
- }\r
- \r
- \r
- public HSqlDbDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-package eu.etaxonomy.cdm.database.types;\r
-\r
-public interface IDatabaseType {\r
- /**\r
- * @return\r
- */\r
- public String getName();\r
- /**\r
- * @return\r
- */\r
- public String getClassString();\r
- /**\r
- * @return\r
- */\r
- public String getUrlString();\r
- /**\r
- * @return\r
- */\r
- public int getDefaultPort();\r
- \r
- /**\r
- * @return\r
- */\r
- public String getHibernateDialect();\r
- \r
- /**\r
- * Returns the connection String for the given parameters\r
- * @param server the server, e.g. IP-Address\r
- * @param database the database name on the server (e.g. "testDB")\r
- * @param port the port number\r
- * @return the connection String\r
- */\r
- public String getConnectionString(String server, String database, int port);\r
- \r
- /**\r
- * Returns the connection String for the given parameters, using default port\r
- * @param server the server, e.g. IP-Address\r
- * @param database the database name on the server (e.g. "testDB")\r
- * @return the connection String\r
- */\r
- public String getConnectionString(String server, String database);\r
- \r
-}
\ No newline at end of file
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class MySQLDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "MySQL";\r
- \r
- //class\r
- protected String classString = "com.mysql.jdbc.Driver";\r
- \r
- //url\r
- protected String urlString = "jdbc:mysql://";\r
- \r
- //port\r
- private int defaultPort = 3306;\r
- \r
- \r
- //hibernate dialect\r
- private String hibernateDialect = "MySQLDialect";\r
-\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + "/" + database;\r
- } \r
- \r
- public MySQLDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * TODO not tested yet !!\r
- * \r
- * @author a.mueller\r
- *\r
- */\r
-public class OdbcDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "ODBC";\r
- \r
- //class\r
- protected String classString = "sun.jdbc.odbc.JdbcOdbcDriver";\r
- \r
- //url\r
- protected String urlString = "jdbc:odbc:";\r
- \r
- //port\r
- private int defaultPort = 0;\r
- \r
- //hibernate dialect\r
- //TODO\r
- private String hibernateDialect = "xxx";\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server ;\r
- } \r
- \r
- //constructor\r
- public OdbcDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class OracleDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "Oracle";\r
- //class\r
- protected String classString = "oracle.jdbc.driver.OracleDriver";\r
- //url\r
- protected String urlString = "jdbc:oracle:thin:@";\r
- //port\r
- private int defaultPort = 1521;\r
- //hibernate dialect\r
- private String hibernateDialect = "OracleDialect";\r
-\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + ":" + database;\r
- } \r
- \r
- public OracleDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class PostgreSQLDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "PostgreSQL";\r
- //class\r
- protected String classString = "org.postgresql.Driver";\r
- //url\r
- protected String urlString = "jdbc:postgresql://";\r
- //port\r
- private int defaultPort = 5432;\r
- //hibernate dialect\r
- private String hibernateDialect = "PostgreSQLDialect";\r
-\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + "/" + database;\r
- } \r
- \r
- public PostgreSQLDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public class SqlServerDatabaseType extends AbstractDatabaseType {\r
-\r
- //name\r
- protected String typeName = "SQL Server";\r
- \r
- //driver class\r
- protected String classString = "com.microsoft.jdbc.sqlserver.SQLServerDriver";\r
- \r
- //url\r
- protected String urlString = "jdbc:microsoft:sqlserver://";\r
- \r
- //default port\r
- private int defaultPort = 1433;\r
- \r
- //hibernate dialect\r
- private String hibernateDialect = "SQLServerDialect";\r
- \r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + ";databaseName=" + database+";SelectMethod=cursor";\r
- }\r
- \r
- //Constructor\r
- public SqlServerDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-}
\ No newline at end of file
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.database.types;\r
-\r
-\r
-/**\r
- * !! UNTESTED !!\r
- * @author a.mueller\r
- *\r
- */\r
-public class SybaseDatabaseType extends AbstractDatabaseType {\r
-\r
- //typeName\r
