http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/PutIdentifiedOperation.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/PutIdentifiedOperation.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/PutIdentifiedOperation.java deleted file mode 100644 index d05febe..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/PutIdentifiedOperation.java +++ /dev/null @@ -1,38 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.annotations; - -import static java.lang.annotation.ElementType.METHOD; -import static java.lang.annotation.RetentionPolicy.RUNTIME; - -import java.lang.annotation.Retention; -import java.lang.annotation.Target; - -/** - * Applied to methods in Dao implementations which store or update data in the - * backing store. - * - * @author Tom Oinn - */ -@Retention(RUNTIME) -@Target(METHOD) -public @interface PutIdentifiedOperation { -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/package.html ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/package.html b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/package.html deleted file mode 100644 index 0d38e1e..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/annotations/package.html +++ /dev/null @@ -1,4 +0,0 @@ -<body> -Annotations to make methods in the data access object implementations -for cache injection. -</body> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateComponentClass.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateComponentClass.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateComponentClass.java deleted file mode 100644 index f8f2076..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateComponentClass.java +++ /dev/null @@ -1,38 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.h3; - -/** - * A marker used to denote that the class should be pre-loaded into hibernate's - * class mapping. Used for component classes which are not going to be mapped to - * the RDBMS but which must be loadable for mapped classes to instantiate - * correctly. Basically if you refer to a class that isn't itself going to be - * mapped in hibernate within a mapping definition you'll need to add that - * component class to this SPI or hibernate won't be able to find it as it won't - * know that it should associate it with the appropriate class loader. - * <p> - * This should be used as an SPI marker, and set as the first SPI registry in - * the preloadRegistries property of the SpiRegistryAwareLocalSessionFactoryBean - * - * @author Tom Oinn - */ -public interface HibernateComponentClass { -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateMappedEntity.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateMappedEntity.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateMappedEntity.java deleted file mode 100644 index ae77e1d..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/HibernateMappedEntity.java +++ /dev/null @@ -1,39 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.h3; - -import net.sf.taverna.t2.reference.ExternalReferenceSPI; -import net.sf.taverna.t2.reference.ReferenceSet; - -/** - * A marker interface used to denote that the component should be registered - * with the Hibernate ORM system prior to any {@link ExternalReferenceSPI} - * implementations. This is here to allow implementations of e.g. - * {@link ReferenceSet} to be in the implementation package where they belong - * and still guarantee that they are registered before any other plugins. - * <p> - * This should be used as an SPI marker, and set as the first SPI registry in - * the spiRegistries property of the SpiRegistryAwareLocalSessionFactoryBean - * - * @author Tom Oinn - */ -public interface HibernateMappedEntity { -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/package.html ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/package.html b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/package.html deleted file mode 100644 index 4ffba14..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/h3/package.html +++ /dev/null @@ -1,8 +0,0 @@ -<body> -Contains the marker interfaces used by the implementation package to -ensure that all appropriate classes are mapped in hibernate -<em>before</em> -implementations of classes that depend upon them, and to ensure that -'static' classes such as the implementations of reference set etc are -mapped correctly. -</body> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/package.html ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/package.html b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/package.html deleted file mode 100644 index 503dc3b..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/package.html +++ /dev/null @@ -1,43 +0,0 @@ -<body> -<p>Interfaces for the Taverna 2 reference manager. This replaces the -(badly named) DataManager and is, in effect, a version 2 of that system. -While these APIs are implementation neutral the intent is heavily -towards the use of an object relational mapping (ORM) tool such as -Hibernate backed by a relational database to hold the various -collection, external reference and error documents managed by the -reference manager.</p> -<p>For those familiar with the previous DataManager code the table -below shows the old class names and the equivalent (where appropriate) -in the new code: -</p> -<table> - <tr> - <td>DataDocument</td> - <td>{@link net.sf.taverna.t2.reference.ReferenceSet}</td> - </tr> - <tr> - <td>ReferenceScheme</td> - <td>{@link net.sf.taverna.t2.reference.ExternalReferenceSPI}</td> - </tr> - <tr> - <td>EntityIdentifier</td> - <td>{@link net.sf.taverna.t2.reference.T2Reference}</td> - </tr> - <tr> - <td colspan="2">...</td> - </tr> -</table> -<p>One fundamental change is a move to runtime exceptions rather -than checked exceptions. This follows the pattern used by Spring and -Hibernate. The rationale is the same as in those systems - in general -checked exceptions are not handled properly by client code. The loss of -compiler level functionality from moving to runtime exceptions is -countered by much higher readability of code which in itself leads to -more robust and reliable systems.</p> -<p>A second change is the availability of asynchronous versions of -all the critical APIs. Reference construction or translation in -particular can be a costly process taking substantial time to complete. -Synchronous versions of the get methods still exist but in general the -simple callback based asynchronous ones are recommended over them for -most applications.</p> -</body> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/resources/net/sf/taverna/t2/reference/AbstractExternalReference.hbm.xml ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/resources/net/sf/taverna/t2/reference/AbstractExternalReference.hbm.xml b/taverna-reference-api/src/main/resources/net/sf/taverna/t2/reference/AbstractExternalReference.hbm.xml deleted file mode 100644 index e8851e9..0000000 --- a/taverna-reference-api/src/main/resources/net/sf/taverna/t2/reference/AbstractExternalReference.hbm.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0"?> -<!DOCTYPE hibernate-mapping PUBLIC - "-//Hibernate/Hibernate Mapping DTD 3.0//EN" - "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd";> -<!-- Hibernate mapping for the abstract superclass of --> -<!-- ExternalReferenceSPI implementations --> -<hibernate-mapping> - <class name="net.sf.taverna.t2.reference.AbstractExternalReference" - abstract="true"> - <!