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Posted to commits@taverna.apache.org by re...@apache.org on 2015/03/23 17:38:10 UTC
[26/51] [partial] incubator-taverna-engine git commit:
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-services-api/src/main/java/uk/org/taverna/commons/services/ServiceRegistry.java
----------------------------------------------------------------------
diff --git a/taverna-services-api/src/main/java/uk/org/taverna/commons/services/ServiceRegistry.java b/taverna-services-api/src/main/java/uk/org/taverna/commons/services/ServiceRegistry.java
deleted file mode 100644
index 62e45b4..0000000
--- a/taverna-services-api/src/main/java/uk/org/taverna/commons/services/ServiceRegistry.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2013 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 uk.org.taverna.commons.services;
-
-import java.net.URI;
-import java.util.Set;
-
-import org.apache.taverna.scufl2.api.port.InputActivityPort;
-import org.apache.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * Register of Taverna services.
- *
- * @author David Withers
- */
-public interface ServiceRegistry {
-
- /**
- * Returns the activity types in the registry.
- *
- * @return the activity types in the registry
- */
- public Set<URI> getActivityTypes();
-
- /**
- * Returns the JSON Schema for the configuration required by an activity.
- *
- * @param activityType
- * the activity type
- * @return the JSON Schema for the configuration required by an activity
- * @throws ActivityTypeNotFoundException
- * if the activity type is not in the registry
- */
- public JsonNode getActivityConfigurationSchema(URI activityType)
- throws InvalidConfigurationException, ActivityTypeNotFoundException;
-
- /**
- * Returns the input ports that the activity type requires to be present in order to execute
- * with the specified configuration.
- * <p>
- * If the activity does not require any input port for the configuration then an empty set is
- * returned.
- *
- * @param configuration
- * the activity configuration
- * @throws ActivityTypeNotFoundException
- * if the activity type is not in the registry
- * @return the input ports that the activity requires to be present in order to execute
- */
- public Set<InputActivityPort> getActivityInputPorts(URI activityType,
- JsonNode configuration) throws InvalidConfigurationException, ActivityTypeNotFoundException;
-
- /**
- * Returns the output ports that the activity type requires to be present in order to execute
- * with the specified configuration.
- * <p>
- * If the activity type does not require any output ports for the configuration then an empty
- * set is returned.
- *
- * @param configuration
- * the activity configuration
- * @throws ActivityTypeNotFoundException
- * if the activity type is not in the registry
- * @return the output ports that the activity requires to be present in order to execute
- */
- public Set<OutputActivityPort> getActivityOutputPorts(URI activityType,
- JsonNode configuration) throws InvalidConfigurationException, ActivityTypeNotFoundException;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-services-impl/src/main/java/org/apache/taverna/commons/services/impl/ServiceRegistryImpl.java
----------------------------------------------------------------------
diff --git a/taverna-services-impl/src/main/java/org/apache/taverna/commons/services/impl/ServiceRegistryImpl.java b/taverna-services-impl/src/main/java/org/apache/taverna/commons/services/impl/ServiceRegistryImpl.java
new file mode 100644
index 0000000..1aaf1de
--- /dev/null
+++ b/taverna-services-impl/src/main/java/org/apache/taverna/commons/services/impl/ServiceRegistryImpl.java
@@ -0,0 +1,91 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.commons.services.impl;
+
+import java.net.URI;
+import java.util.Set;
+
+import org.apache.taverna.commons.services.ActivityTypeNotFoundException;
+import org.apache.taverna.commons.services.InvalidConfigurationException;
+import org.apache.taverna.commons.services.ServiceRegistry;
+import org.apache.taverna.platform.capability.api.ActivityConfigurationException;
+import org.apache.taverna.platform.capability.api.ActivityNotFoundException;
+import org.apache.taverna.platform.capability.api.ActivityService;
+import org.apache.taverna.scufl2.api.port.InputActivityPort;
+import org.apache.taverna.scufl2.api.port.OutputActivityPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * Simple implementation of a ServiceRegistry that discovers available services from the
+ * ActivityService.