- protected String typeName = "Sybase";\r
- //class\r
- protected String classString = "com.sybase.jdbc2.jdbc.SybDriver";\r
- //url\r
- protected String urlString = "jdbc:sybase:Tds:";\r
- //port\r
- private int defaultPort = 4100;\r
- //hibernate dialect\r
- private String hibernateDialect = "SybaseDialect";\r
-\r
- \r
- //connection String\r
- public String getConnectionString(String server, String database, int port){\r
- return urlString + server + ":" + port + "/" + database;\r
- } \r
- \r
- public SybaseDatabaseType() {\r
- init (typeName, classString, urlString, defaultPort, hibernateDialect );\r
- }\r
-\r
-\r
-\r
-\r
-}\r
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.springframework.stereotype.Repository;\r
-\r
-import eu.etaxonomy.cdm.model.agent.Agent;\r
-\r
-\r
-@Repository\r
-public class AgentDaoImpl extends IdentifiableDaoBase<Agent> implements IAgentDao{\r
- private static final Logger logger = Logger.getLogger(AgentDaoImpl.class);\r
-\r
- public AgentDaoImpl() {\r
- super(Agent.class); \r
- }\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.common;\r
-\r
-import java.io.Serializable;\r
-import java.util.List;\r
-import java.util.UUID;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.hibernate.Criteria;\r
-import org.hibernate.Query;\r
-import org.hibernate.Session;\r
-import org.hibernate.SessionFactory;\r
-import org.hibernate.Transaction;\r
-import org.hibernate.criterion.Order;\r
-import org.hibernate.criterion.Restrictions;\r
-import org.springframework.beans.factory.annotation.Autowired;\r
-import org.springframework.dao.DataAccessException;\r
-import org.springframework.transaction.annotation.Transactional;\r
-\r
-import eu.etaxonomy.cdm.model.common.CdmBase;\r
-\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public abstract class CdmEntityDaoBase<T extends CdmBase> extends DaoBase implements ICdmEntityDao<T> {\r
-\r
- static Logger logger = Logger.getLogger(CdmEntityDaoBase.class);\r
-\r
- protected Class<T> type;\r
- \r
- public CdmEntityDaoBase(Class<T> type){\r
- this.type = type;\r
- logger.debug("Creating DAO of type [" + type.getSimpleName() + "]");\r
- }\r
- \r
- public UUID saveCdmObj(CdmBase cdmObj) throws DataAccessException {\r
- getSession().saveOrUpdate(cdmObj);\r
- return cdmObj.getUuid();\r
- }\r
-\r
- public UUID saveOrUpdate(T transientObject) throws DataAccessException {\r
- getSession().saveOrUpdate(transientObject);\r
- return transientObject.getUuid();\r
- }\r
-\r
- public UUID save(T newInstance) throws DataAccessException {\r
- getSession().save(newInstance);\r
- return newInstance.getUuid();\r
- }\r
- \r
- public UUID update(T transientObject) throws DataAccessException {\r
- getSession().update(transientObject);\r
- return transientObject.getUuid();\r
- }\r
- \r
- public UUID delete(T persistentObject) throws DataAccessException {\r
- getSession().delete(persistentObject);\r
- return persistentObject.getUuid();\r
- }\r
-\r
- public T findById(int id) throws DataAccessException {\r
- return (T) getSession().get(type, id);\r
- }\r
-\r
- public T findByUuid(UUID uuid) throws DataAccessException{\r
- Session session = getSession();\r
- \r
- Criteria crit = session.createCriteria(type);\r
- crit.add(Restrictions.eq("strUuid", uuid.toString()));\r
- crit.addOrder(Order.desc("created"));\r
- List<T> results = crit.list();\r
- if (results.isEmpty()){\r
- return null;\r
- }else{\r
- return results.get(0); \r
- }\r
- }\r
- \r
- public Boolean exists(UUID uuid) {\r
- if (findByUuid(uuid)==null){\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- public List<T> list(int limit, int start) {\r
- Criteria crit = getSession().createCriteria(type); \r
- crit.setFirstResult(start);\r
- crit.setMaxResults(limit);\r
- return crit.list(); \r
- }\r
-\r
-}\r
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import java.util.List;
-
-import org.springframework.stereotype.Repository;
-import org.springframework.transaction.annotation.Transactional;
-
-import eu.etaxonomy.cdm.model.common.CdmBase;
-
-@Repository
-public class CdmGenericDaoImpl extends CdmEntityDaoBase<CdmBase> implements ICdmGenericDao{
-
- public CdmGenericDaoImpl() {
- super(CdmBase.class);
- }
-
-}
-
-
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-public abstract class DaoBase {
- @Autowired
- private SessionFactory factory;
-
- protected Session getSession(){