-- Let hibernate choose the primary key generation strategy --> - <id name="primaryKey" unsaved-value="0" column="bean_id"> - <generator class="native" /> - </id> - </class> -</hibernate-mapping> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/.gitignore ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/.gitignore b/taverna-reference-impl/.gitignore deleted file mode 100644 index 1298c5f..0000000 --- a/taverna-reference-impl/.gitignore +++ /dev/null @@ -1 +0,0 @@ -derby.log http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/pom.xml b/taverna-reference-impl/pom.xml deleted file mode 100644 index 0eb9e8c..0000000 --- a/taverna-reference-impl/pom.xml +++ /dev/null @@ -1,134 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>org.apache.taverna.engine</groupId> - <artifactId>taverna-engine</artifactId> - <version>3.1.0-incubating-SNAPSHOT</version> - </parent> - <artifactId>taverna-reference-impl</artifactId> - <packaging>bundle</packaging> - <name>Apache Taverna Reference Manager Implementation</name> - <description> - Implementations of the core APIs, not including extension point - implementations. - This package contains implementations of the data access objects, translator - infrastructure etc. - The extension point implementations that can be - considered as core functionality (files, URLs etc) are held in - the taverna-reference-types module. - </description> - - <properties> - <aspectj.version>1.6.0</aspectj.version> - </properties> - - <build> - <plugins> - <plugin> - <groupId>org.apache.felix</groupId> - <artifactId>maven-bundle-plugin</artifactId> - <extensions>true</extensions> - <configuration> - <instructions> - <Import-Package> - org.aspectj.lang, - org.springframework.orm.*, - org.hibernate.*, - org.hibernate.cfg, - org.hibernate.proxy, * - </Import-Package> - <!-- <Import-Package> org.aspectj.lang;resolution:=optional, org.springframework.orm.*;resolution:=optional, - org.hibernate.*;resolution:=optional, org.hibernate.proxy;resolution:=optional, - org.apache.derby.jdbc, * </Import-Package> --> - </instructions> - </configuration> - </plugin> - </plugins> - </build> - <dependencies> - <dependency> - <groupId>${project.parent.groupId}</groupId> - <artifactId>taverna-reference-api</artifactId> - <version>${project.parent.version}</version> - </dependency> - <dependency> - <groupId>${project.parent.groupId}</groupId> - <artifactId>taverna-database-configuration-api</artifactId> - <version>${project.parent.version}</version> - </dependency> - <dependency> - <groupId>org.springframework</groupId> - <artifactId>org.springframework.orm</artifactId> - <version>${spring.version}</version> - </dependency> - <dependency> - <groupId>org.springframework</groupId> - <artifactId>org.springframework.transaction</artifactId> - <version>${spring.version}</version> - </dependency> - <dependency> - <groupId>org.aspectj</groupId> - <artifactId>com.springsource.org.aspectj.weaver</artifactId> - <version>${aspectj.version}</version> - </dependency> - <dependency> - <groupId>${project.parent.groupId}</groupId> - <artifactId>taverna-reference-testhelpers</artifactId> - <version>${project.parent.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.hibernate</groupId> - <artifactId>com.springsource.org.hibernate</artifactId> - <version>${hibernate.version}</version> - <!-- <optional>true</optional> --> - <exclusions> - <exclusion> - <groupId>javax.transaction</groupId> - <artifactId>jta</artifactId> - </exclusion> - <exclusion> - <groupId>net.sf.ehcache</groupId> - <artifactId>ehcache</artifactId> - </exclusion> - <exclusion> - <groupId>asm</groupId> - <artifactId>asm-attrs</artifactId> - </exclusion> - <exclusion> - <groupId>antlr</groupId> - <artifactId>antlr</artifactId> - </exclusion> - </exclusions> - </dependency> - <dependency> - <groupId>javax.transaction</groupId> - <artifactId>com.springsource.javax.transaction</artifactId> - <version>${javax.transaction.version}</version> - </dependency> - <dependency> - <groupId>log4j</groupId> - <artifactId>log4j</artifactId> - <version>${log4j.version}</version> - </dependency> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>org.apache.derby</groupId> - <artifactId>com.springsource.org.apache.derby</artifactId> - <version>${derby.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>geronimo-spec</groupId> - <artifactId>geronimo-spec-jta</artifactId> - <version>${geronimo.spec.jta.version}</version> - <scope>test</scope> - </dependency> - </dependencies> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/TemporaryJDBC.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/TemporaryJDBC.java b/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/TemporaryJDBC.java deleted file mode 100644 index d041320..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/TemporaryJDBC.java +++ /dev/null @@ -1,75 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.platform.spring.jdbc; - -import static java.io.File.createTempFile; - -import java.io.File; -import java.io.IOException; - -/** - * Create JDBC connection strings for temporary use (ie. from tests) - * <p> - * {@link #getTemporaryDerbyJDBC()} creates a temporary directory that is used - * to construct the JDBC connection string for a local Derby database. - * </p> - * <p> - * This is most useful from a spring configuration, for example when using - * {@link InterpolatingDriverManagerDataSource}: - * </p> - * - * <pre> - * <!-- Apache Derby rooted at a temporary directory --> - * <bean id="t2reference.jdbc.temporaryjdbc" - * class="net.sf.taverna.platform.spring.jdbc.TemporaryJDBC"> - * </bean> - * <bean id="t2reference.jdbc.url" class="java.lang.String" - * factory-bean="t2reference.jdbc.temporaryjdbc" - * factory-method="getTemporaryDerbyJDBC" /> - * <bean id="t2reference.jdbc.datasource" - * class="net.sf.taverna.platform.spring.jdbc.InterpolatingDriverManagerDataSource"> - * <property name="driverClassName"> - * <value>org.apache.derby.jdbc.EmbeddedDriver</value> - * </property> - * <property name="url"> - * <ref bean="t2reference.jdbc.url" /> - * </property> - * <property name="repository"> - * <ref bean="raven.repository" /> - * </property> - * <property name="driverArtifact"> - * <value>org.apache.derby:derby:10.4.1.3</value> - * </property> - * </bean> - * </pre> - * - * @author Stian Soiland-Reyes - */ -public class TemporaryJDBC { - public String getTemporaryDerbyJDBC() throws IOException { - File tmpDir = createTempFile("t2platform-", ".db"); - tmpDir.delete(); - if (!tmpDir.mkdir()) - throw new IOException("Could not create temporary directory " - + tmpDir); - return "jdbc:derby:" + tmpDir.getPath() + "/database;create=true"; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/package.html ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/package.html b/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/package.html deleted file mode 100644 index 2355a14..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/platform/spring/jdbc/package.html +++ /dev/null @@ -1,6 +0,0 @@ -<body> -Extensions to the JDBC parts of Spring, and support for proxying of JDBC -drivers so we can load them dynamically from raven artifacts. The proxy -approach is inspired by http://www.jroller.com/tackline/entry/dynamically_loading_jdbc_drivers -with additions to build from raven rather than from existing jar files. -</body> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractEntityImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractEntityImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractEntityImpl.java deleted file mode 100644 index 8559607..