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Posted to commits@taverna.apache.org by re...@apache.org on 2015/03/23 17:38:09 UTC
[25/51] [partial] incubator-taverna-engine git commit:
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Curateable.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Curateable.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Curateable.java
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-/*******************************************************************************
- * 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.annotation;
-
-import java.util.Date;
-import java.util.List;
-
-/**
- * Implemented by objects which can have curation assertions attached to them.
- * In our model this includes the AnnotationAssertion but also includes the
- * CurationEvent itself, in this way we allow curation of curation assertions
- * and thence a conversational model of annotation.
- *
- * @author Tom Oinn
- *
- */
-public interface Curateable {
-
- /**
- * Curateable instances have a list of curation events which are used to
- * determine whether the implementing object is valid given a particular
- * interpretive context. If this list is empty the event is unchallenged.
- *
- * @return
- */
- public List<CurationEvent<?>> getCurationAssertions();
-
- /**
- * All curation events are marked with their creation date, this is the date
- * at which the curation event was associated with its target.
- *
- * @return
- */
- public Date getCreationDate();
-
- /**
- * Each curateable has a list of people associated with it, frequently one
- * person and in some cases none, although this should be avoided if
- * possible.
- *
- * @return
- */
- public List<? extends Person> getCreators();
-
- /**
- * Each annotation or curation has a resource from which the event is
- * inherently derived, for example if the annotation was created manually
- * after reading a paper the source would unambiguously specify the
- * publication.
- *
- * @return
- */
- public AnnotationSourceSPI getSource();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEvent.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEvent.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEvent.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEvent.java
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-/*******************************************************************************
- * 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.annotation;
-
-/**
- * Represents a single act of curation, parameterized on a bean encapsulating
- * the necessary and sufficient information to describe the specifics of the
- * curation event.
- *
- * @author Tom Oinn
- *
- * @param <T>
- */
-public interface CurationEvent<CurationType extends CurationEventBeanSPI> {
-
- public CurationType getDetail();
-
- /**
- * The curation event type specifies whether this curation event is a
- * validation, repudiation or neither of its target.
- *
- * @return
- */
- public CurationEventType getType();
-
- /**
- * The curation event applies to a specific other event, either another
- * curation event or an annotation assertion.
- *
- * @return the event which this event is curating
- */
- public Curateable getTarget();
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventBeanSPI.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventBeanSPI.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventBeanSPI.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventBeanSPI.java
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-/*******************************************************************************
- * 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.annotation;
-
-/**
- * Contains the detail for a single curation event. In many cases this will be a
- * plain base curation object with very little information but it allows for us
- * to specify additional parameters to the curation event which can then be used
- * by the AnnotationPerspective instance to determine whether it believes the
- * curator.
- *
- * @author Tom Oinn
- *
- */
-public interface CurationEventBeanSPI {
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventType.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventType.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventType.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/CurationEventType.java
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@@ -1,43 +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.annotation;
-
-public enum CurationEventType {
-
- /**
- * The curation event asserts that the event it is attached to was correct,
- * effectively signing off an approval on the attached event.
- */
- VALIDATION,
-
- /**
- * The curation event repudiates the information in the attached event,
- * denying its validity.
- */
- REPUDIATION,
-
- /**
- * The curation event neither validates nor repudiates the information in
- * the attached event.
- */
- NEUTRAL;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyRole.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyRole.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyRole.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyRole.java
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-/*******************************************************************************
- * 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.annotation;
-
-/**
- * Possible relationships between entities in a hierarchical context. This is
- * used as a property of the HierarchyTraversal annotation on members which
- * traverse a conceptual object hierarchy such as a parent-child containment
- * relationship. As an example the getProcessors() method in Dataflow is
- * annotated with <code>&HierarchyRole(role=CHILD)</code> to indicate that
- * it accesses child members of the workflow model containment hierarchy.
- *
- * @author Tom Oinn
- *
- */
-public enum HierarchyRole {
-
- CHILD,
-
- PARENT;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyTraversal.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyTraversal.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyTraversal.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/HierarchyTraversal.java
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-/*******************************************************************************
- * 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.annotation;
-
-import java.lang.annotation.Documented;
-import java.lang.annotation.ElementType;
-import java.lang.annotation.Retention;
-import java.lang.annotation.RetentionPolicy;
-import java.lang.annotation.Target;
-
-/**
- * Applied to getFoo methods to indicate that the returned type is related to
- * the annotated type by some hierarchical relationship, either parent or child.
- * This can then be used by annotation tools to determine the structure of an
- * object under annotation in order to find any child objects without
- * accidentally traversing outside of the bound of the object to be annotated.
- * <p>
- * As annotations are not inherited any annotation tool should traverse up the
- * type structure of an object under annotation to determine the possible
- * child-parent relationships from superclasses and implemented interfaces.