- return factory.getCurrentSession();
- }
-
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.springframework.stereotype.Repository;
-import org.hibernate.Query;
-
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-
-@Repository
-public class DefinedTermDaoImpl extends CdmEntityDaoBase<DefinedTermBase> implements IDefinedTermDao{
- private static final Logger logger = Logger.getLogger(DefinedTermDaoImpl.class);
-
- public DefinedTermDaoImpl() {
- super(DefinedTermBase.class);
- }
-
- public List<DefinedTermBase> findByTitle(String queryString) {
- Query query = getSession().createQuery("select term from DefinedTermBase term join fetch term.representations representation where representation.label = :label");
- query.setParameter("label", queryString);
- return (List<DefinedTermBase>) query.list();
- }
-
-// @Override
-// public List<DefinedTermBase> list(int limit, int start) {
-// Query query = getSession().createQuery("select term from DefinedTermBase term join fetch term.representations representation ");
-// query.setMaxResults(limit);
-// query.setFirstResult(start);
-// return (List<DefinedTermBase>) query.list();
-// }
-
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;\r
-\r
-import eu.etaxonomy.cdm.model.agent.Agent;\r
-\r
-public interface IAgentDao extends IIdentifiableDao<Agent> {\r
- \r
-}\r
+++ /dev/null
-/**
-* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.log4j.Logger;
-import org.springframework.dao.DataAccessException;
-import org.springframework.orm.hibernate3.HibernateTemplate;
-
-
-import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
-
-/**
- * an data access interface that all data access classes implement
- * @author m.doering
- * @version 1.0
- * @created 02-Nov-2007 19:36:10
- */
-public interface ICdmEntityDao<T extends CdmBase> {
-
- public UUID saveOrUpdate(T transientObject) throws DataAccessException;
-
- public UUID save(T newOrManagedObject) throws DataAccessException;
-
- public UUID update(T transientObject) throws DataAccessException;
-
- public UUID delete(T persistentObject) throws DataAccessException;
-
- public List<T> list(int limit, int start) throws DataAccessException;
-
- public T findById(int id) throws DataAccessException;
-
- public T findByUuid(UUID Uuid) throws DataAccessException;
-
- public Boolean exists(UUID uuid) throws DataAccessException;
-
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import java.util.UUID;
-
-import org.springframework.dao.DataAccessException;
-
-import eu.etaxonomy.cdm.model.common.CdmBase;
-
-public interface ICdmGenericDao {
-
- public UUID saveOrUpdate(CdmBase transientObject) throws DataAccessException;
-
- public UUID save(CdmBase newOrManagedObject) throws DataAccessException;
-
- public UUID update(CdmBase transientObject) throws DataAccessException;
-
- public UUID delete(CdmBase persistentObject) throws DataAccessException;
-
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-
-
-public interface IDefinedTermDao extends ICdmEntityDao<DefinedTermBase>, ITitledDao<DefinedTermBase>{
-
-
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-
-public interface IIdentifiableDao <T extends IdentifiableEntity> extends ICdmEntityDao<T>, ITitledDao<T>{
-
-}
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.common;\r
-\r
-import eu.etaxonomy.cdm.model.common.init.IVocabularySaver;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public interface ITermVocabularyDao extends ICdmEntityDao, IVocabularySaver {\r
- \r
- \r
-}\r
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import java.util.List;
-
-import eu.etaxonomy.cdm.model.common.CdmBase;
-
-public interface ITitledDao<T extends CdmBase> {
-
- public List<T> findByTitle(String queryString);
-}
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.hibernate.Criteria;
-import org.hibernate.criterion.Order;
-import org.hibernate.criterion.Restrictions;
-
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
-
-public class IdentifiableDaoBase<T extends IdentifiableEntity> extends CdmEntityDaoBase<T> implements IIdentifiableDao<T>{
- static Logger logger = Logger.getLogger(IdentifiableDaoBase.class);
-
-
- public IdentifiableDaoBase(Class<T> type) {
- super(type);
- }
-
- public List<T> findByTitle(String queryString) {
- Criteria crit = getSession().createCriteria(type);