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractEntityImpl.java +++ /dev/null @@ -1,66 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import net.sf.taverna.t2.reference.T2Reference; - -/** - * Abstract superclass of ReferenceSetImpl, IdentifiedArrayList and - * ErrorDocumentImpl, manages the T2Reference field for these types and their - * hibernate backing. - * - * @author Tom Oinn - */ -public class AbstractEntityImpl { - private T2ReferenceImpl id; - private String compactId = null; - - public T2Reference getId() { - return id; - } - - /** - * This method is only ever called from within Hibernate, and is used to - * initialize the unique ID of this reference set. - */ - public void setTypedId(T2ReferenceImpl newId) { - id = newId; - } - - /** - * Used because technically you can't accept and return implementation types - * in the methods on a bean which implements an interface, but Hibernate - * needs to construct concrete input and output types! - */ - public T2ReferenceImpl getTypedId() { - return id; - } - - public void setInternalId(String newId) { - compactId = newId; - } - - public final String getInternalId() { - if (compactId == null) - compactId = id.getCompactForm(); - return compactId; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractErrorDocumentServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractErrorDocumentServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractErrorDocumentServiceImpl.java deleted file mode 100644 index ccabf5a..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractErrorDocumentServiceImpl.java +++ /dev/null @@ -1,119 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import net.sf.taverna.t2.reference.DaoException; -import net.sf.taverna.t2.reference.ErrorDocument; -import net.sf.taverna.t2.reference.ErrorDocumentDao; -import net.sf.taverna.t2.reference.ErrorDocumentService; -import net.sf.taverna.t2.reference.ErrorDocumentServiceCallback; -import net.sf.taverna.t2.reference.ErrorDocumentServiceException; -import net.sf.taverna.t2.reference.ListServiceException; -import net.sf.taverna.t2.reference.ReferenceContext; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.T2ReferenceGenerator; - -/** - * Abstract implementation of ErrorDocumentService, inject with an appropriate - * ErrorDocumentDao and T2ReferenceGenerator to enable. Contains injectors for - * id generation and dao along with other bookkeeping, leaving the - * implementation of the actual service logic to the subclass. - * - * @author Tom Oinn - */ -public abstract class AbstractErrorDocumentServiceImpl extends - AbstractServiceImpl implements ErrorDocumentService { - protected ErrorDocumentDao errorDao = null; - protected T2ReferenceGenerator t2ReferenceGenerator = null; - - /** - * Inject the error document data access object. - */ - public final void setErrorDao(ErrorDocumentDao dao) { - errorDao = dao; - } - - /** - * Inject the T2Reference generator used to allocate new IDs when - * registering ErrorDocuments - */ - public final void setT2ReferenceGenerator(T2ReferenceGenerator t2rg) { - t2ReferenceGenerator = t2rg; - } - - /** - * Check that the list dao is configured - * - * @throws ListServiceException - * if the dao is still null - */ - protected final void checkDao() throws ErrorDocumentServiceException { - if (errorDao == null) - throw new ErrorDocumentServiceException( - "ErrorDocumentDao not initialized, error document " - + "service operations are not available"); - } - - /** - * Check that the t2reference generator is configured - * - * @throws ListServiceException - * if the generator is still null - */ - protected final void checkGenerator() throws ErrorDocumentServiceException { - if (t2ReferenceGenerator == null) - throw new ErrorDocumentServiceException( - "T2ReferenceGenerator not initialized, error document " - + "service operations not available"); - } - - @Override - public final void getErrorAsynch(final T2Reference id, - final ErrorDocumentServiceCallback callback) - throws ErrorDocumentServiceException { - checkDao(); - Runnable r = new Runnable() { - @Override - public void run() { - try { - ErrorDocument e = errorDao.get(id); - callback.errorRetrieved(e); - } catch (DaoException de) { - callback.errorRetrievalFailed(new ErrorDocumentServiceException( - de)); - } - } - }; - executeRunnable(r); - } - - @Override - public final ErrorDocument registerError(String message, int depth, - ReferenceContext context) throws ErrorDocumentServiceException { - return registerError(message, (Throwable) null, depth, context); - } - - @Override - public final ErrorDocument registerError(Throwable t, int depth, - ReferenceContext context) throws ErrorDocumentServiceException { - return registerError("", t, depth, context); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractListServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractListServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractListServiceImpl.java deleted file mode 100644 index ad564fb..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractListServiceImpl.java +++ /dev/null @@ -1,100 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import net.sf.taverna.t2.reference.ListDao; -import net.sf.taverna.t2.reference.ListService; -import net.sf.taverna.t2.reference.ListServiceCallback; -import net.sf.taverna.t2.reference.ListServiceException; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.T2ReferenceGenerator; - -/** - * Abstract implementation of ListService, inject with an appropriate ListDao - * and T2ReferenceGenerator to enable. Contains injectors for id generation and - * dao along with other bookkeeping, leaving the implementation of the actual - * service logic to the subclass. - * - * @author Tom Oinn - * - */ -public abstract class AbstractListServiceImpl extends AbstractServiceImpl - implements ListService { - protected ListDao listDao = null; - protected T2ReferenceGenerator t2ReferenceGenerator = null; - - /** - * Inject the list data access object. - */ - public final void setListDao(ListDao dao) { - listDao = dao; - } - - /** - * Inject the T2Reference generator used to allocate new IDs when - * registering lists of T2Reference - */ - public final void setT2ReferenceGenerator(T2ReferenceGenerator t2rg) { - t2ReferenceGenerator = t2rg; - } - - /** - * Check that the list dao is configured - * - * @throws ListServiceException - * if the dao is still null - */ - protected final void checkDao() throws ListServiceException { - if (listDao == null) - throw new ListServiceException("ListDao not initialized, list " - + "service operations are not available"); - } - - /** - * Check that the t2reference generator is configured - * - * @throws ListServiceException - * if the generator is still null - */ - protected final void checkGenerator() throws ListServiceException { - if (t2ReferenceGenerator == null) - throw new ListServiceException( - "T2ReferenceGenerator not initialized, list " - + "service operations not available"); - } - - @Override - public final void getListAsynch(final T2Reference id, - final ListServiceCallback callback) throws ListServiceException { - checkDao(); - Runnable r = new Runnable() { - @Override - public void run() { - try { - callback.listRetrieved(getList(id)); - } catch (ListServiceException lse) { - callback.listRetrievalFailed(lse); - } - } - }; - executeRunnable(r); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceServiceImpl.java deleted file mode 100644 index 3ef8e9b..