+ *
+ * @author David Withers
+ */
+public class ServiceRegistryImpl implements ServiceRegistry {
+
+ private ActivityService activityService;
+
+ @Override
+ public Set<URI> getActivityTypes() {
+ return activityService.getActivityTypes();
+ }
+
+ @Override
+ public JsonNode getActivityConfigurationSchema(URI activityType)
+ throws InvalidConfigurationException, ActivityTypeNotFoundException {
+ try {
+ return activityService.getActivityConfigurationSchema(activityType);
+ } catch (ActivityConfigurationException e) {
+ throw new InvalidConfigurationException(e);
+ } catch (ActivityNotFoundException e) {
+ throw new ActivityTypeNotFoundException(e);
+ }
+ }
+
+ @Override
+ public Set<InputActivityPort> getActivityInputPorts(URI activityType, JsonNode configuration)
+ throws InvalidConfigurationException, ActivityTypeNotFoundException {
+ try {
+ return activityService.getActivityInputPorts(activityType, configuration);
+ } catch (ActivityConfigurationException e) {
+ throw new InvalidConfigurationException(e);
+ } catch (ActivityNotFoundException e) {
+ throw new ActivityTypeNotFoundException(e);
+ }
+ }
+
+ @Override
+ public Set<OutputActivityPort> getActivityOutputPorts(URI activityType, JsonNode configuration)
+ throws InvalidConfigurationException, ActivityTypeNotFoundException {
+ try {
+ return activityService.getActivityOutputPorts(activityType, configuration);
+ } catch (ActivityConfigurationException e) {
+ throw new InvalidConfigurationException(e);
+ } catch (ActivityNotFoundException e) {
+ throw new ActivityTypeNotFoundException(e);
+ }
+ }
+
+ public void setActivityService(ActivityService activityService) {
+ this.activityService = activityService;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-services-impl/src/main/java/uk/org/taverna/commons/services/impl/ServiceRegistryImpl.java
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diff --git a/taverna-services-impl/src/main/java/uk/org/taverna/commons/services/impl/ServiceRegistryImpl.java b/taverna-services-impl/src/main/java/uk/org/taverna/commons/services/impl/ServiceRegistryImpl.java
deleted file mode 100644
index bb5a0d0..0000000
--- a/taverna-services-impl/src/main/java/uk/org/taverna/commons/services/impl/ServiceRegistryImpl.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2013 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 uk.org.taverna.commons.services.impl;
-
-import java.net.URI;
-import java.util.Set;
-
-import uk.org.taverna.commons.services.ActivityTypeNotFoundException;
-import uk.org.taverna.commons.services.InvalidConfigurationException;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import org.apache.taverna.platform.capability.api.ActivityConfigurationException;
-import org.apache.taverna.platform.capability.api.ActivityNotFoundException;
-import org.apache.taverna.platform.capability.api.ActivityService;
-import org.apache.taverna.scufl2.api.port.InputActivityPort;
-import org.apache.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * Simple implementation of a ServiceRegistry that discovers available services from the
- * ActivityService.
- *
- * @author David Withers
- */
-public class ServiceRegistryImpl implements ServiceRegistry {
-
- private ActivityService activityService;
-
- @Override
- public Set<URI> getActivityTypes() {
- return activityService.getActivityTypes();
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema(URI activityType)
- throws InvalidConfigurationException, ActivityTypeNotFoundException {
- try {
- return activityService.getActivityConfigurationSchema(activityType);
- } catch (ActivityConfigurationException e) {
- throw new InvalidConfigurationException(e);
- } catch (ActivityNotFoundException e) {
- throw new ActivityTypeNotFoundException(e);
- }
- }
-
- @Override
- public Set<InputActivityPort> getActivityInputPorts(URI activityType, JsonNode configuration)
- throws InvalidConfigurationException, ActivityTypeNotFoundException {
- try {
- return activityService.getActivityInputPorts(activityType, configuration);
- } catch (ActivityConfigurationException e) {
- throw new InvalidConfigurationException(e);
- } catch (ActivityNotFoundException e) {
- throw new ActivityTypeNotFoundException(e);
- }
- }
-
- @Override
- public Set<OutputActivityPort> getActivityOutputPorts(URI activityType, JsonNode configuration)
- throws InvalidConfigurationException, ActivityTypeNotFoundException {
- try {
- return activityService.getActivityOutputPorts(activityType, configuration);
- } catch (ActivityConfigurationException e) {
- throw new InvalidConfigurationException(e);
- } catch (ActivityNotFoundException e) {
- throw new ActivityTypeNotFoundException(e);
- }
- }
-
- public void setActivityService(ActivityService activityService) {
- this.activityService = activityService;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
index 70fdfef..b33d451 100644
--- a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
+++ b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context-osgi.xml
@@ -6,7 +6,7 @@
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi.xsd">
- <service ref="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+ <service ref="serviceRegistry" interface="org.apache.taverna.commons.services.ServiceRegistry" />
<reference id="activityService" interface="uk.org.taverna.platform.capability.api.ActivityService" />
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml
----------------------------------------------------------------------
diff --git a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml
index 72c88d1..4ee6119 100644
--- a/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml
+++ b/taverna-services-impl/src/main/resources/META-INF/spring/taverna-services-context.xml
@@ -3,7 +3,7 @@
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd">
- <bean id="serviceRegistry" class="uk.org.taverna.commons.services.impl.ServiceRegistryImpl">
+ <bean id="serviceRegistry" class="org.apache.taverna.commons.services.impl.ServiceRegistryImpl">
<property name="activityService" ref="activityService" />
</bean>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivity.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivity.java b/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivity.java
deleted file mode 100644
index 7248f90..0000000
--- a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivity.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.stringconstant;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * An Activity that holds a constant string value.
- * <p>
- * It is automatically configured to have no input ports and only one output port named
- * <em>value</em>.