- * <p>
- * There is no guarantee that the return types from annotated members implement
- * Annotated, in these cases traversal should still be followed to cover cases
- * where a grandchild of an object is annotatable even though all children are
- * not.
- * <p>
- * This should only be applied to method with no arguments, if this is not the
- * case an annotation tool is free to not follow such methods (as it has no way
- * to determine what should be applied as arguments)
- *
- * @author Tom Oinn
- *
- */
-@Retention(RetentionPolicy.RUNTIME)
-@Target(ElementType.METHOD)
-@Documented
-public @interface HierarchyTraversal {
-
- /**
- * The role the return type of the annotated method plays in the named
- * hierarchy relative to the containing type.
- *
- * @return role in hierarchy at corresponding index in the Hierarchies
- * property, currently either CHILD or PARENT
- */
- HierarchyRole[] role();
-
- /**
- * It is possible for multiple orthogonal containment hierarchies to exist,
- * to allow for this the hierarchies are named using this field.
- *
- * @return name of the hierarchy to which this relationship applies
- */
- String[] hierarchies();
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Person.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Person.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Person.java
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-/*******************************************************************************
- * 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.annotation;
-
-/**
- * All metadata assertions and curation assertions have a person who is
- * ultimately responsible for the assertion (although this may not necessarily
- * imply that the assertion was created interactively).
- *
- * TODO this needs to have some members! Cross reference with myExperiment user
- * model I suspect.
- *
- * @author Tom Oinn
- *
- */
-public interface Person {
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericRangeAssertion.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericRangeAssertion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericRangeAssertion.java
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-/*******************************************************************************
- * 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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-
-/**
- * Generic annotation containing a pair of numeric values with precision
- * determined by the type parameter which form a bound.
- *
- * @author Tom Oinn
- *
- */
-@AppliesTo(targetObjectType = { Object.class }, many = true)
-public abstract class AbstractNumericRangeAssertion<NumericType extends Number>
- implements AnnotationBeanSPI {
-
- private NumericType upperNumericValue;
-
- private NumericType lowerNumericValue;
-
- /**
- * Default constructor as mandated by java bean specification
- */
- protected AbstractNumericRangeAssertion() {
- //
- }
-
- public NumericType getUpperNumericValue() {
- return upperNumericValue;
- }
-
- public void setUpperNumericValue(NumericType upperNumericValue) {
- this.upperNumericValue = upperNumericValue;
- }
-
- public NumericType getLowerNumericValue() {
- return lowerNumericValue;
- }
-
- public void setLowerNumericValue(NumericType lowerNumericValue) {
- this.lowerNumericValue = lowerNumericValue;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericValueAssertion.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericValueAssertion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractNumericValueAssertion.java
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-/*******************************************************************************
- * 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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-
-/**
- * Generic annotation containing a single number of precision specified by the
- * type variable
- *
- * @author Tom Oinn
- *
- */
-@AppliesTo(targetObjectType = { Object.class }, many = true)
-public abstract class AbstractNumericValueAssertion<NumericType extends Number>
- implements AnnotationBeanSPI {
-
- private NumericType numericValue;
-
- /**
- * Default constructor as mandated by java bean specification
- */
- protected AbstractNumericValueAssertion() {
- //
- }
-
- public NumericType getNumericValue() {
- return numericValue;
- }
-
- public void setNumericValue(NumericType numericValue) {
- this.numericValue = numericValue;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractTextualValueAssertion.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractTextualValueAssertion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/AbstractTextualValueAssertion.java
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-/*******************************************************************************
- * 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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-
-/**
- * Generic bit of free text that can be stuck to anything, subclass for more
- * specific uses
- *
- * @author Tom Oinn
- *
- */
-@AppliesTo(targetObjectType = { Object.class }, many = true)
-public abstract class AbstractTextualValueAssertion implements AnnotationBeanSPI {
-
- private String text;
-
- /**
- * Default constructor as mandated by java bean specification
- */
- protected AbstractTextualValueAssertion() {
- //
- }
-
- public String getText() {
- return text;
- }
-
- public void setText(String text) {
- this.text = text;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Author.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Author.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Author.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Author.java
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-/*******************************************************************************
- * 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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-
-/**
- * The name of an author of a dataflow held as a String
- *
- * It should allow many but currently only allows one
- *
- * @author Alan R Williams
- *
- */
-@AppliesTo(targetObjectType = { Dataflow.class }, many = false)
-public class Author extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public Author() {
- //
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DescriptiveTitle.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DescriptiveTitle.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DescriptiveTitle.java
deleted file mode 100644
index f9defd6..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DescriptiveTitle.java
+++ /dev/null
@@ -1,42 +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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-
-/**
- * The descriptive title of a dataflow held as a String
- *
- * @author Alan R Williams
- *
- */
-@AppliesTo(targetObjectType = { Dataflow.class }, many = false)
-public class DescriptiveTitle extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public DescriptiveTitle() {