- crit.add(Restrictions.ilike("titleCache", queryString));
- List<T> results = crit.list();
- return results;
- }
-
-}
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.common;\r
-\r
-import org.springframework.stereotype.Repository;\r
-\r
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;\r
-import eu.etaxonomy.cdm.model.common.TermVocabulary;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-@Repository\r
-public class TermVocabularyDaoImpl extends CdmEntityDaoBase implements\r
- ITermVocabularyDao {\r
-\r
- /**\r
- * @param type\r
- */\r
- public TermVocabularyDaoImpl() {\r
- super(TermVocabulary.class);\r
- }\r
-\r
- /* (non-Javadoc)\r
- * @see eu.etaxonomy.cdm.model.common.init.IVocabularySaver#saveOrUpdate(eu.etaxonomy.cdm.model.common.TermVocabulary)\r
- */\r
- public void saveOrUpdate(TermVocabulary<DefinedTermBase> vocabulary) {\r
- super.saveOrUpdate(vocabulary);\r
- }\r
-\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.name;\r
-\r
-import java.util.List;\r
-\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public interface ITaxonNameDao extends IIdentifiableDao<TaxonNameBase> {\r
- \r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.name;\r
-\r
-import java.util.List;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.hibernate.Criteria;\r
-import org.hibernate.Session;\r
-import org.hibernate.criterion.Expression;\r
-import org.springframework.dao.DataAccessException;\r
-import org.springframework.orm.hibernate3.HibernateCallback;\r
-import org.springframework.orm.hibernate3.HibernateTemplate;\r
-import org.springframework.stereotype.Repository;\r
-\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.CdmEntityDaoBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IdentifiableDaoBase;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-@Repository\r
-public class TaxonNameDaoHibernateImpl \r
- extends IdentifiableDaoBase<TaxonNameBase> implements ITaxonNameDao {\r
- static Logger logger = Logger.getLogger(TaxonNameDaoHibernateImpl.class);\r
-\r
- public TaxonNameDaoHibernateImpl() {\r
- super(TaxonNameBase.class); \r
- }\r
- \r
-}
\ No newline at end of file
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.reference;\r
-\r
-import java.util.List;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;\r
-import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public interface IReferenceDao extends IIdentifiableDao<ReferenceBase>, ITitledDao<ReferenceBase> {\r
- \r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.reference;\r
-\r
-import org.apache.log4j.Logger;\r
-import org.springframework.stereotype.Repository;\r
-\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IdentifiableDaoBase;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-@Repository\r
-public class ReferenceDaoHibernateImpl extends IdentifiableDaoBase<ReferenceBase> implements IReferenceDao {\r
- static Logger logger = Logger.getLogger(ReferenceDaoHibernateImpl.class);\r
-\r
- public ReferenceDaoHibernateImpl() {\r
- super(ReferenceBase.class);\r
- }\r
-\r
- \r
-}
\ No newline at end of file
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.taxon;\r
-\r
-import java.util.List;\r
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;\r
-import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase> {\r
- \r
- public List<TaxonBase> getTaxaByName(String name, ReferenceBase sec);\r
- \r
- public List<Taxon> getRootTaxa(ReferenceBase sec);\r
-}\r
+++ /dev/null
-/**\r
- * \r
- */\r
-package eu.etaxonomy.cdm.persistence.dao.taxon;\r
-\r
-import java.util.List;\r
-import org.apache.log4j.Logger;\r
-import org.hibernate.Criteria;\r
-import org.hibernate.criterion.Restrictions;\r
-import org.springframework.stereotype.Repository;\r
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;\r
-import eu.etaxonomy.cdm.model.taxon.Taxon;\r
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;\r
-import eu.etaxonomy.cdm.persistence.dao.common.IdentifiableDaoBase;\r
-\r
-/**\r
- * @author a.mueller\r
- *\r
- */\r
-@Repository\r
-public class TaxonDaoHibernateImpl extends IdentifiableDaoBase<TaxonBase> implements ITaxonDao {\r
- static Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);\r
-\r
- public TaxonDaoHibernateImpl() {\r
- super(TaxonBase.class);\r
- }\r
-\r
- public List<Taxon> getRootTaxa(ReferenceBase sec) {\r
- // TODO add reference filter\r
