http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-reference-api/pom.xml b/taverna-reference-api/pom.xml deleted file mode 100644 index 1c2664d..0000000 --- a/taverna-reference-api/pom.xml +++ /dev/null @@ -1,40 +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-api</artifactId> - <packaging>bundle</packaging> - <name>Apache Taverna Reference Manager API</name> - <description> - Core APIs and extension points for the T2 reference manager. - This includes the SPIs for external references, translators and - publishers. - </description> - <build> - <plugins> - <plugin> - <groupId>org.apache.felix</groupId> - <artifactId>maven-bundle-plugin</artifactId> - <configuration> - <instructions> - <Import-Package> - org.hibernate.proxy;resolution:=optional, - org.springframework.transaction.*;resolution:=optional, * - </Import-Package> - </instructions> - </configuration> - </plugin> - </plugins> - </build> - <dependencies> - <dependency> - <groupId>org.springframework</groupId> - <artifactId>org.springframework.transaction</artifactId> - <version>${spring.version}</version> - </dependency> - </dependencies> -</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/AbstractExternalReference.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/AbstractExternalReference.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/AbstractExternalReference.java deleted file mode 100644 index 599d0bb..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/AbstractExternalReference.java +++ /dev/null @@ -1,89 +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; - -import static net.sf.taverna.t2.reference.ReferencedDataNature.*; - -/** - * A trivial implementation of ExternalReference. This abstract class should be - * used as the superclass of any ExternalReference implementations as it - * provides base metadata for the hibernate-based persistence system used by the - * main reference manager implementation. While the interface contract cannot - * require this your extensions will likely not work properly unless you use - * this class. - * - * @author Tom Oinn - */ -public abstract class AbstractExternalReference implements ExternalReferenceSPI { - // Used internally by Hibernate for this class and subclasses - private int primaryKey; - - /** - * Used by Hibernate internally to establish a foreign key relationship - * between this abstract superclass and tables corresponding to - * implementations of the ExternalReference interface. Has no impact on any - * application level code, this method is only ever used by the internals of - * the hibernate framework. - */ - public final void setPrimaryKey(int newKey) { - this.primaryKey = newKey; - } - - /** - * Used by Hibernate internally to establish a foreign key relationship - * between this abstract superclass and tables corresponding to - * implementations of the ExternalReference interface. Has no impact on any - * application level code, this method is only ever used by the internals of - * the hibernate framework. - */ - public final int getPrimaryKey() { - return this.primaryKey; - } - - /** - * Default to returning DataReferenceNature.UNKNOWN - */ - @Override - public ReferencedDataNature getDataNature() { - return UNKNOWN; - } - - /** - * Default to returning null for charset - */ - @Override - public String getCharset() { - return null; - } - - /** - * Default to a value of 0.0f for the resolution cost, but implementations - * should at least attempt to set this to a more sensible level! - */ - @Override - public float getResolutionCost() { - return 0.0f; - } - - @Override - public abstract ExternalReferenceSPI clone() - throws CloneNotSupportedException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ContextualizedT2Reference.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ContextualizedT2Reference.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ContextualizedT2Reference.java deleted file mode 100644 index a5699b0..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ContextualizedT2Reference.java +++ /dev/null @@ -1,47 +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; - -/** - * Used by the {@link ReferenceService#traverseFrom(T2Reference, int)} when - * traversing a collection structure. Each contextualized t2reference contains - * the {@link T2Reference} along with an integer array index representing the - * position of that reference within the traversal structure. The index - * [i<sub>0</sub>,i<sub>1</sub>,i<sub>2</sub> ... i<sub>n</sub>] is interpreted - * such that the reference is located at - * parent.get(i<sub>0</sub>).get(i<sub>1</sub - * >).get(i<sub>2</sub>)....get(i<sub>n</sub>). If the index is empty then the - * T2Reference <em>is</em> the original reference supplied to the - * {@link ReferenceService#traverseFrom(T2Reference, int) traverseFrom} method. - * - * @author Tom Oinn - */ -public interface ContextualizedT2Reference { - /** - * @return the T2Reference to which the associated index applies. - */ - T2Reference getReference(); - - /** - * @return the index of this T2Reference - */ - int[] getIndex(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DaoException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DaoException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DaoException.java deleted file mode 100644 index 7de38df..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DaoException.java +++ /dev/null @@ -1,47 +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; - -/** - * Thrown by the Data Access Object interface methods, wrapping any underlying - * exception. - * - * @author Tom Oinn - */ -public class DaoException extends RuntimeException { - static final long serialVersionUID = 8496141798637577803L; - - public DaoException() { - super(); - } - - public DaoException(String message) { - super(message); - } - - public DaoException(Throwable cause) { - super(cause); - } - - public DaoException(String message, Throwable cause) { - super(message, cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DereferenceException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DereferenceException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DereferenceException.java deleted file mode 100644 index d2f814f..