- //
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DocumentationUrl.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DocumentationUrl.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DocumentationUrl.java
deleted file mode 100644
index 96fe397..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/DocumentationUrl.java
+++ /dev/null
@@ -1,58 +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.annotation.annotationbeans;
-
-import java.net.URL;
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Port;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * A link to documentation for the target element contained at a particular
- * Uniform Resource Locator (URL)
- *
- * @author Tom Oinn
- * @author Alan Williams
- */
-@AppliesTo(targetObjectType = { Port.class, Activity.class, Processor.class, Dataflow.class }, many = true)
-public class DocumentationUrl implements AnnotationBeanSPI {
-
- private URL documentationURL;
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public DocumentationUrl() {
- //
- }
-
- public URL getDocumentationURL() {
- return documentationURL;
- }
-
- public void setDocumentationURL(URL documentationURL) {
- this.documentationURL = documentationURL;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/ExampleValue.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/ExampleValue.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/ExampleValue.java
deleted file mode 100644
index dd8540c..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/ExampleValue.java
+++ /dev/null
@@ -1,43 +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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.DataflowInputPort;
-import net.sf.taverna.t2.workflowmodel.DataflowOutputPort;
-
-/**
- * A String containing an example or a description of an example
- *
- * @author Alan R Williams
- *
- */
-@AppliesTo(targetObjectType = { DataflowInputPort.class , DataflowOutputPort.class }, many = false)
-public class ExampleValue extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public ExampleValue() {
- //
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/FreeTextDescription.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/FreeTextDescription.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/FreeTextDescription.java
deleted file mode 100644
index c871ec5..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/FreeTextDescription.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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Condition;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.DataflowPort;
-import net.sf.taverna.t2.workflowmodel.Datalink;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * An unconstrained textual description held as a String
- *
- * @author Tom Oinn
- *
- */
-@AppliesTo(targetObjectType = { Dataflow.class, Processor.class,
- Activity.class, DataflowPort.class, Datalink.class, Condition.class }, many = false)
-public class FreeTextDescription extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public FreeTextDescription() {
- //
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/HostInstitution.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/HostInstitution.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/HostInstitution.java
deleted file mode 100644
index db35cd3..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/HostInstitution.java
+++ /dev/null
@@ -1,45 +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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * The host institution for an activity implementation
- *
- * @author Tom Oinn
- * @author Alan Williams
- */
-@AppliesTo(targetObjectType = { Activity.class }, many = false)
-public class HostInstitution extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public HostInstitution() {
- super();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/IdentificationAssertion.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/IdentificationAssertion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/IdentificationAssertion.java
deleted file mode 100644
index 44bd587..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/IdentificationAssertion.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-
-/**
- * An IdentificationAssertion is used to hold previous identifications of an
- * object.
- *
- * @author alanrw
- *
- */
-@AppliesTo(targetObjectType = { Dataflow.class }, many = false, pruned = false)
-public class IdentificationAssertion implements AnnotationBeanSPI {
-
- private String identification;
-
- /**
- * @return The identification. This will be a previous identifier of the
- * annotated object.
- */
- public String getIdentification() {
- return identification;
- }
-
- /**
- * @param identification
- * A previous identified of the annotated object.
- */
- public void setIdentification(String identification) {
- this.identification = identification;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/MimeType.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/MimeType.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/MimeType.java
deleted file mode 100644
index eb09c61..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/MimeType.java
+++ /dev/null
@@ -1,60 +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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Port;
-
-/**
- * A single MIME type, intended to be used to annotate an input or output port
- * within the workflow to denote the type within that system of data produced or
- * consumed by the port.
- *
- * @author Tom Oinn
- *
- */
-@AppliesTo(targetObjectType = { Port.class })
-public class MimeType extends AbstractTextualValueAssertion {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public MimeType() {
- super();
- }
-
- /**
- * Return the MIME type as a string, mime types look like 'part/part'. We
- * may want to consider whether it's possible to make this a genuine
- * enumeration driven off a canonical list of MIME types or whether it's
- * best kept as the current (free) string. The advantage of an enumerated
- * type is that we could attach description to the MIME types which would
- * help with the UI construction but maybe this isn't the place to put it
- * (should this link be in the UI layer? probably)
- *
- * @return the MIME type as a string.
- */
- @Override
- public String getText() {
- return super.getText();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Optional.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Optional.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Optional.java
deleted file mode 100644
index 3f18282..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/Optional.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.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.workflowmodel.InputPort;
-
-/**
- * A declaration that the bound input port is optional, if this annotation is
- * refuted then the interpretation should be that the input port is required.