- Criteria crit = getSession().createCriteria(Taxon.class);\r
- crit.add(Restrictions.isNull("taxonomicParentCache"));\r
- List<Taxon> results = crit.list();\r
- return results;\r
- }\r
-\r
- public List<TaxonBase> getTaxaByName(String name, ReferenceBase sec) {\r
- // TODO add reference filter\r
- return this.findByTitle(name);\r
- }\r
- \r
-}
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<beans xmlns="http://www.springframework.org/schema/beans"\r
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"\r
- xmlns:context="http://www.springframework.org/schema/context"\r
- xsi:schemaLocation="http://www.springframework.org/schema/beans \r
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd\r
- http://www.springframework.org/schema/context\r
- http://www.springframework.org/schema/context/spring-context-2.5.xsd">\r
-\r
- <bean id="defaultDataSource" lazy-init="true" class="org.springframework.jdbc.datasource.DriverManagerDataSource">\r
- <property name="driverClassName" value="com.mysql.jdbc.Driver" />\r
- <property name="url" value="jdbc:mysql://192.168.2.10/cdm_test_lib" />\r
- <property name="username" value="edit" />\r
- <property name="password" value="wp5" />\r
- </bean>\r
- <bean id="testSqlServerDataSource" lazy-init="true"\r
- class="org.springframework.jdbc.datasource.DriverManagerDataSource" >\r
- <property name="driverClassName" value="com.microsoft.jdbc.sqlserver.SQLServerDriver" />\r
- <property name="url" value="jdbc:microsoft:sqlserver://LAPTOPHP:1433;databaseName=cdmTest;SelectMethod=cursor" />\r
- <property name="username" value="edit" />\r
- <property name="password" value="wp5" />\r
- </bean>\r
- <bean id="testPostgreDataSource" lazy-init="true" class="org.springframework.jdbc.datasource.DriverManagerDataSource">\r
- <property name="driverClassName" value="org.postgresql.Driver" />\r
- <property name="url" value="jdbc:postgresql://192.168.1.17:5432/cdm_test" />\r
- <property name="username" value="edit" />\r
- <property name="password" value="schalke" />\r
- \r
- </bean>\r
- <bean id="localMysqlDataSource" lazy-init="true" class="org.springframework.jdbc.datasource.DriverManagerDataSource">
- <property name="driverClassName" value="com.mysql.jdbc.Driver" />
- <property name="url" value="jdbc:mysql://localhost/cdm" />
- <property name="username" value="edit" />
- <property name="password" value="wp5" />
- </bean>
- <bean id="localDefaultHsqlDataSource" \r
- lazy-init="true"\r
- class="eu.etaxonomy.cdm.database.LocalHsqldb" \r
- init-method="init"\r
- destroy-method="destroy"\r
- >\r
- <property name="driverClassName" value="org.hsqldb.jdbcDriver"/>\r
- <property name="username" value="sa"/>\r
- <property name="password" value=""/>\r
- <property name="startServer" value="true"/>\r
- <property name="silent" value="true"/>\r
- <!-- property name="pureUrl" value="jdbc:hsqldb:hsql://localhost/"/-->\r
- <!-- property name="dbName" value="cdm"/> -->\r
- <!-- <property name="databasePath" value="C:\tmp\cdmDb\"/> -->\r
- </bean>\r
-</beans>\r
-\r
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:context="http://www.springframework.org/schema/context"
- xmlns:tx="http://www.springframework.org/schema/tx"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context-2.5.xsd
- http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
- ">
-
- <context:component-scan base-package="eu/etaxonomy/cdm"/>
-
- <!-- enable the configuration of transactional behavior based on annotations -->
- <tx:annotation-driven transaction-manager="transactionManager"/>
-
- <bean id="transactionManager" class="org.springframework.orm.hibernate3.HibernateTransactionManager">
- <property name="sessionFactory" ref="sessionFactory" />
- </bean>
-
-<bean id="sessionFactory"
- class="org.springframework.orm.hibernate3.annotation.AnnotationSessionFactoryBean">
- <property name="dataSource" ref="defaultDataSource"/>
- <property name="namingStrategy">
- <bean class="org.hibernate.cfg.DefaultComponentSafeNamingStrategy" />\r
- </property>\r
- <property name="annotatedPackages">
- <list>
- <value>eu.etaxonomy.cdm.model.common</value>
- </list>
- </property>\r
- <property name="annotatedClasses">
- <list>
- <value>eu.etaxonomy.cdm.model.agent.Address</value>
- <value>eu.etaxonomy.cdm.model.agent.Agent</value>
- <value>eu.etaxonomy.cdm.model.agent.Contact</value>