- *
- * @author Stuart Owen
- * @author David Withers
- */
-public class StringConstantActivity extends AbstractAsynchronousActivity<JsonNode> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/constant";
-
- private static final Logger logger = Logger.getLogger(StringConstantActivity.class);
-
- private String value;
-
- private JsonNode json;
-
- @Override
- public void configure(JsonNode json) throws ActivityConfigurationException {
- this.json = json;
- this.value = json.get("string").asText();
-// if (outputPorts.size() == 0) {
-// addOutput("value", 0, "text/plain");
-// }
- }
-
- public String getStringValue() {
- return json.get("string").asText();
- }
-
- @Override
- public JsonNode getConfiguration() {
- return json;
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- @Override
- public void run() {
- ReferenceService referenceService = callback.getContext().getReferenceService();
- try {
- T2Reference id = referenceService.register(value, 0, true,
- callback.getContext());
- Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
- outputData.put("value", id);
- callback.receiveResult(outputData, new int[0]);
- } catch (ReferenceServiceException e) {
- callback.fail(e.getMessage(), e);
- }
- }
-
- });
-
- }
-
-// protected void addOutput(String portName, int portDepth, String type) {
-// ActivityOutputPort port = edits.createActivityOutputPort(portName, portDepth, portDepth);
-// MimeType mimeType = new MimeType();
-// mimeType.setText(type);
-// try {
-// edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
-// } catch (EditException e) {
-// logger.debug("Error adding MimeType annotation to port", e);
-// }
-// outputPorts.add(port);
-// }
-
- public String getExtraDescription() {
- if (value.length() > 60) {
- return value.substring(0, 60 - 3) + "...";
- }
- return value;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactory.java
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diff --git a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactory.java b/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactory.java
deleted file mode 100644
index d11d15e..0000000
--- a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactory.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 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.activities.stringconstant;
-
-import java.io.IOException;
-import java.net.URI;
-import java.util.HashSet;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * An {@link ActivityFactory} for creating <code>StringConstantActivity</code>.
- *
- * @author David Withers
- */
-public class StringConstantActivityFactory implements ActivityFactory {
-
- private Edits edits;
-
- @Override
- public StringConstantActivity createActivity() {
- return new StringConstantActivity();
- }
-
- @Override
- public URI getActivityType() {
- return URI.create(StringConstantActivity.URI);
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema() {
- ObjectMapper objectMapper = new ObjectMapper();
- try {
- return objectMapper.readTree(getClass().getResource("/schema.json"));
- } catch (IOException e) {
- return objectMapper.createObjectNode();
- }
- }
-
- @Override
- public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
- return new HashSet<>();
- }
-
- @Override
- public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
- Set<ActivityOutputPort> outputPorts = new HashSet<>();
- outputPorts.add(edits.createActivityOutputPort("value", 0, 0));
- return outputPorts;
- }
-
- public void setEdits(Edits edits) {
- this.edits = edits;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityHealthChecker.java
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diff --git a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityHealthChecker.java b/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityHealthChecker.java
deleted file mode 100644
index 27cef3f..0000000
--- a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityHealthChecker.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.activities.stringconstant;
-
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-
-public class StringConstantActivityHealthChecker implements HealthChecker<StringConstantActivity> {
-
- public boolean canVisit(Object subject) {
- return subject!=null && subject instanceof StringConstantActivity;
- }
-
- public VisitReport visit(StringConstantActivity activity, List<Object> ancestors) {
- Processor p = (Processor) VisitReport.findAncestor(ancestors, Processor.class);
- if (p == null) {
- return null;
- }
- String value = activity.getConfiguration().get("string").asText();
- if (value==null) {
- return new VisitReport(HealthCheck.getInstance(), p,"No value", HealthCheck.NULL_VALUE, Status.SEVERE);
- }
- if ("Add your own value here".equals(value)) {
- VisitReport vr = new VisitReport(HealthCheck.getInstance(), p, "Default value", HealthCheck.DEFAULT_VALUE, Status.WARNING);
- vr.setProperty("value", value);
- return vr;
- }
- return new VisitReport(HealthCheck.getInstance(), p, "StringConstant is OK", HealthCheck.NO_PROBLEM, Status.OK);
- }
-
- public boolean isTimeConsuming() {
- return false;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantConfigurationBean.java
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diff --git a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantConfigurationBean.java b/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantConfigurationBean.java
deleted file mode 100644
index f4ae082..0000000
--- a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/StringConstantConfigurationBean.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.activities.stringconstant;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Configuration bean for setting up a StringConstantActivity.<br>
- * The only thing to be configured is the string value, since the ports are fixed.
- *
- * @author Stuart Owen
- * @see StringConstantActivity
- */
-@ConfigurationBean(uri = StringConstantActivity.URI + "#Config")
-public class StringConstantConfigurationBean {
- private String value;
-
- public String getValue() {
- return value;
- }
-
- @ConfigurationProperty(name = "string", label = "Constant String Value", description = "The value of the string constant")
- public void setValue(String value) {
- this.value = value;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/package.html
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/package.html b/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/package.html
deleted file mode 100644
index 400b576..0000000
--- a/taverna-stringconstant-activity/src/main/java/net/sf/taverna/t2/activities/stringconstant/package.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<body>
-Contains the activity classes required in the execution of Beanshell scripts.
-</body>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivity.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivity.java b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivity.java
new file mode 100644
index 0000000..28d723d
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivity.java
@@ -0,0 +1,118 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.taverna.annotation.annotationbeans.MimeType;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.ReferenceServiceException;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.workflowmodel.EditException;
+import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback;
+
+import org.apache.log4j.Logger;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * An Activity that holds a constant string value.