- *
- * @author Tom Oinn
- * @author Alan Williams
- */
-@AppliesTo(targetObjectType = { InputPort.class }, many = false)
-public class Optional implements AnnotationBeanSPI {
-
- /**
- * Default constructor as mandated by java bean specification
- */
- public Optional() {
- //
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/SemanticAnnotation.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/SemanticAnnotation.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/SemanticAnnotation.java
deleted file mode 100644
index 02dced3..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/annotationbeans/SemanticAnnotation.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.annotation.annotationbeans;
-
-import net.sf.taverna.t2.annotation.AnnotationBeanSPI;
-import net.sf.taverna.t2.annotation.AppliesTo;
-import net.sf.taverna.t2.workflowmodel.Condition;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Datalink;
-import net.sf.taverna.t2.workflowmodel.Merge;
-import net.sf.taverna.t2.workflowmodel.Port;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayer;
-
-/**
- * A SemanticAssertion holds a String which contains RDF about an Object
- * @author alanrw
- *
- */
-@AppliesTo(targetObjectType = { Dataflow.class, Processor.class, Port.class, Activity.class, Datalink.class, Merge.class, Condition.class, DispatchLayer.class }, many = false)
-public class SemanticAnnotation implements AnnotationBeanSPI {
-
- private String mimeType = "text/rdf+n3";
-
- private String content = "";
-
- public String getMimeType() {
- return mimeType;
- }
-
- public void setMimeType(String mimeType) {
- this.mimeType = mimeType;
- }
-
- /**
- * @param content the content to set
- */
- public void setContent(String content) {
- this.content = content;
- }
-
- /**
- * @return the content
- */
- public String getContent() {
- return content;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/package.html
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/package.html b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/package.html
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/package.html
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-<body>
-Entities within the workflow object model may be marked as annotated.
-When marked as such they contract to provide one or more of a variety of
-forms of metadata, whether generic or specific to the type of object
-within the model. This description is deliberately kept vague for now
-because we haven't yet enumerated what classes of annotation exist on
-each entity.
-<p>From this point in we will use the term 'metadata' to distinguish
-between annotations in terms of properties of the workflow and
-annotations in terms of the Java 5 language feature. This is
-particularly important we we use Java Annotations to implement the
-workflow annotations. Yay.
-<p>In keeping with the read-only model of the API package all
-metadata interfaces only specify the get methods for their respective
-contents. Modification of metadata instances is performed through Edit
-objects.
-</body>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/FacadeListener.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/FacadeListener.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/FacadeListener.java
deleted file mode 100644
index 35d6fef..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/FacadeListener.java
+++ /dev/null
@@ -1,49 +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.facade;
-
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade.State;
-
-/**
- * Used to communicate a failure of the overall workflow to interested parties.
- *
- * @author Tom Oinn
- */
-public interface FacadeListener {
- /**
- * Called if the workflow fails in a critical and fundamental way. Most
- * internal failures of individual process instances will not trigger this,
- * being handled either by the per processor dispatch stack through retry,
- * failover etc or by being converted into error tokens and injected
- * directly into the data stream. This therefore denotes a catastrophic and
- * unrecoverable problem.
- *
- * @param message
- * Description of what happened
- * @param t
- * The cause of the failure
- */
- void workflowFailed(WorkflowInstanceFacade facade, String message,
- Throwable t);
-
- void stateChange(WorkflowInstanceFacade facade, State oldState,
- State newState);
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/ResultListener.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/ResultListener.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/ResultListener.java
deleted file mode 100644
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/ResultListener.java
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@@ -1,43 +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.facade;
-
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-
-/**
- * Implement and use with the WorkflowInstanceFacade to listen for data
- * production events from the underlying workflow instance
- *
- * @author Tom Oinn
- */
-public interface ResultListener {
- /**
- * Called when a new result token is produced by the workflow instance.
- *
- * @param token
- * the WorkflowDataToken containing the result.