- <value>eu.etaxonomy.cdm.model.agent.Institution</value>
- <value>eu.etaxonomy.cdm.model.agent.InstitutionalMembership</value>
- <value>eu.etaxonomy.cdm.model.agent.InstitutionType</value>
- <value>eu.etaxonomy.cdm.model.agent.Person</value>
- <value>eu.etaxonomy.cdm.model.agent.Team</value>
- <value>eu.etaxonomy.cdm.model.common.AnnotatableEntity</value>
- <value>eu.etaxonomy.cdm.model.common.Annotation</value>
- <value>eu.etaxonomy.cdm.model.common.AudioFile</value>
- <value>eu.etaxonomy.cdm.model.common.CdmBase</value>
- <value>eu.etaxonomy.cdm.model.common.DefinedTermBase</value>
- <value>eu.etaxonomy.cdm.model.common.EventBase</value>
- <value>eu.etaxonomy.cdm.model.common.Extension</value>
- <value>eu.etaxonomy.cdm.model.common.ExtensionType</value>
- <value>eu.etaxonomy.cdm.model.common.Figure</value>
- <value>eu.etaxonomy.cdm.model.common.IDefTerm</value>
- <value>eu.etaxonomy.cdm.model.common.IdentifiableEntity</value>
- <value>eu.etaxonomy.cdm.model.common.IdentifyableMediaEntity</value>
- <value>eu.etaxonomy.cdm.model.common.IEvent</value>
- <value>eu.etaxonomy.cdm.model.common.ImageFile</value>
- <value>eu.etaxonomy.cdm.model.common.IMediaDocumented</value>
- <value>eu.etaxonomy.cdm.model.common.IOriginalSource</value>
- <value>eu.etaxonomy.cdm.model.common.IReferencedEntity</value>
- <value>eu.etaxonomy.cdm.model.common.Keyword</value>
- <value>eu.etaxonomy.cdm.model.common.Language</value>
- <value>eu.etaxonomy.cdm.model.common.LanguageString</value>
- <value>eu.etaxonomy.cdm.model.common.Marker</value>
- <value>eu.etaxonomy.cdm.model.common.MarkerType</value>
- <value>eu.etaxonomy.cdm.model.common.Media</value>
- <value>eu.etaxonomy.cdm.model.common.MediaInstance</value>
- <value>eu.etaxonomy.cdm.model.common.MovieFile</value>
- <value>eu.etaxonomy.cdm.model.common.MultilanguageSet</value>
- <value>eu.etaxonomy.cdm.model.common.NoDefinedTermClassException</value>
- <value>eu.etaxonomy.cdm.model.common.OrderedTermBase</value>
- <value>eu.etaxonomy.cdm.model.common.OriginalSource</value>
- <value>eu.etaxonomy.cdm.model.common.ReferencedEntityBase</value>
- <value>eu.etaxonomy.cdm.model.common.ReferencedMedia</value>
- <value>eu.etaxonomy.cdm.model.common.RelationshipTermBase</value>
- <value>eu.etaxonomy.cdm.model.common.Representation</value>
- <value>eu.etaxonomy.cdm.model.common.Rights</value>
- <value>eu.etaxonomy.cdm.model.common.RightsTerm</value>
- <value>eu.etaxonomy.cdm.model.common.TermBase</value>
- <value>eu.etaxonomy.cdm.model.common.TermVocabulary</value>
- <value>eu.etaxonomy.cdm.model.common.TimePeriod</value>
- <value>eu.etaxonomy.cdm.model.common.VersionableEntity</value>
- <value>eu.etaxonomy.cdm.model.common.WrongTermTypeException</value>
- <value>eu.etaxonomy.cdm.model.description.AbsenceTerm</value>
- <value>eu.etaxonomy.cdm.model.description.CategoricalData</value>
- <value>eu.etaxonomy.cdm.model.description.CharacterTree</value>
- <value>eu.etaxonomy.cdm.model.description.CommonTaxonName</value>
- <value>eu.etaxonomy.cdm.model.description.DescriptionBase</value>
- <value>eu.etaxonomy.cdm.model.description.Distribution</value>
- <value>eu.etaxonomy.cdm.model.description.FeatureBase</value>
- <value>eu.etaxonomy.cdm.model.description.FeatureType</value>
- <value>eu.etaxonomy.cdm.model.description.IdentificationKey</value>
- <value>eu.etaxonomy.cdm.model.description.IndividualsAssociation</value>
- <value>eu.etaxonomy.cdm.model.description.MeasurementUnit</value>
- <value>eu.etaxonomy.cdm.model.description.Modifier</value>
- <value>eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase</value>
- <value>eu.etaxonomy.cdm.model.description.PresenceTerm</value>
- <value>eu.etaxonomy.cdm.model.description.QuantitativeData</value>
- <value>eu.etaxonomy.cdm.model.description.Scope</value>
- <value>eu.etaxonomy.cdm.model.description.Sex</value>
- <value>eu.etaxonomy.cdm.model.description.SpecimenDescription</value>
- <value>eu.etaxonomy.cdm.model.description.Stage</value>
- <value>eu.etaxonomy.cdm.model.description.State</value>
- <value>eu.etaxonomy.cdm.model.description.StateData</value>
- <value>eu.etaxonomy.cdm.model.description.StatisticalMeasure</value>
- <value>eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue</value>
- <value>eu.etaxonomy.cdm.model.description.TaxonDescription</value>
- <value>eu.etaxonomy.cdm.model.description.TaxonInteraction</value>