+ * <p>
+ * It is automatically configured to have no input ports and only one output port named
+ * <em>value</em>.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class StringConstantActivity extends AbstractAsynchronousActivity<JsonNode> {
+
+ public static final String URI = "http://ns.taverna.org.uk/2010/activity/constant";
+
+ private static final Logger logger = Logger.getLogger(StringConstantActivity.class);
+
+ private String value;
+
+ private JsonNode json;
+
+ @Override
+ public void configure(JsonNode json) throws ActivityConfigurationException {
+ this.json = json;
+ this.value = json.get("string").asText();
+// if (outputPorts.size() == 0) {
+// addOutput("value", 0, "text/plain");
+// }
+ }
+
+ public String getStringValue() {
+ return json.get("string").asText();
+ }
+
+ @Override
+ public JsonNode getConfiguration() {
+ return json;
+ }
+
+ @Override
+ public void executeAsynch(final Map<String, T2Reference> data,
+ final AsynchronousActivityCallback callback) {
+ callback.requestRun(new Runnable() {
+
+ @Override
+ public void run() {
+ ReferenceService referenceService = callback.getContext().getReferenceService();
+ try {
+ T2Reference id = referenceService.register(value, 0, true,
+ callback.getContext());
+ Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
+ outputData.put("value", id);
+ callback.receiveResult(outputData, new int[0]);
+ } catch (ReferenceServiceException e) {
+ callback.fail(e.getMessage(), e);
+ }
+ }
+
+ });
+
+ }
+
+// protected void addOutput(String portName, int portDepth, String type) {
+// ActivityOutputPort port = edits.createActivityOutputPort(portName, portDepth, portDepth);
+// MimeType mimeType = new MimeType();
+// mimeType.setText(type);
+// try {
+// edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
+// } catch (EditException e) {
+// logger.debug("Error adding MimeType annotation to port", e);
+// }
+// outputPorts.add(port);
+// }
+
+ public String getExtraDescription() {
+ if (value.length() > 60) {
+ return value.substring(0, 60 - 3) + "...";
+ }
+ return value;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactory.java b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactory.java
new file mode 100644
index 0000000..ceab1b5
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactory.java
@@ -0,0 +1,80 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+/**
+ * An {@link ActivityFactory} for creating <code>StringConstantActivity</code>.
+ *
+ * @author David Withers
+ */
+public class StringConstantActivityFactory implements ActivityFactory {
+
+ private Edits edits;
+
+ @Override
+ public StringConstantActivity createActivity() {
+ return new StringConstantActivity();
+ }
+
+ @Override
+ public URI getActivityType() {
+ return URI.create(StringConstantActivity.URI);
+ }
+
+ @Override
+ public JsonNode getActivityConfigurationSchema() {
+ ObjectMapper objectMapper = new ObjectMapper();
+ try {
+ return objectMapper.readTree(getClass().getResource("/schema.json"));
+ } catch (IOException e) {
+ return objectMapper.createObjectNode();
+ }
+ }
+
+ @Override
+ public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
+ return new HashSet<>();
+ }
+
+ @Override
+ public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
+ Set<ActivityOutputPort> outputPorts = new HashSet<>();
+ outputPorts.add(edits.createActivityOutputPort("value", 0, 0));
+ return outputPorts;
+ }
+
+ public void setEdits(Edits edits) {
+ this.edits = edits;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityHealthChecker.java b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityHealthChecker.java
new file mode 100644
index 0000000..3557547
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantActivityHealthChecker.java
@@ -0,0 +1,57 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+import java.util.List;
+
+import org.apache.taverna.workflowmodel.Processor;
+import org.apache.taverna.workflowmodel.health.HealthCheck;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+import org.apache.taverna.visit.VisitReport;
+import org.apache.taverna.visit.VisitReport.Status;
+
+public class StringConstantActivityHealthChecker implements HealthChecker<StringConstantActivity> {
+
+ public boolean canVisit(Object subject) {
+ return subject!=null && subject instanceof StringConstantActivity;
+ }
+
+ public VisitReport visit(StringConstantActivity activity, List<Object> ancestors) {
+ Processor p = (Processor) VisitReport.findAncestor(ancestors, Processor.class);
+ if (p == null) {
+ return null;
+ }
+ String value = activity.getConfiguration().get("string").asText();
+ if (value==null) {
+ return new VisitReport(HealthCheck.getInstance(), p,"No value", HealthCheck.NULL_VALUE, Status.SEVERE);
+ }
+ if ("Add your own value here".equals(value)) {
+ VisitReport vr = new VisitReport(HealthCheck.getInstance(), p, "Default value", HealthCheck.DEFAULT_VALUE, Status.WARNING);
+ vr.setProperty("value", value);
+ return vr;
+ }
+ return new VisitReport(HealthCheck.getInstance(), p, "StringConstant is OK", HealthCheck.NO_PROBLEM, Status.OK);
+ }
+
+ public boolean isTimeConsuming() {
+ return false;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantConfigurationBean.java b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantConfigurationBean.java
new file mode 100644
index 0000000..c176aa4
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/StringConstantConfigurationBean.java
@@ -0,0 +1,44 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Configuration bean for setting up a StringConstantActivity.<br>
+ * The only thing to be configured is the string value, since the ports are fixed.