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/DereferenceException.java +++ /dev/null @@ -1,48 +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; - -/** - * Thrown when a problem occurs during de-reference of an ExternalReferenceSPI - * implementation. This include operations which implicitly de-reference the - * reference such as those infering character set or data natures. - * - * @author Tom Oinn - */ -public class DereferenceException extends RuntimeException { - private static final long serialVersionUID = 8054381613840005541L; - - public DereferenceException() { - // - } - - public DereferenceException(String message) { - super(message); - } - - public DereferenceException(Throwable cause) { - super(cause); - } - - public DereferenceException(String message, Throwable cause) { - super(message, cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocument.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocument.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocument.java deleted file mode 100644 index 06a20e3..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocument.java +++ /dev/null @@ -1,56 +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; - -import java.util.List; -import java.util.Set; - -/** - * Contains the definition of an error token within the workflow system. - * - * @author Tom Oinn - * @author David Withers - */ -public interface ErrorDocument extends Identified { - /** - * If the error document is created from a {@link Throwable} it will have a - * stack trace, in this case the stack trace is represented as a list of - * {@link StackTraceElement} beans - */ - List<StackTraceElementBean> getStackTraceStrings(); - - /** - * If the error document is created from a {@link Throwable}, this contains - * the message part of the {@link Throwable}. - */ - String getExceptionMessage(); - - /** - * Error documents can carry an arbitrary string message, this returns it. - */ - String getMessage(); - - /** - * If the error document is created from set of references that contain - * error documents, this method returns them. - */ - Set<T2Reference> getErrorReferences(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentDao.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentDao.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentDao.java deleted file mode 100644 index 72fabf1..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentDao.java +++ /dev/null @@ -1,64 +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; - -import static org.springframework.transaction.annotation.Propagation.REQUIRED; -import static org.springframework.transaction.annotation.Propagation.SUPPORTS; - -import org.springframework.transaction.annotation.Transactional; - -/** - * Data access object handling ErrorDocument instances. - * - * @author Tom Oinn - */ -public interface ErrorDocumentDao { - /** - * Store a named ErrorDocument to the database. - * - * @param errorDoc - * error document to store - * @throws DaoException - * if any exception is thrown when connecting to the underlying - * store or when storing the error document - */ - @Transactional(propagation = REQUIRED, readOnly = false) - void store(ErrorDocument errorDoc) throws DaoException; - - /** - * Retrieves a named and populated ErrorDocument - * - * @param reference - * id of the error document to retrieve - * @return a previously stored ErrorDocument instance - * @throws DaoException - * if any exception is thrown when connecting to the underlying - * data store or when attempting retrieval of the error document - */ - @Transactional(propagation = SUPPORTS, readOnly = true) - ErrorDocument get(T2Reference reference) throws DaoException; - - @Transactional(propagation = SUPPORTS, readOnly = false) - boolean delete(ErrorDocument errorDoc) throws DaoException; - - @Transactional(propagation = SUPPORTS, readOnly = false) - void deleteErrorDocumentsForWFRun(String workflowRunId) throws DaoException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentService.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentService.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentService.java deleted file mode 100644 index 6eee715..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentService.java +++ /dev/null @@ -1,152 +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; - -import java.util.Set; - -import org.springframework.transaction.annotation.Propagation; -import org.springframework.transaction.annotation.Transactional; - -/** - * Provides facilities to register list of T2References, register empty lists at - * any given depth and to resolve appropriate T2Reference instances back to - * these lists. Registration operations assign names and lock the list contents - * as a result. This service operates strictly on T2References, it neither tries - * to nor is capable of any form of reference resolution, so aspects such as - * collection traversal are not handled here (these are performed by the top - * level reference service) - * - * @author Tom Oinn - */ -@Transactional(propagation = Propagation.SUPPORTS, readOnly = true) -public interface ErrorDocumentService { - /** - * Register a new error document. - * <p> - * The created reference will be related with a workflow run id passed - * through ReferenceContext so we can track all data referenced by a - * specific run. - * - * @param message - * a free text message describing the error, if