- <value>eu.etaxonomy.cdm.model.description.TextData</value>
- <value>eu.etaxonomy.cdm.model.description.TextFormat</value>
- <value>eu.etaxonomy.cdm.model.location.Continent</value>
- <value>eu.etaxonomy.cdm.model.location.NamedArea</value>
- <value>eu.etaxonomy.cdm.model.location.NamedAreaLevel</value>
- <value>eu.etaxonomy.cdm.model.location.NamedAreaType</value>
- <value>eu.etaxonomy.cdm.model.location.Point</value>
- <value>eu.etaxonomy.cdm.model.location.ReferenceSystem</value>
- <value>eu.etaxonomy.cdm.model.location.WaterbodyOrCountry</value>
- <value>eu.etaxonomy.cdm.model.molecular.DnaSample</value>
- <value>eu.etaxonomy.cdm.model.molecular.GenBankAccession</value>
- <value>eu.etaxonomy.cdm.model.molecular.Locus</value>
- <value>eu.etaxonomy.cdm.model.molecular.PhylogeneticTree</value>
- <value>eu.etaxonomy.cdm.model.molecular.Sequence</value>
- <value>eu.etaxonomy.cdm.model.name.BacterialName</value>
- <value>eu.etaxonomy.cdm.model.name.BotanicalName</value>
- <value>eu.etaxonomy.cdm.model.name.CultivarPlantName</value>
- <value>eu.etaxonomy.cdm.model.name.HomotypicalGroup</value>
- <value>eu.etaxonomy.cdm.model.name.HybridRelationship</value>
- <value>eu.etaxonomy.cdm.model.name.HybridRelationshipType</value>
- <value>eu.etaxonomy.cdm.model.name.NameRelationship</value>
- <value>eu.etaxonomy.cdm.model.name.NameRelationshipType</value>
- <value>eu.etaxonomy.cdm.model.name.NameTypeDesignation</value>
- <value>eu.etaxonomy.cdm.model.name.NomenclaturalStatus</value>
- <value>eu.etaxonomy.cdm.model.name.NomenclaturalStatusType</value>
- <value>eu.etaxonomy.cdm.model.name.NonViralName</value>
- <value>eu.etaxonomy.cdm.model.name.Rank</value>
- <value>eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation</value>
- <value>eu.etaxonomy.cdm.model.name.TaxonNameBase</value>
- <value>eu.etaxonomy.cdm.model.name.TypeDesignationStatus</value>
- <value>eu.etaxonomy.cdm.model.name.ViralName</value>
- <value>eu.etaxonomy.cdm.model.name.ZoologicalName</value>
- <value>eu.etaxonomy.cdm.model.occurrence.Collection</value>
- <value>eu.etaxonomy.cdm.model.occurrence.DerivationEvent</value>
- <value>eu.etaxonomy.cdm.model.occurrence.DerivationEventType</value>
- <value>eu.etaxonomy.cdm.model.occurrence.DerivedUnit</value>
- <value>eu.etaxonomy.cdm.model.occurrence.DeterminationEvent</value>
- <value>eu.etaxonomy.cdm.model.occurrence.DeterminationModifier</value>
- <value>eu.etaxonomy.cdm.model.occurrence.FieldObservation</value>
- <value>eu.etaxonomy.cdm.model.occurrence.Fossil</value>
- <value>eu.etaxonomy.cdm.model.occurrence.GatheringEvent</value>
- <value>eu.etaxonomy.cdm.model.occurrence.LivingBeing</value>
- <value>eu.etaxonomy.cdm.model.occurrence.Observation</value>
- <value>eu.etaxonomy.cdm.model.occurrence.PreservationMethod</value>
- <value>eu.etaxonomy.cdm.model.occurrence.Specimen</value>
- <value>eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase</value>
- <value>eu.etaxonomy.cdm.model.reference.Article</value>
- <value>eu.etaxonomy.cdm.model.reference.BibtexEntryType</value>
- <value>eu.etaxonomy.cdm.model.reference.BibtexReference</value>
- <value>eu.etaxonomy.cdm.model.reference.Book</value>
- <value>eu.etaxonomy.cdm.model.reference.BookSection</value>
- <value>eu.etaxonomy.cdm.model.reference.CdDvd</value>
- <value>eu.etaxonomy.cdm.model.reference.ConferenceProceedings</value>
- <value>eu.etaxonomy.cdm.model.reference.Database</value>
- <value>eu.etaxonomy.cdm.model.reference.Generic</value>
- <value>eu.etaxonomy.cdm.model.reference.INomenclaturalReference</value>
- <value>eu.etaxonomy.cdm.model.reference.InProceedings</value>
- <value>eu.etaxonomy.cdm.model.reference.Journal</value>
- <value>eu.etaxonomy.cdm.model.reference.Map</value>
- <value>eu.etaxonomy.cdm.model.reference.Patent</value>
- <value>eu.etaxonomy.cdm.model.reference.PersonalCommunication</value>
- <value>eu.etaxonomy.cdm.model.reference.PrintedUnitBase</value>
- <value>eu.etaxonomy.cdm.model.reference.PrintSeries</value>
- <value>eu.etaxonomy.cdm.model.reference.Proceedings</value>
- <value>eu.etaxonomy.cdm.model.reference.PublicationBase</value>
- <value>eu.etaxonomy.cdm.model.reference.ReferenceBase</value>
- <value>eu.etaxonomy.cdm.model.reference.Report</value>
- <value>eu.etaxonomy.cdm.model.reference.SectionBase</value>