- * @param portName
- * The name of the output port on the workflow from which this
- * token is produced, this now folds in the owning process which
- * was part of the signature for this method
- */
- void resultTokenProduced(WorkflowDataToken token, String portName);
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowInstanceFacade.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowInstanceFacade.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowInstanceFacade.java
deleted file mode 100644
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowInstanceFacade.java
+++ /dev/null
@@ -1,237 +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.facade;
-
-import java.lang.ref.WeakReference;
-import java.util.WeakHashMap;
-
-import net.sf.taverna.t2.invocation.InvocationContext;
-import net.sf.taverna.t2.invocation.TokenOrderException;
-import net.sf.taverna.t2.invocation.WorkflowDataToken;
-import net.sf.taverna.t2.monitor.MonitorNode;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.utility.TypedTreeModel;
-import net.sf.taverna.t2.workflowmodel.ControlBoundary;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-
-/**
- * The interaction point with a workflow instance. Technically there is no such
- * thing as a workflow instance in Taverna2, at least not in any real sense in
- * the code itself. The instance is more literally an identifier used as the
- * root of all data and error objects within this workflow and by which the top
- * level DataFlow or similar object is identified in the state tree. The
- * implementation of this interface should hide this though, automatically
- * prepending the internally stored (and hidden) identifier to all data push
- * messages and providing a subtree of the state model rooted at the internal
- * ID.
- * <p>
- * TODO - we should probably have callbacks for failure states here, but that
- * would need a decent definition (and maybe even ontology of) what failure
- * means. It's less obvious in a data streaming world what a failure is. At the
- * moment the dispatch stack can potentially treat unhandled error messages as
- * failing the processor, how do we get this exception information back up to
- * the workflow level?
- *
- * @author Tom Oinn
- * @author Alex Nenadic
- * @author Stian Soiland-Reyes
- * @author Alan R Williams
- */
-@ControlBoundary
-public interface WorkflowInstanceFacade {
- public static enum State {
- /**
- * Workflow has not yet been started using
- * {@link WorkflowInstanceFacade#fire()}
- */
- prepared,
- /**
- * Workflow is running (or have been resumed using
- * {@link WorkflowInstanceFacade#fire()})
- */
- running,
- /**
- * Workflow has been paused using
- * {@link WorkflowInstanceFacade#pauseWorkflowRun()}
- */
- paused,
- /**
- * Workflow has completed, all processors are finished and all data
- * delivered to all output ports.
- */
- completed,
- /**
- * Workflow has been cancelled using
- * {@link WorkflowInstanceFacade#cancelWorkflowRun()}
- */
- cancelled;
- }
-
- /**
- * A weak hash map of all workflow run IDs mapped against the corresponding
- * WorkflowInstanceFacadeS. This is needed for activities with dependencies
- * (such as beanshell and API consumer) to gain access to the current
- * workflow via the WorkflowInstanceFacade.
- */
- static final WeakHashMap<String, WeakReference<WorkflowInstanceFacade>> workflowRunFacades = new WeakHashMap<>();
-
- /**
- * Push a data token into the specified port. If the token is part of a
- * stream the index contains the index of this particular token. If not the
- * index should be the empty integer array.
- *
- * @param token
- * A WorkflowDataToken containing the data to be pushed to the
- * workflow along with its current owning process identifier and
- * index
- * @param portName
- * Port name to use
- * @throws TokenOrderException
- * if ordering constraints on the token stream to each input
- * port are violated
- */
- void pushData(WorkflowDataToken token, String portName)
- throws TokenOrderException;
-
- /**
- * Where a workflow has no inputs this method will cause it to start
- * processing. Any processors within the workflow with no inputs are fired.
- *
- * @throws IllegalStateException
- * if the workflow has already been fired or has had data pushed
- * to it.
- */
- void fire() throws IllegalStateException;
-
- /**
- * The result listener is used to handle data tokens produced by the
- * workflow.
- * <p>
- * If the listener is registered after the workflow has already produced
- * results it will be immediately called with any results previously
- * produced. Where the workflow has completed a stream of results it may
- * only message the listener with the highest level one, so for a case where
- * a list of results is emited one at a time the listener may either get the
- * individual items followed by the list token or if registered after the
- * list token has been emited only receive the list token.
- *
- * @param listener
- */
- void addResultListener(ResultListener listener);
-
- /**
- * Remove a previously registered result listener
- *
- * @param listener
- */
- void removeResultListener(ResultListener listener);
-
- /**
- * A failure listener reports on overall workflow failure. It is not
- * triggered by the failure of individual processors unless that processor
- * is marked as critical. In fact in T2 all processors are marked as
- * critical by default as there are ways of handling errors within the data
- * stream, if the processor actually fails something really bad has
- * happened.
- * <p>
- * As with the result listener a failure listener registered after the
- * workflow has already failed will be immediately called with the failure
- * data.
- */
- void addFacadeListener(FacadeListener listener);
-
- /**
- * Remove a previously registered failure listener
- */
- void removeFacadeListener(FacadeListener listener);
-
- /**
- * Workflow state is available through a sub-tree of the monitor tree. For
- * security reasons the full monitor tree is never accessible through this
- * interface but the sub-tree rooted at the node representing this workflow
- * instance is and can be used for both monitoring and steering functions.
- * <p>
- * Uses the standard TreeModel-like mechanisms for registering change events
- * and can be plugged into a JTree for display purposes through the
- * TreeModelAdapter class.