available. If - * there is no message use the empty string here. - * @param t - * a Throwable describing the underlying fault causing this error - * document to be registered, if any. If there is no Throwable - * associated use null. - * @param depth - * depth of the error, used when returning an error document - * instead of an identified list. - * @return a new ErrorDocument instance, constructed fully and stored in the - * underlying storage system - */ - @Transactional(propagation = Propagation.REQUIRED, readOnly = false) - ErrorDocument registerError(String message, Throwable t, int depth, - ReferenceContext context) throws ErrorDocumentServiceException; - - /** - * Equivalent to <code>registerError(message, null, depth, context)</code>. - */ - @Transactional(propagation = Propagation.REQUIRED, readOnly = false) - ErrorDocument registerError(String message, int depth, - ReferenceContext context) throws ErrorDocumentServiceException; - - /** - * Equivalent to <code>registerError("", t, depth, context)</code>. - */ - @Transactional(propagation = Propagation.REQUIRED, readOnly = false) - ErrorDocument registerError(Throwable t, int depth, ReferenceContext context) - throws ErrorDocumentServiceException; - - /** - * Register a new error document. - * <p> - * The created reference will be related with a workflow run id passed - * through ReferenceContext so we can track all data referenced by a - * specific run. - * - * @param message - * a free text message describing the error, if available. If - * there is no message use the empty string here. - * @param errors - * a set of references that contain error documents. - * @param depth - * depth of the error, used when returning an error document - * instead of an identified list. - * @return a new ErrorDocument instance, constructed fully and stored in the - * underlying storage system - */ - @Transactional(propagation = Propagation.REQUIRED, readOnly = false) - ErrorDocument registerError(String message, Set<T2Reference> errors, - int depth, ReferenceContext context) - throws ErrorDocumentServiceException; - - /** - * Retrieve a previously named and registered ErrorDocument from the backing - * store - * - * @param id - * identifier of the error document to retrieve - * @return an ErrorDocument - * @throws ErrorDocumentServiceException - * if anything goes wrong with the retrieval process or if there - * is something wrong with the reference (such as it being of - * the wrong reference type). - */ - ErrorDocument getError(T2Reference id) throws ErrorDocumentServiceException; - - /** - * Functionality the same as {@link #getError(T2Reference) getError} but in - * asynchronous mode, returning immediately and using the supplied callback - * to communicate its results. - * - * @param id - * a {@link T2Reference} identifying an {@link ErrorDocument} to - * retrieve - * @param callback - * a {@link ErrorDocumentServiceCallback} used to convey the - * results of the asynchronous call - * @throws ErrorDocumentServiceException - * if the reference set service is not correctly configured. - * Exceptions encountered when performing the asynchronous call - * are not returned here, for obvious reasons, and are instead - * messaged through the callback interface. - */ - void getErrorAsynch(T2Reference id, ErrorDocumentServiceCallback callback) - throws ErrorDocumentServiceException; - - /** - * Return the T2Reference for the sole child of an error document - * identifier. - */ - T2Reference getChild(T2Reference errorId) - throws ErrorDocumentServiceException; - - @Transactional(propagation = Propagation.SUPPORTS, readOnly = false) - boolean delete(T2Reference reference) throws ReferenceServiceException; - - /** - * Delete all {@link ErrorDocument}S used by the specific workflow run. - */ - @Transactional(propagation = Propagation.SUPPORTS, readOnly = false) - void deleteErrorDocumentsForWorkflowRun(String workflowRunId) - throws ReferenceServiceException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceCallback.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceCallback.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceCallback.java deleted file mode 100644 index 5e55672..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceCallback.java +++ /dev/null @@ -1,47 +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; - -/** - * Callback interface used by asynchronous methods in the - * {@link ErrorDocumentService} interface - * - * @author Tom Oinn - */ -public interface ErrorDocumentServiceCallback { - /** - * Called when the requested {@link ReferenceSet} has been successfully - * retrieved. - * - * @param errorDoc - * the ErrorDocument requested - */ - void errorRetrieved(ErrorDocument errorDoc); - - /** - * Called if the retrieval failed for some reason - * - * @param cause - * an ErrorDocumentServiceException explaining the retrieval - * failure - */ - void errorRetrievalFailed(ErrorDocumentServiceException cause); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceException.java deleted file mode 100644 index 3959c6a..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ErrorDocumentServiceException.java +++ /dev/null @@ -1,48 +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; - -/** - * RuntimeException subclass thrown by the error document service layer - * interfaces. All underlying exceptions are either handled by the service layer - * or wrapped in this exception (or a subclass) and rethrown. - * - * @author Tom Oinn - */ -public class ErrorDocumentServiceException extends RuntimeException { - private static final long serialVersionUID = 5556399589785258956L; - - public ErrorDocumentServiceException() { - super(); - } - - public ErrorDocumentServiceException(String message, Throwable cause) { - super(message, cause); - } - - public ErrorDocumentServiceException(String message) { - super(message); - } - - public ErrorDocumentServiceException(Throwable cause) { - super(cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceBuilderSPI.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceBuilderSPI.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceBuilderSPI.java deleted file mode 100644 index 2dfb340..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceBuilderSPI.java +++ /dev/null @@ -1,90 +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; - -import java.io.InputStream; - -/** - * Constructs an ExternalReferenceSPI instance from a byte stream. Used by the - * {@link ReferenceSetAugmentor} when there isn't a direct reference to - * reference translation path available for a desired target type, but available - * for external use wherever this functionality is needed. - * <p> - * Where an underlying resource is required this is extracted from the supplied - * ReferenceContext, this implies that all methods in implementations of this - * interface should be thread safe, allowing multiple concurrent threads - * cleanly. For SPI purposes implementations should be java beans with default - * constructors. - * - * @author Tom Oinn - */ -public interface ExternalReferenceBuilderSPI<TargetType extends ExternalReferenceSPI> { - /** - * Given a stream of bytes, build the appropriate target - * ExternalReferenceSPI implementation which would de-reference to the value - * of that stream and return it. - * - * @param byteStream - * the bytestream to read target from. - * @param context - * a reference resolution context, needed potentially to - * construct the new ExternalReferenceSchemeSPI, especially in - * cases where the context contains security agents giving access - * to a remote data staging system * - * @throws ExternalReferenceConstructionException - * if an error occurs instantiating the new reference. - * @return the newly constructed ExternalReferenceSPI instance. - */ - TargetType createReference(InputStream byteStream, ReferenceContext context); - - /** - * Expose the type of the ExternalReferenceSPI that this builder can - * construct - * - * @return the class of ExternalReferenceSPI returned by the create - * reference methods. - */ - Class<TargetType> getReferenceType(); - - /** - * Because the reference builder may rely on facilities provided to it - * through the context this method is available to check whether these - * facilities are sufficient. - * - * @param context - * the reference context that will be used to construct new - * references - * @return whether the context contains necessary resources for the - * reference construction process - */ - boolean isEnabled(ReferenceContext context); - - /** - * Return an approximate complexity cost of the reference construction. In - * general we can't make any guarantees about this because the complexity of - * the construction depends on more than just the type involved - it can - * depend on local configuration, network location relative to the data - * stores referenced and in some cases on the data themselves. For now - * though we assign an approximation, the default value is 1.0f and lower - * values represent less costly operations. - */ - float getConstructionCost(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceConstructionException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceConstructionException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceConstructionException.java deleted file mode 100644 index 0892ecc..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceConstructionException.java +++ /dev/null @@ -1,50 +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; - -/** - * Thrown when an exception occurs during construction of an - * ExternalReferenceSPI instance. This includes construction through direct - * method invocation, through the ExternalReferenceBuilderSPI interface and - * through the ExternalReferenceTranslatorSPI interface. - * - * @author Tom Oinn - */ -public class ExternalReferenceConstructionException extends RuntimeException { - private static final long serialVersionUID = 8334725795238353354L; - - public ExternalReferenceConstructionException() { - super(); - } - - public ExternalReferenceConstructionException(String message) { - super(message); - } - - public ExternalReferenceConstructionException(Throwable cause) { - super(cause); - } - - public ExternalReferenceConstructionException(String message, - Throwable cause) { - super(message, cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceSPI.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceSPI.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceSPI.java deleted file mode 100644 index 4d6a047..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceSPI.java +++ /dev/null @@ -1,132 +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; - -import java.io.InputStream; - -/** - * A reference to a single piece of data. This may or may not be within the - * enactment infrastructure, it could refer to data held in a file, a URL, a - * grid storage system or anything of that nature. Ideally the data this - * reference points to should not change - we'd like to say 'must not change' at - * this point but this isn't always possible, implementations should aim to - * provide the appearance that data are immutable. - * <p> - * When used within the workflow engine implementations of this interface are - * always contained in a ReferenceSet instance. - * <p> - * Implementors of this interface are strongly advised to use the - * AbstractExternalReference superclass - this provides the necessary primary - * key information used by hibernate-based implementations of the reference - * manager. Technically we don't require it as it's possible that other backend - * stores may exist, but the core store used by T2 