+ *
+ * @author Stuart Owen
+ * @see StringConstantActivity
+ */
+@ConfigurationBean(uri = StringConstantActivity.URI + "#Config")
+public class StringConstantConfigurationBean {
+ private String value;
+
+ public String getValue() {
+ return value;
+ }
+
+ @ConfigurationProperty(name = "string", label = "Constant String Value", description = "The value of the string constant")
+ public void setValue(String value) {
+ this.value = value;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/package.html
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/package.html b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/package.html
new file mode 100644
index 0000000..400b576
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/java/org/apache/taverna/activities/stringconstant/package.html
@@ -0,0 +1,3 @@
+<body>
+Contains the activity classes required in the execution of Beanshell scripts.
+</body>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-stringconstant-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index ed959fb..0000000
--- a/taverna-stringconstant-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.stringconstant.StringConstantActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker b/taverna-stringconstant-activity/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker
new file mode 100644
index 0000000..11c7f33
--- /dev/null
+++ b/taverna-stringconstant-activity/src/main/resources/META-INF/services/org.apache.taverna.workflowmodel.health.HealthChecker
@@ -0,0 +1 @@
+org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context-osgi.xml b/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context-osgi.xml
index d6750b1..098154d 100644
--- a/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context-osgi.xml
+++ b/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context-osgi.xml
@@ -6,10 +6,10 @@
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi.xsd">
- <service ref="stringconstantActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
+ <service ref="stringconstantActivityHealthChecker" interface="org.apache.taverna.workflowmodel.health.HealthChecker" />
- <service ref="stringconstantActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
+ <service ref="stringconstantActivityFactory" interface="org.apache.taverna.workflowmodel.processor.activity.ActivityFactory" />
- <reference id="edits" interface="net.sf.taverna.t2.workflowmodel.Edits" />
+ <reference id="edits" interface="org.apache.taverna.workflowmodel.Edits" />
</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml b/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml
index 4df863a..806bb1f 100644
--- a/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml
+++ b/taverna-stringconstant-activity/src/main/resources/META-INF/spring/stringconstant-activity-context.xml
@@ -3,9 +3,9 @@
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd">
- <bean id="stringconstantActivityHealthChecker" class="net.sf.taverna.t2.activities.stringconstant.StringConstantActivityHealthChecker" />
+ <bean id="stringconstantActivityHealthChecker" class="org.apache.taverna.activities.stringconstant.StringConstantActivityHealthChecker" />
- <bean id="stringconstantActivityFactory" class="net.sf.taverna.t2.activities.stringconstant.StringConstantActivityFactory">
+ <bean id="stringconstantActivityFactory" class="org.apache.taverna.activities.stringconstant.StringConstantActivityFactory">
<property name="edits" ref="edits" />
</bean>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactoryTest.java b/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactoryTest.java
deleted file mode 100644
index 61560f2..0000000
--- a/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityFactoryTest.java
+++ /dev/null
@@ -1,64 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 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.activities.stringconstant;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.net.URI;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- *
- * @author David Withers
- */
-public class StringConstantActivityFactoryTest {
-
- private StringConstantActivityFactory factory;
-
- /**
- * @throws java.lang.Exception
- */
- @Before
- public void setUp() throws Exception {
- factory = new StringConstantActivityFactory();
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.beanshell.BeanshellActivityFactory#createActivity()}.
- */
- @Test
- public void testCreateActivity() {
- StringConstantActivity createActivity = factory.createActivity();
- assertNotNull(createActivity);
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.beanshell.BeanshellActivityFactory#getActivityType()}.
- */
- @Test
- public void testGetActivityURI() {
- assertEquals(URI.create(StringConstantActivity.URI), factory.getActivityType());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityTest.java b/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityTest.java
deleted file mode 100644
index a191e8e..0000000
--- a/taverna-stringconstant-activity/src/test/java/net/sf/taverna/t2/activities/stringconstant/StringConstantActivityTest.java
+++ /dev/null
@@ -1,68 +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.activities.stringconstant;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
-import net.sf.taverna.t2.workflowmodel.AbstractPort;
-
-import org.junit.Test;
-
-/**
- * Tests the StringConstantActivity
- * @author Stuart Owen
- *
- */
-public class StringConstantActivityTest {
-
- /**
- * Simple invocation test. Also tests Activity.configure sets up the correct output port.