- *
- * @return Typed version of TreeModel representing the state of this
- * workflow. Nodes in the tree are instances of MonitorNode
- */
- TypedTreeModel<MonitorNode> getStateModel();
-
- /**
- * Return the dataflow this facade facades
- */
- Dataflow getDataflow();
-
- /**
- * Return the invocation context used by this facade
- */
- InvocationContext getContext();
-
- /**
- * Return a map of the data pushed on the named port
- */
- WeakHashMap<String, T2Reference> getPushedDataMap();
-
- /**
- * Get the unique id of the wf run inside the facede.
- */
- String getWorkflowRunId();
-
- /**
- * Cancel the workflow run corresponding to this facade
- *
- * @return true if the workflow run was successfully cancelled. Note that
- * this does not mean that all of the invocations associated with
- * the run have finished.
- */
- boolean cancelWorkflowRun() throws IllegalStateException;
-
- /**
- * Pause the workflow run corresponding to this facade
- *
- * @return true if the workflow run was successfully paused.
- */
- boolean pauseWorkflowRun() throws IllegalStateException;
-
- /**
- * Resume the workflow run corresponding to this facade
- *
- * @return true if the workflow run was successfully resumed
- */
- boolean resumeWorkflowRun() throws IllegalStateException;
-
- /**
- * Return the current workflow {@link State}.
- *
- * @return The workflow state.
- */
- State getState();
-
- /**
- * An identifier that is unique to this facade.
- *
- * @return a String representing a unique internal identifier.
- */
- String getIdentifier();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowRunCancellation.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowRunCancellation.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowRunCancellation.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/WorkflowRunCancellation.java
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-/**
- *
- */
-package net.sf.taverna.t2.facade;
-
-/**
- * A WorkflowRunCancellation is passed to listeners when a workflow run is
- * cancelled.
- *
- * @author alanrw
- */
-@SuppressWarnings("serial")
-public class WorkflowRunCancellation extends Throwable {
- /**
- * The id of the workflow run that was cancelled
- */
- private String cancelledWorkflowRunId;
-
- public WorkflowRunCancellation (String runId) {
- cancelledWorkflowRunId = runId;
- }
-
- /**
- * @return the id of the workflow run that was cancelled.
- */
- public String getCancelledWorkflowRunId() {
- return cancelledWorkflowRunId;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/package.html
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/package.html b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/facade/package.html
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-<body>
-Facade interfaces to represent a workflow instance within the enactor.
-<p>Although T2 has no 'real' concept of a workflow instance, using
-identifiers on data instead, it is useful to treat it as if it does. The
-facade classes are the external 'invoke only' interface to the enactment
-system, providing wrappers around the actual single instance model. This
-also hides the shared state tree, exposing only the sub-tree rooted at
-the base ID internal to the facade layer. The state tree acts both as
-monitoring and steering infrastructure, the facade therefore prevents a
-process accessing the state of another workflow either maliciously or
-inadvertently.
-<p>The construction of these facade objects is not defined here, a
-factory method in the implementation package is the most likely
-candidate but there are other options, for example a peer to peer cloud
-may expose services to create new facades and allow access as might a
-web service based interface. The interfaces here are intended to be as
-easy to access remotely as possible.
-<p>For the same reasons there are no methods in the workflow facade
-concerning security or the management of data access - it is assumed
-that the constructor of the facade layer has embedded such concerns
-within it. There is therefore a clear split between initiation of the
-workflow session and manipulation of it with this package only
-addressing the latter of the two.
-</body>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Completion.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Completion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Completion.java
deleted file mode 100644
index c9f84f2..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Completion.java
+++ /dev/null
@@ -1,107 +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.invocation;
-
-/**
- * Contains a (possibly partial) completion event. The completion event is a
- * statement that no further events will occur on this channel with an index
- * prefixed by the completion index. As with Job events completion events have
- * an owning process with the same semantics as that of the Job class
- * <p>
- * The conceptual depth of a completion is the sum of the length of index array
- * for any data tokens the completion shares a stream with and the depth of
- * those tokens. This should be constant for any given token stream.