- <value>eu.etaxonomy.cdm.model.reference.StrictReferenceBase</value>
- <value>eu.etaxonomy.cdm.model.reference.Thesis</value>
- <value>eu.etaxonomy.cdm.model.reference.WebPage</value>
- <value>eu.etaxonomy.cdm.model.taxon.ConceptRelationshipType</value>
- <value>eu.etaxonomy.cdm.model.taxon.Synonym</value>
- <value>eu.etaxonomy.cdm.model.taxon.SynonymRelationship</value>
- <value>eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType</value>
- <value>eu.etaxonomy.cdm.model.taxon.Taxon</value>
- <value>eu.etaxonomy.cdm.model.taxon.TaxonBase</value>
- <value>eu.etaxonomy.cdm.model.taxon.TaxonRelationship</value>
- <value>eu.etaxonomy.cdm.model.view.View</value>
- </list>
- </property>
- <property name="hibernateProperties">
- <props>
- <prop key="hibernate.hbm2ddl.auto">create</prop>
- <prop key="hibernate.dialect">org.hibernate.dialect.MySQLDialect</prop>
- <prop key="hibernate.cache.provider_class">org.hibernate.cache.NoCacheProvider</prop>
- <prop key="hibernate.show_sql">false</prop>
- <prop key="hibernate.format_sql">false</prop>
- </props>
- </property>
-</bean>
-
- </beans>
+++ /dev/null
-package eu.etaxonomy.cdm.persistence.dao.common;
-
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.log4j.Logger;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import eu.etaxonomy.cdm.model.common.DefinedTermBase;
-import eu.etaxonomy.cdm.model.common.Keyword;
-import eu.etaxonomy.cdm.model.common.TermVocabulary;
-import eu.etaxonomy.cdm.model.common.WrongTermTypeException;
-import eu.etaxonomy.cdm.test.unit.CdmUnitTestBase;
-
-public class DefinedTermDaoImplTest extends CdmUnitTestBase{
- static Logger logger = Logger.getLogger(DefinedTermDaoImplTest.class);
-
- @Autowired
- private IDefinedTermDao dao;
-
-
- //@Test
- public void save() throws WrongTermTypeException {
- TermVocabulary<DefinedTermBase> vocabulary = new TermVocabulary<DefinedTermBase>("Biological subdomains","biodomain","http://myterms.org/biodomain");
- String [] repres = {"genetics","physiology","systematics","taxonomy","nomenclature"};
- for (String r : repres){
- Keyword term = new Keyword(r,r);
- vocabulary.addTerm(term);
- }
- for (DefinedTermBase dt : vocabulary){
- dao.save(dt);
- }
- }
-
- @Test
- public void findByTitle() {
- List<DefinedTermBase> terms = dao.findByTitle("En");
- logger.debug("Results: "+terms.size());
- for (DefinedTermBase dt:terms){
- logger.debug(dt.toString());
- }
- //assertTrue(terms.contains(this.vocabulary));
- }
-
- @Test
- public void listOneTerm() {
- logger.debug("TEST: List 1 defined term");
- List<DefinedTermBase> terms = dao.list(1, 1);
- for (DefinedTermBase dt:terms){
- logger.debug("Loaded term: "+dt.toString());
- }
- }
-
- @Test
- public void getTermByUUID() {
- String strUuid = "eeaea868-c4c1-497f-b9fe-52c9fc4aca53";
- logger.debug("TEST: getTermByUUID " + strUuid);
- DefinedTermBase dt = dao.findByUuid(UUID.fromString(strUuid));
- //logger.debug("Loaded term: "+dt.toString());
- }
-
- @Test
- public void listManyTerms() {
- logger.debug("TEST: List 10 defined terms");
- List<DefinedTermBase> terms = dao.list(10, 0);
- for (DefinedTermBase dt:terms){
- logger.debug("Loaded term: "+dt.toString());
- }
- }
-}
import java.util.UUID;\r
import org.junit.Test;\r
\r
-import eu.etaxonomy.cdm.model.taxon.ConceptRelationshipType;\r
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;\r
\r
/**\r
* @author a.mueller\r
*/\r
@Test\r
public final void testTermsAreLoaded() {\r
- ConceptRelationshipType rel = ConceptRelationshipType.TAXONOMICALLY_INCLUDED_IN();\r
+ TaxonRelationshipType rel = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();\r
assertNotNull(rel);\r
UUID expectedUuid = UUID.fromString("d13fecdf-eb44-4dd7-9244-26679c05df1c");\r
assertEquals(expectedUuid, rel.getUuid());\r
import eu.etaxonomy.cdm.api.service.TermServiceImplTest;\r
\r
\r
-import eu.etaxonomy.cdm.persistence.dao.common.DefinedTermDaoImplTest;\r
-\r
\r
@RunWith(Suite.class)\r
@Suite.SuiteClasses( \r
{ \r
- TermServiceImplTest.class,\r
- DefinedTermDaoImplTest.class\r
+ TermServiceImplTest.class\r
}\r
)\r
public class CdmTestSuite {\r
//console test //TODO test\r
public static void consoleRun() {\r
org.junit.runner.JUnitCore.runClasses(\r
- TermServiceImplTest.class,\r
- DefinedTermDaoImplTest.class\r
+ TermServiceImplTest.class\r
);\r
}\r
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / commitdiff