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceServiceImpl.java +++ /dev/null @@ -1,171 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import java.util.List; -import java.util.Set; - -import net.sf.taverna.t2.reference.ErrorDocumentService; -import net.sf.taverna.t2.reference.ExternalReferenceSPI; -import net.sf.taverna.t2.reference.ListService; -import net.sf.taverna.t2.reference.ReferenceContext; -import net.sf.taverna.t2.reference.ReferenceService; -import net.sf.taverna.t2.reference.ReferenceServiceException; -import net.sf.taverna.t2.reference.ReferenceServiceResolutionCallback; -import net.sf.taverna.t2.reference.ReferenceSetService; -import net.sf.taverna.t2.reference.StreamToValueConverterSPI; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.ValueToReferenceConverterSPI; - -/** - * Implementation of ReferenceService, inject with ReferenceSetService, - * ErrorDocumentService and ListService to enable. Inject with an instance - * registry of ValueToReferenceConvertorSPI to enable on the fly registration of - * otherwise illegal object types. This class contains the basic injection - * functionality and the getters for the sub-services, mostly to isolate these - * mundane bits of code from the more interesting actual implementation of the - * reference service logic. - * - * @author Tom Oinn - */ -public abstract class AbstractReferenceServiceImpl extends AbstractServiceImpl - implements ReferenceService { - protected ErrorDocumentService errorDocumentService = null; - protected ReferenceSetService referenceSetService = null; - protected ListService listService = null; - protected List<ValueToReferenceConverterSPI> converters = null; - @SuppressWarnings("rawtypes") - protected List<StreamToValueConverterSPI> valueBuilders = null; - - /** - * Inject value to reference convertor SPI - */ - public final void setConverters( - List<ValueToReferenceConverterSPI> converters) { - this.converters = converters; - } - - /** - * Inject stream to value converter SPI - */ - @SuppressWarnings("rawtypes") - public final void setValueBuilders( - List<StreamToValueConverterSPI> valueBuilders) { - this.valueBuilders = valueBuilders; - } - - /** - * Inject error document service - */ - public final void setErrorDocumentService(ErrorDocumentService eds) { - this.errorDocumentService = eds; - } - - /** - * Inject reference set service - */ - public final void setReferenceSetService(ReferenceSetService rss) { - this.referenceSetService = rss; - } - - /** - * Inject list service - */ - public final void setListService(ListService ls) { - this.listService = ls; - } - - /** - * Throw a ReferenceServiceException if methods in ReferenceService are - * called without the necessary sub-services configured. - */ - protected final void checkServices() throws ReferenceServiceException { - if (errorDocumentService == null) - throw new ReferenceServiceException( - "Reference service must be configued with an " - + "instance of ErrorDocumentService to function"); - if (referenceSetService == null) - throw new ReferenceServiceException( - "Reference service must be configued with an " - + "instance of ReferenceSetService to function"); - if (listService == null) - throw new ReferenceServiceException( - "Reference service must be configued with an " - + "instance of ListService to function"); - } - - /** - * Check whether the converter registry has been defined, throw a - * ReferenceServiceException if not - */ - protected final void checkConverterRegistry() - throws ReferenceServiceException { - if (converters == null) - throw new ReferenceServiceException( - "Reference service must be configued with an " - + "instance registry of ValueToReferenceConvertorSPI " - + "to enable on the fly mapping of arbitrary objects " - + "during compound registration"); - } - - @Override - public final ErrorDocumentService getErrorDocumentService() { - checkServices(); - return this.errorDocumentService; - } - - @Override - public final ListService getListService() { - checkServices(); - return this.listService; - } - - @Override - public final ReferenceSetService getReferenceSetService() { - checkServices(); - return this.referenceSetService; - } - - /** - * Wraps the synchronous form, using the executeRunnable method to schedule - * it. - */ - @Override - public void resolveIdentifierAsynch(final T2Reference id, - final Set<Class<ExternalReferenceSPI>> ensureTypes, - final ReferenceContext context, - final ReferenceServiceResolutionCallback callback) - throws ReferenceServiceException { - checkServices(); - Runnable r = new Runnable() { - @Override - public void run() { - try { - callback.identifierResolved(resolveIdentifier(id, - ensureTypes, context)); - } catch (ReferenceServiceException rse) { - callback.resolutionFailed(rse); - } - } - }; - executeRunnable(r); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceSetServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceSetServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceSetServiceImpl.java deleted file mode 100644 index 9c930a5..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractReferenceSetServiceImpl.java +++ /dev/null @@ -1,160 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import java.util.Set; - -import net.sf.taverna.t2.reference.DaoException; -import net.sf.taverna.t2.reference.ExternalReferenceSPI; -import net.sf.taverna.t2.reference.ReferenceContext; -import net.sf.taverna.t2.reference.ReferenceSet; -import net.sf.taverna.t2.reference.ReferenceSetAugmentor; -import net.sf.taverna.t2.reference.ReferenceSetDao; -import net.sf.taverna.t2.reference.ReferenceSetService; -import net.sf.taverna.t2.reference.ReferenceSetServiceCallback; -import net.sf.taverna.t2.reference.ReferenceSetServiceException; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.T2ReferenceGenerator; - -/** - * Abstract implementation of ReferenceSetService, inject with an appropriate - * ReferenceSetDao to enable. Implements translation functionality as long as an - * appropriate ReferenceSetAugmentor implementation is injected. Contains - * injectors for id generation and dao along with other bookkeeping, leaving the - * implementation of the actual service logic to the subclass. - * - * @author Tom Oinn - */ -public abstract class AbstractReferenceSetServiceImpl extends - AbstractServiceImpl implements ReferenceSetService { - protected ReferenceSetDao referenceSetDao = null; - protected T2ReferenceGenerator t2ReferenceGenerator = null; - protected ReferenceSetAugmentor referenceSetAugmentor = null; - - /** - * Inject the reference set data access object. - */ - public final void setReferenceSetDao(ReferenceSetDao dao) { - this.referenceSetDao = dao; - } - - /** - * Inject the T2Reference generator used to allocate new IDs when - * registering sets of ExternalReferenceSPI - */ - public final void setT2ReferenceGenerator(T2ReferenceGenerator t2rg) { - this.t2ReferenceGenerator = t2rg; - } - - /** - * Inject the ReferenceSetAugmentor used to translate or construct new - * ExternalReferenceSPI instances within a ReferenceSet - */ - public final void setReferenceSetAugmentor(ReferenceSetAugmentor rse) { - this.referenceSetAugmentor = rse; - } - - /** - * Check that the reference set dao is configured - * - * @throws ReferenceSetServiceException - * if the dao is still null - */ - protected final void checkDao() throws ReferenceSetServiceException { - if (referenceSetDao == null) - throw new ReferenceSetServiceException( - "ReferenceSetDao not initialized, reference set " - + "service operations are not available"); - } - - /** - * Check that the t2reference generator is configured - * - * @throws ReferenceSetServiceException - * if the generator is still null - */ - protected final void checkGenerator() throws ReferenceSetServiceException { - if (t2ReferenceGenerator == null) - throw new ReferenceSetServiceException( - "T2ReferenceGenerator not initialized, reference " - + "set service operations not available"); - } - - /** - * Check that the reference set augmentor is configured - * - * @throws ReferenceSetServiceException - * if the reference set augmentor is still null - */ - protected final void checkAugmentor() throws ReferenceSetServiceException { - if (referenceSetAugmentor == null) - throw new ReferenceSetServiceException( - "ReferenceSetAugmentor not initialized, reference " - + "set service operations not available"); - } - - @Override - public final void getReferenceSetAsynch(final T2Reference id, - final ReferenceSetServiceCallback callback) - throws ReferenceSetServiceException { - checkDao(); - Runnable r = new Runnable() { - @Override - public void run() { - try { - ReferenceSet rs = referenceSetDao.get(id); - callback.referenceSetRetrieved(rs); - } catch (DaoException de) { - callback.referenceSetRetrievalFailed(new ReferenceSetServiceException( - de)); - } - } - }; - executeRunnable(r); - } - - /** - * {@inheritDoc} - */ - @Override - public final void getReferenceSetWithAugmentationAsynch( - final T2Reference id, - final Set<Class<ExternalReferenceSPI>> ensureTypes, - final ReferenceContext context, - final ReferenceSetServiceCallback callback) - throws ReferenceSetServiceException { - checkDao(); - checkAugmentor(); - Runnable r = new Runnable() { - @Override - public void run() { - try { - callback.referenceSetRetrieved(getReferenceSetWithAugmentation( - id, ensureTypes, context)); - } catch (ReferenceSetServiceException rsse) { - callback.referenceSetRetrievalFailed(rsse); - } - } - }; - executeRunnable(r); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractServiceImpl.java deleted file mode 100644 index c24981e..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractServiceImpl.java +++ /dev/null @@ -1,44 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -/** - * Abstract superclass for all service implementation objects, will be used to - * allow injection of thread pooling logic as and when we implement it. - * - * @author Tom Oinn - */ -public class AbstractServiceImpl { - /** - * Schedule a runnable for execution - current naive implementation uses a - * new thread and executes immediately, but this is where any thread pool - * logic would go if we wanted to add that. - * - * @param r - */ - protected void executeRunnable(Runnable r) { - makeExecutionThread(r).start(); - } - - protected Thread makeExecutionThread(Runnable r) { - return new Thread(r); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractT2ReferenceGenerator.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractT2ReferenceGenerator.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractT2ReferenceGenerator.java deleted file mode 100644 index dedcc67..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/AbstractT2ReferenceGenerator.java +++ /dev/null @@ -1,111 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import static net.sf.taverna.t2.reference.T2ReferenceType.ErrorDocument; -import static net.sf.taverna.t2.reference.T2ReferenceType.IdentifiedList; -import static net.sf.taverna.t2.reference.T2ReferenceType.ReferenceSet; - -import java.util.List; - -import net.sf.taverna.t2.reference.ReferenceContext; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.T2ReferenceGenerator; -import net.sf.taverna.t2.reference.WorkflowRunIdEntity; - -/** - * An abstract class for implementing simple {@link T2ReferenceGenerator}s. - * - * @author Stian Soiland-Reyes - */ -public abstract class AbstractT2ReferenceGenerator implements - T2ReferenceGenerator { - public AbstractT2ReferenceGenerator() { - super(); - } - - private void initReferenceNamespace(T2ReferenceImpl r, ReferenceContext context) { - if (context == null) { - // this is not good, just use the default namespace - r.setNamespacePart(getNamespace()); - return; - } - - List<WorkflowRunIdEntity> workflowRunIdEntities = context - .getEntities(WorkflowRunIdEntity.class); - if (workflowRunIdEntities == null || workflowRunIdEntities.isEmpty()) { - // this is not good, just use the default namespace - r.setNamespacePart(getNamespace()); - return; - } - - // there should be only one wf run id entity - String workflowRunId = ((WorkflowRunIdEntity) workflowRunIdEntities - .get(0)).getWorkflowRunId(); - r.setNamespacePart(workflowRunId); - } - - @Override - public synchronized T2Reference nextReferenceSetReference( - ReferenceContext context) { - T2ReferenceImpl r = new T2ReferenceImpl(); - initReferenceNamespace(r, context); - r.setLocalPart(getNextLocalPart()); - r.setReferenceType(ReferenceSet); - r.setDepth(0); - r.setContainsErrors(false); - return r; - } - - /** - * Generate a new local part for a new {@link T2Reference reference}. The - * local part should be unique within this - * {@link T2ReferenceGenerator#getNamespace() namespace}. - * - * @return A new, unique local part to identify a new reference. - */ - protected abstract String getNextLocalPart(); - - @Override - public T2Reference nextListReference(boolean containsErrors, int listDepth, - ReferenceContext context) { - T2ReferenceImpl r = new T2ReferenceImpl(); - initReferenceNamespace(r, context); - r.setLocalPart(getNextLocalPart()); - r.setReferenceType(IdentifiedList); - r.setDepth(listDepth); - r.setContainsErrors(containsErrors); - return r; - } - - @Override - public T2Reference nextErrorDocumentReference(int depth, - ReferenceContext context) { - T2ReferenceImpl r = new T2ReferenceImpl(); - initReferenceNamespace(r, context); - r.setLocalPart(getNextLocalPart()); - r.setReferenceType(ErrorDocument); - r.setDepth(depth); - // This is an error document, it contains errors by definition - r.setContainsErrors(true); - return r; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/CacheAspect.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/CacheAspect.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/CacheAspect.java deleted file mode 100644 index 59b5e04..