- *
- * @author Tom Oinn
- *
- */
-public class Completion extends IterationInternalEvent<Completion> {
-
- /**
- * Construct a new optionally partial completion event with the specified
- * owner and completion index
- *
- * @param owningProcess
- * @param completionIndex
- */
- public Completion(String owningProcess, int[] completionIndex,
- InvocationContext context) {
- super(owningProcess, completionIndex, context);
- }
-
- /**
- * Construct a new final completion event, equivalent to calling new
- * Completion(owningProcess, new int[0]);
- *
- * @param owningProcess
- */
- public Completion(String owningProcess, InvocationContext context) {
- super(owningProcess, new int[0], context);
- }
-
- @Override
- public String toString() {
- StringBuffer sb = new StringBuffer();
- sb.append("Cmp(" + owner + ")[");
- for (int i = 0; i < index.length; i++) {
- if (i > 0) {
- sb.append(",");
- }
- sb.append(index[i] + "");
- }
- sb.append("]");
- return sb.toString();
- }
-
- /**
- * Push the index array onto the owning process name and return the new Job
- * object. Does not modify this object, the method creates a new Job with
- * the modified index array and owning process
- *
- * @return
- */
- @Override
- public Completion pushIndex() {
- return new Completion(getPushedOwningProcess(), new int[] {}, context);
- }
-
- /**
- * Pull the index array previous pushed to the owning process name and
- * prepend it to the current index array
- */
- @Override
- public Completion popIndex() {
- return new Completion(owner.substring(0, owner.lastIndexOf(':')),
- getPoppedIndex(), context);
- }
-
- @Override
- public Completion popOwningProcess() throws ProcessIdentifierException {
- return new Completion(popOwner(), index, context);
- }
-
- @Override
- public Completion pushOwningProcess(String localProcessName)
- throws ProcessIdentifierException {
- return new Completion(pushOwner(localProcessName), index, context);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Event.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Event.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Event.java
deleted file mode 100644
index f0816ac..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/Event.java
+++ /dev/null
@@ -1,168 +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.invocation;
-
-/**
- * Abstract superclass of all 'event' types within a workflow invocation. These
- * are the Job and Completion events which are used internally within a
- * Processor, in particular by the dispatch stack and iteration system, and the
- * WorkflowDataToken which is the only event class that can exist outside of a
- * Processor boundary (and is therefore the most significant one for users of
- * the API)
- *
- * @author Tom Oinn
- */
-public abstract class Event<EventType extends Event<?>> {
- protected String owner;
- protected InvocationContext context;
- protected int[] index;
-
- protected Event(String owner, int[] index, InvocationContext context) {
- this.owner = owner;
- this.index = index;
- this.context = context;
- if (index == null)
- throw new RuntimeException("Job index cannot be null");
- if (owner == null)
- throw new RuntimeException("Owning process cannot be null");
- if (context == null)
- throw new RuntimeException("Invocation context cannot be null");
- }
-
- /**
- * An event is final if its index array is zero length
- *
- * @return true if indexarray.length==0
- */
- public final boolean isFinal() {
- return (index.length == 0);
- }
-
- /**
- * The event has an owner, this is represented as a String object but the
- * ownership is hierarchical in nature. The String is a colon separated list
- * of alphanumeric process identifiers, with identifiers being pushed onto
- * this list on entry to a process and popped off on exit.
- *
- * @return String of colon separated process identifiers owning this Job
- */
- public final String getOwningProcess() {
- return this.owner;
- }
-
- public final InvocationContext getContext() {
- return this.context;
- }
-
- /**
- * Return a copy of the event subclass with the last owning process removed
- * from the owning process list. For example, if the event had owner
- * 'foo:bar' this would return a duplicate event with owner 'foo'. If the
- * owning process is the empty string this is invalid and will throw a
- * ProcessIdentifierException
- *
- * @return a copy of the event with the parent process identifier
- */
- public abstract EventType popOwningProcess()
- throws ProcessIdentifierException;
-
- /**
- * Return a copy of the event subclass with the specified local process name
- * appended to the owning process identifier field. If the original owner
- * was 'foo' and this was called with 'bar' you'd end up with a copy of the
- * subclass with owner 'foo:bar'
- *
- * @param localProcessName
- * name to add
- * @return the modified event
- * @throws ProcessIdentifierException
- * if the local process name contains the ':' character
- */
- public abstract EventType pushOwningProcess(String localProcessName)
- throws ProcessIdentifierException;
-
- /**
- * Events have an index placing them in a conceptual tree structure. This
- * index is carried along with the event and used at various points to drive
- * iteration and ensure that separate jobs are kept that way
- */
- public final int[] getIndex() {
- return this.index;
- }
-
- /**
- * Helper method for implementations of popOwningProcess, this constructs
- * the appropriate process identifier after the leaf has been removed and
- * returns it. If there is no leaf to remove, i.e. the current process
- * identifier is the empty string, then ProcessIdentifierException is thrown
- *
- * @return
- * @throws ProcessIdentifierException
- */
- protected final String popOwner() throws ProcessIdentifierException {
- // Empty string already, can't pop from here, throw exception
- if (owner.isEmpty())
- throw new ProcessIdentifierException(
- "Attempt to pop a null owning process (empty string)");
- // A single ID with no colon in, return the empty string
- if (owner.lastIndexOf(':') < 0)
- return "";
- return owner.substring(0, owner.lastIndexOf(':'));
- }
-
- /**
- * Helper method for implementations of pushOwningProcess, appends the
- * specified local name to the current owning process identifier and returns
- * the new id. This doesn't change the current process identifier. If there
- * is a colon ':' in the specified name this is invalid and will throw
- * ProcessIdentifierException at you.