is based on hibernate so it's - * a very good idea to follow this! Basically if you don't your code won't work - * in the current system. - * <p> - * This interface is an SPI - while implementations are never constructed based - * on the SPI registry it is used to discover all implementing classes and - * automatically register their hibernate mapping files. Implementors should add - * their implementation class name to a - * META-INF/services/net.sf.taverna.t2.reference.ExternalReferenceSPI file in - * the implementation artifact. For examples please refer to the - * t2reference-core-extensions module, this contains implementations of this - * interface for common basic reference types. - * <p> - * Note - if your implementation class has a complex hibernate mapping that uses - * components which are themselves mapped into the database (perfectly legal to - * do) then you must mark those components as instances of HibernateMappedEntity - * so their corresponding mapping and class definitions are loaded by the - * Hibernate backed reference set dao. If your implementation class uses inline - * compound keys or other component types where you reference another class but - * the other class is not mapped itself in hibernate you must instead make the - * component class an instance of HibernateComponentClass - a marker interface - - * for the same reason. Both of these are SPIs themselves, and require the - * appropriate entries to be added to their service metadata files in your - * extension jar. - * - * @author Tom Oinn - */ -public interface ExternalReferenceSPI extends Cloneable { - /** - * Determine, if possible, whether the data this reference refers to is - * textual or binary in nature. If this determination is impossible, either - * because the ExternalReference implementation does not know or because the - * data is not accessible for some reason then this should return - * ReferenceDataNature.UNKNOWN - * - * @return the nature of the referenced data - */ - ReferencedDataNature getDataNature(); - - /** - * For textual data return the character set that should be used to pull - * data into a java String object. Callers must deal with a null return - * value in the event of either unknown charset or unknown or binary data - * types. - * - * @return string character set, for example 'utf-8', or <code>null</code> - * if binary or unknown type. - */ - String getCharset(); - - /** - * Open and return an InputStream to the data referenced using, if required, - * any facilities within the supplied context. - * - * @param context - * the ReferenceContext object used to obtain e.g. security - * agents or other facilities required when de-referencing this - * reference. - * @return an InputStream providing access to the referenced data - * @throws DereferenceException - * if the reference cannot be de-referenced. This may be because - * of problems with the context such as security failures, or it - * may be because the reference is inherently not possible to - * de-reference (as in the case of a non-serializable API - * consumer reference). - */ - InputStream openStream(ReferenceContext context) - throws DereferenceException; - - /** - * Approximate size of the stored data or -1 if we do not know. - */ - Long getApproximateSizeInBytes(); - - /** - * Resolution cost is an informal guide to how costly the process of - * de-referencing this reference would be. It's used when assessing which - * out of a set of ExternalReferenceSPI implementations to use to get the - * value of the reference(s), in particular when rendering to POJOs or when - * translating throught the de-reference / construct from stream route. As - * this property is highly complex and potentially expensive in itself to - * evaluate there's no requirement for it to be absolutely correct, it's - * just used as a guide that, for example, it is easier to get bytes from a - * file on the local disk than to get them from a resource held on a grid on - * the other side of the planet. - * - * @return a float representing some notion of resolution cost, lower values - * represent cheaper de-reference paths. - */ - float getResolutionCost(); - - ExternalReferenceSPI clone() throws CloneNotSupportedException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceTranslatorSPI.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceTranslatorSPI.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceTranslatorSPI.java deleted file mode 100644 index bc46dce..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceTranslatorSPI.java +++ /dev/null @@ -1,96 +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; - -/** - * Constructs an ExternalReference instance from an existing ExternalReference, - * most usually of a different type. Used by the {@link ReferenceSetAugmentor}. - * This SPI should not be used for cases where an ExternalReferenceSPI is - * constructed from a stream of bytes, this is intended for direct reference to - * reference translation with the assumption that this is more efficient for - * whatever reason. For cases where the reference is constructed from a byte - * stream you should implement {@link ExternalReferenceBuilder} instead. - * <p> - * For SPI purposes implementations should be java beans with default - * constructors, any required state such as the location of remote repositories - * to which data can be staged will be passed in in the ReferenceContext. - * - * @author Tom Oinn - */ -public interface ExternalReferenceTranslatorSPI<SourceType extends ExternalReferenceSPI, TargetType extends ExternalReferenceSPI> { - /** - * Given an existing ExternalReferenceSPI, build the appropriate target - * ExternalReferenceSPI implementation and return it. - * - * @param sourceReference - * the reference to be used as source for the translation. - * @param