- * @throws Exception
- */
- @Test
- public void testInvoke() throws Exception {
- return;
-// StringConstantConfigurationBean bean = new StringConstantConfigurationBean();
-// bean.setValue("this_is_a_string");
-// StringConstantActivity activity = new StringConstantActivity();
-// activity.configure(bean);
-//
-// assertEquals("there should be no inputs",0,activity.getInputPorts().size());
-// assertEquals("there should be 1 output",1,activity.getOutputPorts().size());
-// assertEquals("the output port name should be value","value",((AbstractPort)activity.getOutputPorts().toArray()[0]).getName());
-//
-// Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
-// expectedOutputs.put("value", String.class);
-//
-// Map<String,Object> outputs = ActivityInvoker.invokeAsyncActivity(activity, new HashMap<String, Object>(), expectedOutputs);
-//
-// assertEquals("there should be 1 output",1,outputs.size());
-// assertTrue("there should be an output named value",outputs.containsKey("value"));
-// assertEquals("The value of the output should be 'this_is_a_string'","this_is_a_string",outputs.get("value"));
-// assertTrue("The output type should be String",outputs.get("value") instanceof String);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactoryTest.java b/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactoryTest.java
new file mode 100644
index 0000000..f3d6a2c
--- /dev/null
+++ b/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityFactoryTest.java
@@ -0,0 +1,63 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.net.URI;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ *
+ * @author David Withers
+ */
+public class StringConstantActivityFactoryTest {
+
+ private StringConstantActivityFactory factory;
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @Before
+ public void setUp() throws Exception {
+ factory = new StringConstantActivityFactory();
+ }
+
+ /**
+ * Test method for {@link org.apache.taverna.activities.beanshell.BeanshellActivityFactory#createActivity()}.
+ */
+ @Test
+ public void testCreateActivity() {
+ StringConstantActivity createActivity = factory.createActivity();
+ assertNotNull(createActivity);
+ }
+
+ /**
+ * Test method for {@link org.apache.taverna.activities.beanshell.BeanshellActivityFactory#getActivityType()}.
+ */
+ @Test
+ public void testGetActivityURI() {
+ assertEquals(URI.create(StringConstantActivity.URI), factory.getActivityType());
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityTest.java b/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityTest.java
new file mode 100644
index 0000000..d42058a
--- /dev/null
+++ b/taverna-stringconstant-activity/src/test/java/org/apache/taverna/activities/stringconstant/StringConstantActivityTest.java
@@ -0,0 +1,58 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.stringconstant;
+
+
+import org.junit.Test;
+
+/**
+ * Tests the StringConstantActivity
+ * @author Stuart Owen
+ *
+ */
+public class StringConstantActivityTest {
+
+ /**
+ * Simple invocation test. Also tests Activity.configure sets up the correct output port.
+ * @throws Exception
+ */
+ @Test
+ public void testInvoke() throws Exception {
+ return;
+// StringConstantConfigurationBean bean = new StringConstantConfigurationBean();
+// bean.setValue("this_is_a_string");
+// StringConstantActivity activity = new StringConstantActivity();
+// activity.configure(bean);
+//
+// assertEquals("there should be no inputs",0,activity.getInputPorts().size());
+// assertEquals("there should be 1 output",1,activity.getOutputPorts().size());
+// assertEquals("the output port name should be value","value",((AbstractPort)activity.getOutputPorts().toArray()[0]).getName());
+//
+// Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
+// expectedOutputs.put("value", String.class);
+//
+// Map<String,Object> outputs = ActivityInvoker.invokeAsyncActivity(activity, new HashMap<String, Object>(), expectedOutputs);
+//
+// assertEquals("there should be 1 output",1,outputs.size());
+// assertTrue("there should be an output named value",outputs.containsKey("value"));
+// assertEquals("The value of the output should be 'this_is_a_string'","this_is_a_string",outputs.get("value"));
+// assertTrue("The output type should be String",outputs.get("value") instanceof String);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AbstractAnnotatedThing.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AbstractAnnotatedThing.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AbstractAnnotatedThing.java
deleted file mode 100644
index e9dda93..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AbstractAnnotatedThing.java
+++ /dev/null
@@ -1,164 +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;
-
-import static java.util.Collections.unmodifiableSet;
-
-import java.util.HashSet;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.EditException;
-
-/**
- * Convenient abstract superclass for annotated things, manages edits.
- * Subclasses of this must implement the Annotated interface with their own
- * interface type as the parameter, so for example Processor subclasses would
- * implement Annotated<Processor>
- *
- * @author Tom Oinn
- * @author Alan R Williams
- */
-public abstract class AbstractAnnotatedThing<T> implements Annotated<T> {
- private Set<AnnotationChain> annotations = new HashSet<>();
-
- /**
- * Return the set of annotations bound to this annotated object, the set
- * returned is an unmodifiable copy of the internal annotation set, if you
- * need to modify the annotations you should use the get methods for Edit
- * objects to do so.
- *
- * @see net.sf.taverna.t2.annotation.Annotated#getAnnotations()
- */
- @Override
- public final Set<AnnotationChain> getAnnotations() {
- return unmodifiableSet(annotations);
- }
-
- /**
- * Set the annotation chains associated with this annotated object. This is
- * only needed for deserialization and could almost certainly be done in a
- * better way.