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/CacheAspect.java +++ /dev/null @@ -1,127 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import net.sf.taverna.t2.reference.DaoException; -import net.sf.taverna.t2.reference.Identified; -import net.sf.taverna.t2.reference.ReferenceServiceCacheProvider; -import net.sf.taverna.t2.reference.T2Reference; - -import org.aspectj.lang.ProceedingJoinPoint; - -/** - * An aspect used to intercept calls to the various data access objects and - * divert through a write-through cache provider - * - * @author Tom Oinn - */ -public class CacheAspect { - private ReferenceServiceCacheProvider cacheProvider; - - /** - * Return an injected ReferenceServiceCacheProvider - */ - private final ReferenceServiceCacheProvider getCacheProvider() { - return cacheProvider; - } - - /** - * Inject an instance of ReferenceServiceCacheProvider - * - * @param cacheProvider - * the cache provider to use - */ - public final void setCacheProvider( - final ReferenceServiceCacheProvider cacheProvider) { - this.cacheProvider = cacheProvider; - } - - /** - * Handle a 'get by T2Reference' operation on a Dao - * - * @param pjp - * the join point representing the ongoing method call to the dao - * @return the entity identified by the T2Reference supplied to the method - * to which this advice applies - * @throws DaoException - * if anything goes wrong - */ - public final Identified getObject(final ProceedingJoinPoint pjp) - throws DaoException { - Identified result = null; - - // Get the T2Reference from the argument to the get method - T2Reference id = (T2Reference) pjp.getArgs()[0]; - if (id != null) { - result = getCacheProvider().get(id); - if (result != null) - return result; - } - // If we miss the cache then call the method as usual - try { - result = (Identified) pjp.proceed(); - } catch (DaoException e) { - throw e; - } catch (Throwable e) { - throw new DaoException("Unexpected exception type during aspect " - + "based invocation", e); - } - - // Write back to the cache - if (result != null) - getCacheProvider().put(result); - - return result; - } - - /** - * Called around a write or update operation on the backing store, writes - * through to the cache after modifying the state of the backing store and - * before returning from the dao method - * - * @param pjp - * join point representing the ongoing method invocation to cache - * @throws DaoException - * if anything goes wrong - */ - public void putObject(final ProceedingJoinPoint pjp) throws DaoException { - // Get the Identified being stored by the method we're advising - Identified storedObject = (Identified) pjp.getArgs()[0]; - - try { - // Run the store or update method - pjp.proceed(); - } catch (DaoException e) { - throw e; - } catch (Throwable e) { - throw new DaoException("Unexpected exception type during aspect " - + "based invocation", e); - } - - /* - * Assuming the method isn't null and has an identifier (which it will - * if we haven't thrown an exception before now) write it back to the - * cache provider - */ - if (storedObject != null && storedObject.getId() != null) - getCacheProvider().put(storedObject); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ContextualizedT2ReferenceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ContextualizedT2ReferenceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ContextualizedT2ReferenceImpl.java deleted file mode 100644 index 30d8492..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ContextualizedT2ReferenceImpl.java +++ /dev/null @@ -1,61 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import net.sf.taverna.t2.reference.ContextualizedT2Reference; -import net.sf.taverna.t2.reference.T2Reference; - -/** - * Simple implementation of ContextualizedT2Reference - * - * @author Tom Oinn - */ -public class ContextualizedT2ReferenceImpl implements ContextualizedT2Reference { - private T2Reference reference; - private int[] index; - - public ContextualizedT2ReferenceImpl(T2Reference ref, int[] context) { - this.reference = ref; - this.index = context; - } - - @Override - public int[] getIndex() { - return this.index; - } - - @Override - public T2Reference getReference() { - return this.reference; - } - - @Override - public String toString() { - StringBuilder sb = new StringBuilder("["); - String sep = ""; - for (int idx : index) { - sb.append(sep).append(idx); - sep = ","; - } - return sb.append("]").append(reference).toString(); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/EmptyReferenceContext.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/EmptyReferenceContext.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/EmptyReferenceContext.java deleted file mode 100644 index 6af0430..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/EmptyReferenceContext.java +++ /dev/null @@ -1,46 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import java.util.ArrayList; -import java.util.List; - -import net.sf.taverna.t2.reference.ReferenceContext; - -/** - * A trivial implementation of ReferenceContext, used if the context parameter - * to any service method is null. - * - * @author Tom Oinn - */ -public class EmptyReferenceContext implements ReferenceContext { - /** - * Return an empty entity set for all queries. - */ - @Override - public <T> List<T> getEntities(Class<T> arg0) { - return new ArrayList<>(); - } - - @Override - public void addEntity(Object entity) { - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentImpl.java deleted file mode 100644 index da00d59..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentImpl.java +++ /dev/null @@ -1,120 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import java.util.ArrayList; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import net.sf.taverna.t2.reference.ErrorDocument; -import net.sf.taverna.t2.reference.StackTraceElementBean; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.h3.HibernateMappedEntity; - -/** - * Simple bean implementation of ErrorDocument - * - * @author Tom Oinn - */ -public class ErrorDocumentImpl extends AbstractEntityImpl implements - ErrorDocument, HibernateMappedEntity { - private String exceptionMessage = ""; - private String message = ""; - List<StackTraceElementBean> stackTrace; - Set<T2Reference> errorReferences = new HashSet<>(); - - public ErrorDocumentImpl() { - this.stackTrace = new ArrayList<>(); - } - - @Override - public String getExceptionMessage() { - return this.exceptionMessage; - } - - public void setExceptionMessage(String exceptionMessage) { - this.exceptionMessage = exceptionMessage; - } - - @Override - public String getMessage() { - return this.message; - } - - public void setMessage(String message) { - this.message = message; - } - - /** - * From interface, not used by hibernate internally - */ - @Override - public List<StackTraceElementBean> getStackTraceStrings() { - return this.stackTrace; - } - - /** - * Used by Hibernate to bodge around problems with interface types in the - * API - */ - @SuppressWarnings({ "unchecked", "rawtypes" }) - public void setStackTraceList(List newList) { - this.stackTrace = newList; - } - - /** - * Used by Hibernate to bodge around problems with interface types in the - * API - */ - @SuppressWarnings("rawtypes") - public List getStackTraceList() { - return this.stackTrace; - } - - @Override - public Set<T2Reference> getErrorReferences() { - return errorReferences; - } - - /** - * Used by Hibernate to bodge around problems with interface types in the - * API - */ - @SuppressWarnings({ "unchecked", "rawtypes" }) - public void setErrorReferenceSet(Set errorReferenceSet) { - this.errorReferences = errorReferenceSet; - } - - /** - * Used by Hibernate to bodge around problems with interface types in the - * API - */ - @SuppressWarnings("rawtypes") - public Set getErrorReferenceSet() { - return this.errorReferences; - } - - @Override - public String toString() { - return getMessage(); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentServiceImpl.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentServiceImpl.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentServiceImpl.java deleted file mode 100644 index 1e78f92..