context - * a reference resolution context, needed potentially to access - * the existing external references or to construct the new one, - * especially in cases where the context contains security agents - * giving access to a remote data staging system - * @throws ExternalReferenceConstructionException - * if an error occurs instantiating the new reference. - * @return the newly constructed ExternalReferenceSPI instance. - */ - TargetType createReference(SourceType sourceReference, - ReferenceContext context); - - /** - * Return the type of external reference that this translator consumes. - * - * @return ExternalReferenceSPI class corresponding to the reference type - * used as a source by this translator. - */ - Class<SourceType> getSourceReferenceType(); - - /** - * Return the type of external reference this translator constructs. - * - * @return ExternalReferenceSPI class corresponding to the reference type - * emitted by this translator. - */ - Class<TargetType> getTargetReferenceType(); - - /** - * Because the reference translator may rely on facilities provided to it - * through the context this method is available to check whether these - * facilities are sufficient. - * - * @param context - * the reference context that will be used to construct new - * references during the translation process - * @return whether the context contains necessary resources for the - * reference construction process - */ - boolean isEnabled(ReferenceContext context); - - /** - * Return an approximate complexity cost of the translation. In general we - * can't make any guarantees about this because the complexity of the - * translation depends on more than just the types involved - it can depend - * on local configuration, network location relative to the data stores - * referenced and in some cases on the data themselves. For now though we - * assign an approximation, the default value is 1.0f and lower values - * represent less costly operations. - */ - float getTranslationCost(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceValidationException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceValidationException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceValidationException.java deleted file mode 100644 index c8b540d..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ExternalReferenceValidationException.java +++ /dev/null @@ -1,50 +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; - -/** - * Thrown by setter methods and constructors of ExternalReferenceSPI - * implementations when fed parameters which cause some kind of format or - * validation error. These might include badly formed URL or file paths or any - * other property that fails to validate against some reference type specific - * scheme. - * - * @author Tom Oinn - */ -public class ExternalReferenceValidationException extends RuntimeException { - private static final long serialVersionUID = 3031393671457773057L; - - public ExternalReferenceValidationException() { - // - } - - public ExternalReferenceValidationException(String message) { - super(message); - } - - public ExternalReferenceValidationException(Throwable cause) { - super(cause); - } - - public ExternalReferenceValidationException(String message, Throwable cause) { - super(message, cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/Identified.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/Identified.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/Identified.java deleted file mode 100644 index 8e9c5fd..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/Identified.java +++ /dev/null @@ -1,36 +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; - -/** - * Interface for any object that has an associated {@link T2Reference} - * - * @author Tom Oinn - */ -public interface Identified { - /** - * Return an appropriately configured instance of T2Reference for this - * identified object. - * - * @return the id of this object in the form of a T2Reference - */ - T2Reference getId(); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/IdentifiedList.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/IdentifiedList.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/IdentifiedList.java deleted file mode 100644 index 032906f..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/IdentifiedList.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; - -import java.util.List; - -/** - * An identified list is a list which is identified by a T2Reference. Lists are - * immutable once named - if getId() returns a non null value all list methods - * modifying the underlying list data will throw {@link IllegalStateException}. - * In the reference management API this list sub-interface is used to represent - * both collections of identifiers (i.e. 'raw' stored lists) and more fully - * resolved structures where the types in the list can be reference sets, error - * documents and other lists of such. The {@link ListDao} interface uses only - * the 'raw' form consisting of flat lists of identifiers. - * <p> - * The IdentifiedList has a unique T2Reference associated with it. If this is - * null the contents of the list may be modified, otherwise all modification - * operations throw {@link IllegalStateException}. Lists in T2, once named, are - * immutable. - * - * @author Tom Oinn - * - * @param <T> - */ -public interface IdentifiedList<T> extends List<T>, Identified { - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListDao.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListDao.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListDao.java deleted file mode 100644 index 7e064be..