- *
- * @param annotations
- */
- @Override
- public final void setAnnotations(Set<AnnotationChain> annotations) {
- this.annotations = annotations;
- }
-
- /**
- * Superclass of edits to remove, add and replace annotations on instances
- * of the enclosing AbstractAnnotatedThing class
- *
- * @author Tom
- * @param <TargetType>
- */
- private static abstract class AbstractAnnotationEdit<TargetType> implements
- Edit<TargetType> {
- private AbstractAnnotatedThing<TargetType> subject;
- private boolean applied = false;
-
- protected AbstractAnnotationEdit(
- AbstractAnnotatedThing<TargetType> subject) {
- this.subject = subject;
- }
-
- @Override
- @SuppressWarnings("unchecked")
- public final TargetType doEdit() throws EditException {
- synchronized (subject) {
- if (applied)
- throw new EditException("Edit already applied!");
- doEditAction(subject);
- this.applied = true;
- return (TargetType) subject;
- }
- }
-
- protected abstract void doEditAction(AbstractAnnotatedThing<?> subject)
- throws EditException;
-
- protected abstract void undoEditAction(AbstractAnnotatedThing<?> subject);
-
- @Override
- @SuppressWarnings("unchecked")
- public final TargetType getSubject() {
- return (TargetType) subject;
- }
-
- @Override
- public final boolean isApplied() {
- return this.applied;
- }
-
- @Override
- public final void undo() {
- synchronized (subject) {
- if (!applied)
- throw new RuntimeException(
- "Attempt to undo edit that was never applied");
- undoEditAction(subject);
- applied = false;
- }
- }
- }
-
- /**
- * @see net.sf.taverna.t2.annotation.Annotated#getAddAnnotationEdit(net.sf.taverna.t2.annotation.WorkflowAnnotation)
- */
- @Override
- public final Edit<T> getAddAnnotationEdit(
- final AnnotationChain newAnnotation) {
- return new AbstractAnnotationEdit<T>(this) {
- @Override
- protected void doEditAction(AbstractAnnotatedThing<?> subject)
- throws EditException {
- annotations.add(newAnnotation);
- }
-
- @Override
- protected void undoEditAction(AbstractAnnotatedThing<?> subject) {
- annotations.remove(newAnnotation);
- }
- };
- }
-
- /**
- * @see net.sf.taverna.t2.annotation.Annotated#getRemoveAnnotationEdit(net.sf.taverna.t2.annotation.WorkflowAnnotation)
- */
- @Override
- public final Edit<T> getRemoveAnnotationEdit(
- final AnnotationChain annotationToRemove) {
- return new AbstractAnnotationEdit<T>(this) {
- @Override
- protected void doEditAction(AbstractAnnotatedThing<?> subject)
- throws EditException {
- annotations.remove(annotationToRemove);
- }
-
- @Override
- protected void undoEditAction(AbstractAnnotatedThing<?> subject) {
- annotations.add(annotationToRemove);
- }
- };
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Annotated.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Annotated.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Annotated.java
deleted file mode 100644
index ab7ed2c..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/Annotated.java
+++ /dev/null
@@ -1,79 +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;
-
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.Edit;
-
-/**
- * Denotes that the object carries workflow object level annotation. Rather than
- * defining specific annotation types for each workflow entity we work on the
- * basis that multiple annotations of different types may apply, so free text
- * description is one example, semantic annotation of the internal function of a
- * processor might be another.
- * <p>
- * Where annotations are conceptually editable such as free text descriptions
- * the editing framework should internally remove the original annotation and
- * add the replacement rather than modifying the previous annotation in place.
- *
- * @author Tom Oinn
- *
- */
-public interface Annotated<TargetType> {
-
- /**
- * Each annotated object contains a bag of metadata object instances
- *
- * @return set of metadata objects that apply to the annotated object
- */
- Set<? extends AnnotationChain> getAnnotations();
-
- void setAnnotations(Set<AnnotationChain> annotations);
-
- /**
- * Add new workflow object metadata to this annotated entity
- *
- * @param <TargetType>
- * the type of the object being annotated
- * @param newAnnotation
- * metadata object to add to the annotated object
- * @return edit object to perform and undo the metadata assignment
- */
- public Edit<? extends TargetType> getAddAnnotationEdit(
- AnnotationChain newAnnotation);
-
- /**
- * Remove an annotation object from the this annotated entity
- *
- * @param <TargetType>
- * type of the workflow object from which the annotation is
- * removed
- * @param annotationToRemove
- * metadata object to remove
- * @param objectToAnnotate
- * object from which the metadata is removed
- * @return edit object to perform and undo the metadata removal
- */
- public Edit<? extends TargetType> getRemoveAnnotationEdit(
- AnnotationChain annotationToRemove);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationAssertion.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationAssertion.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationAssertion.java
deleted file mode 100644
index 6f68c35..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationAssertion.java
+++ /dev/null
@@ -1,52 +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;
-
-/**
- * Represents a single assertion of information, providing access to a bean
- * containing the information in the assertion and one specifying the source of
- * the information contained.
- *
- * @author Tom Oinn
- *
- */
-public interface AnnotationAssertion<AnnotationBeanType extends AnnotationBeanSPI>
- extends Curateable {
-
- /**
- * Each annotation assertion contains a bean specifying the actual
- * annotation, varying from a simple string for a free text description to
- * more sophisticated semantic annotations or controlled vocabularies.
- *
- * @return the annotation bean specifying this annotation assertion
- */
- public AnnotationBeanType getDetail();
-
- /**
- * The annotation assertion plays one of several roles within the annotation
- * chain, either an initial assertion, a refinement of a previous assertion
- * or a replacement of a previous assertion.