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/ErrorDocumentServiceImpl.java +++ /dev/null @@ -1,163 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import static net.sf.taverna.t2.reference.impl.T2ReferenceImpl.getAsImpl; - -import java.util.Set; - -import net.sf.taverna.t2.reference.ErrorDocument; -import net.sf.taverna.t2.reference.ErrorDocumentService; -import net.sf.taverna.t2.reference.ErrorDocumentServiceException; -import net.sf.taverna.t2.reference.ReferenceContext; -import net.sf.taverna.t2.reference.ReferenceServiceException; -import net.sf.taverna.t2.reference.T2Reference; - -/** - * Implementation of ErrorDocumentService, inject with an appropriate - * ErrorDocumentDao and T2ReferenceGenerator to enable. - * - * @author Tom Oinn - */ -public class ErrorDocumentServiceImpl extends AbstractErrorDocumentServiceImpl - implements ErrorDocumentService { - @Override - public ErrorDocument getError(T2Reference id) - throws ErrorDocumentServiceException { - checkDao(); - try { - return errorDao.get(id); - } catch (Throwable t) { - throw new ErrorDocumentServiceException(t); - } - } - - /** - * Register the specified error and any child errors (which have the same - * namespace and local part but a lower depth, down to depth of zero - */ - @Override - public ErrorDocument registerError(String message, Throwable t, int depth, - ReferenceContext context) throws ErrorDocumentServiceException { - checkDao(); - checkGenerator(); - - T2Reference ref = t2ReferenceGenerator.nextErrorDocumentReference( - depth, context); - T2ReferenceImpl typedId = getAsImpl(ref); - - ErrorDocument docToReturn = null; - for (; depth >= 0; depth--) { - ErrorDocumentImpl edi = new ErrorDocumentImpl(); - if (docToReturn == null) - docToReturn = edi; - edi.setTypedId(typedId); - if (message != null) - edi.setMessage(message); - else - edi.setMessage(""); - if (t != null) { - edi.setExceptionMessage(t.toString()); - for (StackTraceElement ste : t.getStackTrace()) { - StackTraceElementBeanImpl stebi = new StackTraceElementBeanImpl(); - stebi.setClassName(ste.getClassName()); - stebi.setFileName(ste.getFileName()); - stebi.setLineNumber(ste.getLineNumber()); - stebi.setMethodName(ste.getMethodName()); - edi.stackTrace.add(stebi); - } - } else - edi.setExceptionMessage(""); - try { - errorDao.store(edi); - } catch (Throwable t2) { - throw new ErrorDocumentServiceException(t2); - } - if (depth > 0) - typedId = typedId.getDeeperErrorReference(); - } - return docToReturn; - } - - @Override - public ErrorDocument registerError(String message, Set<T2Reference> errors, - int depth, ReferenceContext context) - throws ErrorDocumentServiceException { - checkDao(); - checkGenerator(); - - T2Reference ref = t2ReferenceGenerator.nextErrorDocumentReference( - depth, context); - T2ReferenceImpl typedId = T2ReferenceImpl.getAsImpl(ref); - - ErrorDocument docToReturn = null; - for (; depth >= 0; depth--) { - ErrorDocumentImpl edi = new ErrorDocumentImpl(); - if (docToReturn == null) - docToReturn = edi; - edi.setTypedId(typedId); - if (message != null) - edi.setMessage(message); - else - edi.setMessage(""); - if (errors != null) - edi.setErrorReferenceSet(errors); - edi.setExceptionMessage(""); - - try { - errorDao.store(edi); - } catch (Throwable t2) { - throw new ErrorDocumentServiceException(t2); - } - if (depth > 0) - typedId = typedId.getDeeperErrorReference(); - } - return docToReturn; - } - - @Override - public T2Reference getChild(T2Reference errorId) - throws ErrorDocumentServiceException { - T2ReferenceImpl refImpl = getAsImpl(errorId); - try { - return refImpl.getDeeperErrorReference(); - } catch (Throwable t) { - throw new ErrorDocumentServiceException(t); - } - } - - @Override - public boolean delete(T2Reference reference) - throws ReferenceServiceException { - checkDao(); - ErrorDocument doc = errorDao.get(reference); - if (doc == null) - return false; - return errorDao.delete(doc); - } - - @Override - public void deleteErrorDocumentsForWorkflowRun(String workflowRunId) - throws ReferenceServiceException { - checkDao(); - errorDao.deleteErrorDocumentsForWFRun(workflowRunId); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateErrorDocumentDao.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateErrorDocumentDao.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateErrorDocumentDao.java deleted file mode 100644 index 470a82e..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateErrorDocumentDao.java +++ /dev/null @@ -1,154 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import static net.sf.taverna.t2.reference.T2ReferenceType.ErrorDocument; - -import java.util.List; - -import net.sf.taverna.t2.reference.DaoException; -import net.sf.taverna.t2.reference.ErrorDocument; -import net.sf.taverna.t2.reference.ErrorDocumentDao; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.annotations.DeleteIdentifiedOperation; -import net.sf.taverna.t2.reference.annotations.GetIdentifiedOperation; -import net.sf.taverna.t2.reference.annotations.PutIdentifiedOperation; - -import org.hibernate.Query; -import org.hibernate.Session; -import org.springframework.orm.hibernate3.support.HibernateDaoSupport; - -/** - * An implementation of ErrorDocumentDao based on Spring's HibernateDaoSupport. - * To use this in spring inject a property 'sessionFactory' with either a - * {@link org.springframework.orm.hibernate3.LocalSessionFactoryBean - * LocalSessionFactoryBean} or the equivalent class from the T2Platform module - * to add SPI based implementation discovery and mapping. To use outside of - * Spring ensure you call the setSessionFactory(..) method before using this - * (but really, use it from Spring, so much easier). - * - * @author Tom Oinn - */ -public class HibernateErrorDocumentDao extends HibernateDaoSupport implements - ErrorDocumentDao { - private static final String GET_ERRORS_FOR_RUN = "FROM ErrorDocumentImpl WHERE namespacePart = :workflow_run_id"; - - /** - * Fetch an ErrorDocument list by id - * - * @param ref - * the T2Reference to fetch - * @return a retrieved identified list of T2 references - * @throws DaoException - * if the supplied reference is of the wrong type or if - * something goes wrong fetching the data or connecting to the - * database - */ - @Override - @GetIdentifiedOperation - public ErrorDocument get(T2Reference ref) throws DaoException { - if (ref == null) - throw new DaoException( - "Supplied reference is null, can't retrieve."); - if (!ref.getReferenceType().equals(ErrorDocument)) - throw new DaoException( - "This dao can only retrieve reference of type T2Reference.ErrorDocument"); - if (!(ref instanceof T2ReferenceImpl)) - throw new DaoException( - "Reference must be an instance of T2ReferenceImpl"); - - try { - return (ErrorDocumentImpl) getHibernateTemplate().get( - ErrorDocumentImpl.class, - ((T2ReferenceImpl) ref).getCompactForm()); - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - @PutIdentifiedOperation - public void store(ErrorDocument theDocument) throws DaoException { - if (theDocument.getId() == null) - throw new DaoException( - "Supplied error document set has a null ID, allocate " - + "an ID before calling the store method in the dao."); - if (!theDocument.getId().getReferenceType().equals(ErrorDocument)) - throw new DaoException("Strangely the list ID doesn't have type " - + "T2ReferenceType.ErrorDocument, something has probably " - + "gone badly wrong somewhere earlier!"); - if (!