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListDao.java +++ /dev/null @@ -1,67 +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; - -import static org.springframework.transaction.annotation.Propagation.REQUIRED; -import static org.springframework.transaction.annotation.Propagation.SUPPORTS; - -import org.springframework.transaction.annotation.Transactional; - -/** - * Data access object handling NamedLists of T2Reference instances. - * - * @author Tom Oinn - */ -public interface ListDao { - /** - * Store a named and populated IdentifiedList of T2Reference to the - * database. - * - * @param theList - * list to store - * @throws DaoException - * if any exception is thrown when connecting to the underlying - * store or when storing the list - */ - @Transactional(propagation = REQUIRED, readOnly = false) - void store(IdentifiedList<T2Reference> theList) throws DaoException; - - /** - * Retrieves a named and populated IdentifiedList of T2Reference from the - * database by T2Reference - * - * @param reference - * id of the list to retrieve - * @return a previously stored list of T2References - * @throws DaoException - * if any exception is thrown when connecting to the underlying - * data store or when attempting retrieval of the list - */ - @Transactional(propagation = SUPPORTS, readOnly = true) - IdentifiedList<T2Reference> get(T2Reference reference) throws DaoException; - - @Transactional(propagation = SUPPORTS, readOnly = false) - boolean delete(IdentifiedList<T2Reference> theList) throws DaoException; - - @Transactional(propagation = SUPPORTS, readOnly = false) - void deleteIdentifiedListsForWFRun(String workflowRunId) - throws DaoException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListService.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListService.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListService.java deleted file mode 100644 index dae18af..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListService.java +++ /dev/null @@ -1,144 +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; - -import static org.springframework.transaction.annotation.Propagation.REQUIRED; -import static org.springframework.transaction.annotation.Propagation.SUPPORTS; - -import java.util.List; - -import org.springframework.transaction.annotation.Transactional; - -/** - * Provides facilities to register list of T2References, register empty lists at - * any given depth and to resolve appropriate T2Reference instances back to - * these lists. Registration operations assign names and lock the list contents - * as a result. This service operates strictly on T2References, it neither tries - * to nor is capable of any form of reference resolution, so aspects such as - * collection traversal are not handled here (these are performed by the top - * level reference service) - * - * @author Tom Oinn - */ -@Transactional(propagation = SUPPORTS, readOnly = true) -public interface ListService { - /** - * Register a new list of T2References. The depth of the list will be - * calculated based on the depth of the references within it - if these are - * not uniform the list won't be created (all children of a list in T2 must - * have the same depth as their siblings). Provided this constraint is - * satisfied the list is named and stored in the backing store. The returned - * list is at this point immutable, operations modifying it either directly - * or through the ListIterator will fail with an IllegalStateException. - * Implementations should copy the input list rather than keeping a - * reference to it to preserve this property. - * <p> - * The created references will be related with a workflow run id passed - * through ReferenceContext so we can track all data referenced by a - * specific run. - * - * @param items - * the T2Reference instances to store as a list. - * @return a new IdentifiedList of T2Reference instances allocated with a - * T2Reference itself as the unique name and cached by the backing - * store. - * @throws ListServiceException - * if there is a problem either with the specified list of - * references or with the storage subsystem. - */ - @Transactional(propagation = REQUIRED, readOnly = false) - IdentifiedList<T2Reference> registerList(List<T2Reference> items, - ReferenceContext context) throws ListServiceException; - - /** - * Register a new empty list with the specified depth. This is needed - * because in the case of empty lists we can't calculate the depth from the - * list items (what with there not being any!), but the depth property is - * critical for the T2 iteration and collection management system in the - * enactor - we need to know that this is an empty list that - * <em>would have</em> contained lists, for example. - * <p> - * The created references will be related with a workflow run id passed - * through ReferenceContext so we can track all data referenced by a - * specific run. - * - * @param depth - * the depth of the empty list, must be >=1 - * @return a new empty IdentifiedList allocated with a T2Reference itself as - * the unique name and cached by the backing store. - * @throws ListServiceException - * if there is a problem with the storage subsystem or if called - * with an invalid depth argument - */ - @Transactional(propagation = REQUIRED, readOnly = false) - IdentifiedList<T2Reference> registerEmptyList(int depth, - ReferenceContext context) throws ListServiceException; - - /** - * Retrieve a previously named and registered list of T2Reference instances - * identified by the specified T2Reference (which must be of type - * T2ReferenceType.IdentifiedList) - * - * @param id - * identifier of the list of reference to retrieve - * @return an IdentifiedList of T2References. Note that because this list is - * named it is effectively immutable, if you want to modify the list - * you have to create and register a new list, you cannot modify the - * returned value of this directly. This is why there is no update - * method in the service or dao for reference lists. - * @throws