- *
- * @param newLocalProcess
- * @return
- * @throws ProcessIdentifierException
- */
- protected final String pushOwner(String newLocalProcess)
- throws ProcessIdentifierException {
- if (newLocalProcess.contains(":"))
- throw new ProcessIdentifierException("Can't push '"
- + newLocalProcess + "' as it contains a ':' character");
- if (owner.isEmpty())
- // If the owner was the empty string we don't need to append the
- // colon
- return newLocalProcess;
- return owner + ":" + newLocalProcess;
- }
-
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder();
- sb.append(getClass().getSimpleName());
- sb.append(' ');
- sb.append(owner);
- sb.append('[');
- for (int i : index) {
- sb.append(i);
- sb.append(" ");
- }
- sb.append(']');
- return sb.toString();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/InvocationContext.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/InvocationContext.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/InvocationContext.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/InvocationContext.java
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-/*******************************************************************************
- * 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.invocation;
-
-import net.sf.taverna.t2.provenance.reporter.ProvenanceReporter;
-import net.sf.taverna.t2.reference.ReferenceContext;
-import net.sf.taverna.t2.reference.ReferenceService;
-
-/**
- * Carries the context of a workflow invocation, the necessary data manager,
- * security agents and any other resource shared across the invocation such as
- * provenance injectors.
- *
- * @author Tom Oinn
- */
-public interface InvocationContext extends ReferenceContext {
- /**
- * Return the reference service to be used within this invocation context
- *
- * @return a configured instance of ReferenceService to be used to resolve
- * and register references to data in the workflow
- */
- ReferenceService getReferenceService();
-
- ProvenanceReporter getProvenanceReporter();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/IterationInternalEvent.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/IterationInternalEvent.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/IterationInternalEvent.java
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/invocation/IterationInternalEvent.java
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-/*******************************************************************************
- * 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.invocation;
-
-/**
- * Abstract superclass for event types which have to pass through the iteration
- * system. For this they need the ability to push and pull the iteration index
- * to and from the process identifier, this is done through the popIndex and
- * pushIndex methods. Subclasses of this may be used outside the iteration
- * system but anything which is passed into the iteration system must provide
- * this functionality.
- *
- * @author Tom Oinn
- *
- * @param <EventType>
- * reflexive self type
- */
-public abstract class IterationInternalEvent<EventType extends IterationInternalEvent<?>>
- extends Event<EventType> {
- /**
- * Protected constructor for the minimum fields required by all Event
- * subclasses
- *
- * @param owner
- * @param index
- * @param context
- */
- protected IterationInternalEvent(String owner, int[] index,
- InvocationContext context) {
- super(owner, index, context);
- }
-
- /**
- * Pop a previously pushed index array off the process name and append the
- * current index array to create the new index array. This is applied to a
- * new instance of an Event subclass and does not modify the target.
- *
- * @return new Event subclass with modified owning process and index
- */
- public abstract IterationInternalEvent<EventType> popIndex();
-
- /**
- * Push the index array onto the owning process name and return the new
- * Event subclass object. Does not modify this object, the method creates a
- * new Event subclass with the modified index array and owning process.
- *
- */
- public abstract IterationInternalEvent<EventType> pushIndex();
-
- /**
- * Helper method for the pushIndex operation
- *
- * @return
- */
- protected final String getPushedOwningProcess() {
- StringBuilder sb = new StringBuilder(owner).append(":");
- String sep = "";
- for (int idx : index) {
- sb.append(sep).append(idx);
- sep = ",";
- }
- return sb.toString();
- }
-
- /**
- * Helper method for the popIndex operation, returns the modified index
- * array. Subclasses must still implement logic to get the modified owning
- * process but that's relatively easy : <code>
- * return new <Event subclass>(owner.substring(0, owner.lastIndexOf(':')),getPoppedIndex(), dataMap);
- * </code>
- *
- * @return
- */
- protected final int[] getPoppedIndex() {
- int lastLocation = owner.lastIndexOf(':');
- String indexArrayAsString = owner.substring(lastLocation + 1);
- String[] parts = indexArrayAsString.split(",");
- int[] newIndexArray = new int[index.length + parts.length];
- int pos = 0;
- for (String part : parts)
- newIndexArray[pos++] = Integer.parseInt(part);
- System.arraycopy(index, 0, newIndexArray, pos, index.length);
- return newIndexArray;
- }
-}