- *
- * @return the annotation role of this annotation
- */
- public AnnotationRole getRole();
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationBeanSPI.java
----------------------------------------------------------------------
diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationBeanSPI.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationBeanSPI.java
deleted file mode 100644
index a754148..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationBeanSPI.java
+++ /dev/null
@@ -1,32 +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;
-
-/**
- * Marker interface to denote that a bean class is a container for the
- * information encapsulated by an InformationAssertion object
- *
- * @author Tom Oinn
- *
- */
-public interface AnnotationBeanSPI {
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationChain.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationChain.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationChain.java
deleted file mode 100644
index 6f70faa..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationChain.java
+++ /dev/null
@@ -1,51 +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;
-
-import java.util.List;
-
-/**
- * A fact about an annotated entity is expressed in terms of an annotation
- * chain. The annotation chain contains one or more information assertions in a
- * list ordered by the creation date of each assertion. Annotation chains are
- * then interpreted by an AnnotationPerspective which is responsible for
- * reasoning over the information in the chain and extracting the set of
- * information assertions that are valid according to the rules in the
- * particular AnnotationPerspective.
- *
- * @author Tom Oinn
- *
- */
-public interface AnnotationChain {
-
- /**
- * Returns the ordered list of AnnotationAssertions. This is the 'raw' set
- * of annotations in creation order - this order is not necessarily the
- * order they were curated, and may include refuted or otherwise wrong
- * annotations. Consumers of this API are recommended to use an
- * AnnotationPerspective to resolve any such conflicts appropriately.
- *
- * @return read only copy of the ordered list of AnnotationAssertion
- * instances
- */
- List<AnnotationAssertion<?>> getAssertions();
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationPerspective.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationPerspective.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationPerspective.java
deleted file mode 100644
index 656b026..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationPerspective.java
+++ /dev/null
@@ -1,62 +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;
-
-import java.util.List;
-
-/**
- * Responsible for the interpretation of an AnnotationChain (which may contain
- * conflicting or disputed information) into a set of AnnotationAssertion
- * instances from that chain which are valid given the chain and some
- * interpretation rule.
- *
- * @author Tom Oinn
- *
- */
-public interface AnnotationPerspective {
-
- /**
- * Evaluate the annotations and their curation events in the specified
- * chain, resolve conflicts if possible and return the resultant set of
- * annotations
- *
- * @param chain
- * the annotation chain to evaluate
- * @return the set of annotations which are valid within this chain
- */
- public List<? extends AnnotationAssertion<?>> getAnnotations(
- AnnotationChain chain);
-
- /**
- * Annotation chains may be in a disputed state if there are conflicting
- * mutually exclusive events within them under the interpretation imposed by
- * the annotation perspective and the perspective is unable to sensibly
- * reconcile them. For example, if the perspective is configured to trust
- * two parties equally and they disagree.
- *
- * @param chain
- * the annotation chain to check for conflict
- * @return true if there are conflicts under the interpretation of this
- * annotation perspective
- */
- public boolean isDisputed(AnnotationChain chain);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationRole.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationRole.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationRole.java
deleted file mode 100644
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationRole.java
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@@ -1,51 +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;
-
-/**
- * Specifies the role of an AnnotationAssertion within an AnnotationChain
- *
- * @author Tom Oinn
- */
-public enum AnnotationRole {
-
- /**
- * The information assertion is the first in the chain (if this is applied
- * to an annotation that isn't the earliest in its chain it should be
- * treated as a validation failure)
- */
- INITIAL_ASSERTION,
-
- /**
- * The information assertion was added to the chain to refine the existing
- * annotation assertion or assertions, such as cases where a generic
- * description exists which can be specialized in a particular instance but
- * where the original more generic form is still correct
- */
- REFINEMENT,
-
- /**
- * The information assertion was added to the chain in order to override an
- * earlier information assertion which was regarded as incorrect.
- */
- REPLACEMENT;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationSourceSPI.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationSourceSPI.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationSourceSPI.java
deleted file mode 100644
index 1f7a74d..0000000
--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AnnotationSourceSPI.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;
-
-/**
- * A marker interface that specified that the implementation is a bean
- * containing information about a source of annotations. These might be
- * publications, web URIs, a free text container, a person (etc). We should be
- * able to use existing schemes for identification of sources, publications etc
- * here.
- *
- * @author Tom Oinn
- *
- */
-public interface AnnotationSourceSPI {
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/5f1ddb71/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AppliesTo.java
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diff --git a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AppliesTo.java b/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AppliesTo.java
deleted file mode 100644
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--- a/taverna-workflowmodel-api/src/main/java/net/sf/taverna/t2/annotation/AppliesTo.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.*;
-
-/**
- * Annotation to be used on metadata objects to denote which workflow objects
- * they apply to
- *
- * @author Tom Oinn
- *
- */
-@Retention(RetentionPolicy.RUNTIME)
-@Target(ElementType.TYPE)
-@Documented
-public @interface AppliesTo {
-
- /**
- * The class of the metadata object allowed by this annotation
- */
- Class<?>[] targetObjectType();
-
- /**
- * Can you have more than one of these metadata objects in the resolved set?
- */
- boolean many() default true;
-
- /**
- * Should the annotation be pruned, i.e. only most recent kept, when saving?
- */
- boolean pruned() default true;
-
-
-}