ListServiceException - * if anything goes wrong with the retrieval process or if there - * is something wrong with the reference (such as it being of - * the wrong reference type). - */ - IdentifiedList<T2Reference> getList(T2Reference id) - throws ListServiceException; - - /** - * Functionality the same as {@link #getList(T2Reference) getList} but in - * asynchronous mode, returning immediately and using the supplied callback - * to communicate its results. - * - * @param id - * a {@link T2Reference} identifying an {@link IdentifiedList} to - * retrieve - * @param callback - * a {@link ListServiceCallback} used to convey the results of - * the asynchronous call - * @throws ListServiceException - * if the reference set service is not correctly configured. - * Exceptions encountered when performing the asynchronous call - * are not returned here, for obvious reasons, and are instead - * messaged through the callback interface. - */ - void getListAsynch(T2Reference id, ListServiceCallback callback) - throws ListServiceException; - - @Transactional(propagation = SUPPORTS, readOnly = false) - boolean delete(T2Reference reference) throws ReferenceServiceException; - - /** - * Delete all {@link IdentifiedList}S used by the specific workflow run. - */ - @Transactional(propagation = SUPPORTS, readOnly = false) - void deleteIdentifiedListsForWorkflowRun(String workflowRunId) - throws ReferenceServiceException; -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceCallback.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceCallback.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceCallback.java deleted file mode 100644 index 754caf6..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceCallback.java +++ /dev/null @@ -1,47 +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; - -/** - * Callback interface used by asynchronous methods in the - * {@link ListService} interface - * - * @author Tom Oinn - */ -public interface ListServiceCallback { - /** - * Called when the requested {@link ReferenceSet} has been successfully - * retrieved. - * - * @param references - * the ReferenceSet requested - */ - void listRetrieved(IdentifiedList<T2Reference> references); - - /** - * Called if the retrieval failed for some reason - * - * @param cause - * a ListServiceException explaining the retrieval - * failure - */ - void listRetrievalFailed(ListServiceException cause); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceException.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceException.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceException.java deleted file mode 100644 index 01cdd82..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ListServiceException.java +++ /dev/null @@ -1,48 +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; - -/** - * Thrown by methods in the ListService interface if anything goes wrong with - * list registration or retrieval. Any underlying exceptions that can't be - * handled in the service layer are wrapped in this and re-thrown. - * - * @author Tom Oinn - */ -public class ListServiceException extends RuntimeException { - private static final long serialVersionUID = 5049346991071587866L; - - public ListServiceException() { - super(); - } - - public ListServiceException(String message) { - super(message); - } - - public ListServiceException(Throwable cause) { - super(cause); - } - - public ListServiceException(String message, Throwable cause) { - super(message, cause); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ReferenceContext.java ---------------------------------------------------------------------- diff --git a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ReferenceContext.java b/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ReferenceContext.java deleted file mode 100644 index 0ce2de3..0000000 --- a/taverna-reference-api/src/main/java/net/sf/taverna/t2/reference/ReferenceContext.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; - -import java.util.List; - -/** - * Many operations over the reference manager require access to an appropriate - * context. The context contains hooks out to platform level facilities such as - * the security agent framework (when used in conjunction with the enactor). - * <p> - * This interface is also used to pass in resources required by the external - * reference translation and construction SPIs. An example might be a translator - * from File to URL could work by copying the source file to a web share of some - * kind, but obviously this can't happen unless properties such as the location - * of the web share folder are known. These properties tend to be properties of - * the installation rather than of the code, referring as they do to resources - * on the machine hosting the reference manager (and elsewhere). - * <p> - * Where entities in the context represent properties of the platform rather - * than the 'session' they are likely to be configured in a central location - * such as a Spring context definition, this interface is neutral to those - * concerns. - * - * @author Tom Oinn - */ -public interface ReferenceContext { - /** - * Return a list of all entities in the resolution context which match the - * supplied entity type argument. - * - * @param <T> - * The generic type of the returned entity list. In general the - * compiler is smart enough that you don't need to specify this, - * it can pick it up from the entityType parameter. - * @param entityType - * Class of entity to return. Use Object.class to return all - * entities within the reference context - * @return a list of entities from the reference context which can be cast - * to the specified type. - */ - <T extends Object> List<T> getEntities(Class<T> entityType); - - /** - * Add an entity to the context. - */ - void addEntity(Object entity); -}