(theDocument instanceof ErrorDocumentImpl)) - throw new DaoException( - "Supplied ErrorDocument not an instance of ErrorDocumentImpl"); - - try { - getHibernateTemplate().save(theDocument); - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - @DeleteIdentifiedOperation - public boolean delete(ErrorDocument theDocument) throws DaoException { - if (theDocument.getId() == null) - throw new DaoException( - "Supplied error document set has a null ID, allocate " - + "an ID before calling the store method in the dao."); - if (!theDocument.getId().getReferenceType() - .equals(ErrorDocument)) - throw new DaoException("Strangely the list ID doesn't have type " - + "T2ReferenceType.ErrorDocument, something has probably " - + "gone badly wrong somewhere earlier!"); - if (!(theDocument instanceof ErrorDocumentImpl)) - throw new DaoException( - "Supplied ErrorDocument not an instance of ErrorDocumentImpl"); - - try { - getHibernateTemplate().delete(theDocument); - return true; - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - @SuppressWarnings("unchecked") - @DeleteIdentifiedOperation - public synchronized void deleteErrorDocumentsForWFRun(String workflowRunId) - throws DaoException { - try { - // Select all ErrorDocuments for this wf run - Session session = getSession(); - Query selectQuery = session.createQuery(GET_ERRORS_FOR_RUN); - selectQuery.setString("workflow_run_id", workflowRunId); - List<ErrorDocument> errorDocuments = selectQuery.list(); - session.close(); - /* - * need to close before we do delete otherwise hibernate complains - * that two sessions are accessing collection - */ - getHibernateTemplate().deleteAll(errorDocuments); - } catch (Exception ex) { - throw new DaoException(ex); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateListDao.java ---------------------------------------------------------------------- diff --git a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateListDao.java b/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateListDao.java deleted file mode 100644 index 62ba83f..0000000 --- a/taverna-reference-impl/src/main/java/net/sf/taverna/t2/reference/impl/HibernateListDao.java +++ /dev/null @@ -1,151 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2007 The University of Manchester - * - * Modifications to the initial code base are copyright of their - * respective authors, or their employers as appropriate. - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 of - * the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - * Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public - * License along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 - ******************************************************************************/ -package net.sf.taverna.t2.reference.impl; - -import static net.sf.taverna.t2.reference.T2ReferenceType.IdentifiedList; - -import java.util.List; - -import net.sf.taverna.t2.reference.DaoException; -import net.sf.taverna.t2.reference.IdentifiedList; -import net.sf.taverna.t2.reference.ListDao; -import net.sf.taverna.t2.reference.T2Reference; -import net.sf.taverna.t2.reference.annotations.DeleteIdentifiedOperation; -import net.sf.taverna.t2.reference.annotations.GetIdentifiedOperation; -import net.sf.taverna.t2.reference.annotations.PutIdentifiedOperation; - -import org.hibernate.Query; -import org.hibernate.Session; -import org.springframework.orm.hibernate3.support.HibernateDaoSupport; - -/** - * An implementation of ListDao based on Spring's HibernateDaoSupport. To use - * this in spring inject a property 'sessionFactory' with either a - * {@link org.springframework.orm.hibernate3.LocalSessionFactoryBean - * LocalSessionFactoryBean} or the equivalent class from the T2Platform module - * to add SPI based implementation discovery and mapping. To use outside of - * Spring ensure you call the setSessionFactory(..) method before using this - * (but really, use it from Spring, so much easier). - * - * @author Tom Oinn - */ -public class HibernateListDao extends HibernateDaoSupport implements ListDao { - private static final String GET_LISTS_FOR_RUN = "FROM T2ReferenceListImpl WHERE namespacePart = :workflow_run_id"; - - /** - * Fetch a t2reference list by id - * - * @param ref - * the T2Reference to fetch - * @return a retrieved identified list of T2 references - * @throws DaoException - * if the supplied reference is of the wrong type or if - * something goes wrong fetching the data or connecting to the - * database - */ - @Override - @GetIdentifiedOperation - public IdentifiedList<T2Reference> get(T2Reference ref) throws DaoException { - if (ref == null) - throw new DaoException( - "Supplied reference is null, can't retrieve."); - if (!ref.getReferenceType().equals(IdentifiedList)) - throw new DaoException( - "This dao can only retrieve reference of type T2Reference.IdentifiedList"); - if (!(ref instanceof T2ReferenceImpl)) - throw new DaoException( - "Reference must be an instance of T2ReferenceImpl"); - - try { - return (T2ReferenceListImpl) getHibernateTemplate().get( - T2ReferenceListImpl.class, - ((T2ReferenceImpl) ref).getCompactForm()); - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - @PutIdentifiedOperation - public void store(IdentifiedList<T2Reference> theList) throws DaoException { - if (theList.getId() == null) - throw new DaoException("Supplied list set has a null ID, allocate " - + "an ID before calling the store method in the dao."); - if (!theList.getId().getReferenceType().equals(IdentifiedList)) - throw new DaoException("Strangely the list ID doesn't have type " - + "T2ReferenceType.IdentifiedList, something has probably " - + "gone badly wrong somewhere earlier!"); - if (!(theList instanceof T2ReferenceListImpl)) - throw new DaoException( - "Supplied identifier list not an instance of T2ReferenceList"); - - try { - getHibernateTemplate().save(theList); - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - public boolean delete(IdentifiedList<T2Reference> theList) - throws DaoException { - if (theList.getId() == null) - throw new DaoException("Supplied list set has a null ID, allocate " - + "an ID before calling the store method in the dao."); - if (!theList.getId().getReferenceType().equals(IdentifiedList)) - throw new DaoException("Strangely the list ID doesn't have type " - + "T2ReferenceType.IdentifiedList, something has probably " - + "gone badly wrong somewhere earlier!"); - if (!(theList instanceof T2ReferenceListImpl)) - throw new DaoException( - "Supplied identifier list not an instance of T2ReferenceList"); - - try { - getHibernateTemplate().delete(theList); - return true; - } catch (Exception ex) { - throw new DaoException(ex); - } - } - - @Override - @SuppressWarnings("unchecked") - @DeleteIdentifiedOperation - public synchronized void deleteIdentifiedListsForWFRun(String workflowRunId) - throws DaoException { - try { - // Select all T2Reference lists for this wf run - Session session = getSession(); - Query selectQuery = session.createQuery(GET_LISTS_FOR_RUN); - selectQuery.setString("workflow_run_id", workflowRunId); - List<IdentifiedList<T2Reference>> identifiedLists = selectQuery - .list(); - session.close(); - /* - * need to close before we do delete otherwise hibernate complains - * that two sessions are accessing collection - */ - getHibernateTemplate().deleteAll(identifiedLists); - } catch (Exception ex) { - throw new DaoException(ex); - } - } -}
