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Posted to commits@taverna.apache.org by st...@apache.org on 2018/06/29 10:55:02 UTC
[15/27] incubator-taverna-plugin-component git commit: package rename
folders
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/ComponentHealthCheck.java
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diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/ComponentHealthCheck.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/ComponentHealthCheck.java
deleted file mode 100644
index a3585f4..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/ComponentHealthCheck.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.util;
-
-import static org.apache.log4j.Logger.getLogger;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import io.github.taverna_extras.component.api.ComponentException;
-import io.github.taverna_extras.component.api.ComponentFactory;
-import io.github.taverna_extras.component.api.Version;
-import io.github.taverna_extras.component.ui.ComponentActivityConfigurationBean;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.common.Visitor;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.validation.correctness.DefaultDispatchingVisitor;
-import org.apache.taverna.visit.VisitKind;
-import org.apache.taverna.visit.VisitReport;
-
-public class ComponentHealthCheck extends VisitKind {
- public static final int NO_PROBLEM = 0;
- public static final int OUT_OF_DATE = 10;
- public static final int NON_SHAREABLE = 20;
- public static final int FAILS_PROFILE = 30;
- private static Logger logger = getLogger(ComponentHealthCheck.class);
- private static final String OUTDATED_MSG = "Component out of date";
-
- private ComponentFactory factory;
-
- public void setComponentFactory(ComponentFactory factory) {
- this.factory = factory;
- }
-
- public List<Object> checkForOutdatedComponents(WorkflowBundle bundle) {
- UpgradeChecker uc = new UpgradeChecker();
- bundle.accept(uc);
- return uc.warnings;
- }
-
- private class UpgradeChecker extends DefaultDispatchingVisitor {
- ComponentFactory factory;
- List<Object> warnings = new ArrayList<>();
-
- @Override
- public void visitActivity(Activity activity) {
- ComponentActivityConfigurationBean config = new ComponentActivityConfigurationBean(
- activity.getConfiguration().getJson(), factory);
- Version v;
- try {
- v = config.getVersion();
- } catch (ComponentException e) {
- logger.error("failed to get component description", e);
- warnings.add(e);//FIXME Just putting the exception in here isn't good
- return;
- }
- visitComponent(activity, v);
- }
- protected void visitComponent(Activity activity, Version version) {
- int latest = version.getComponent().getComponentVersionMap().lastKey();
- if (latest > version.getVersionNumber())
- warnings.add(new VisitReport(ComponentHealthCheck.this,
- activity, OUTDATED_MSG, OUT_OF_DATE,
- VisitReport.Status.WARNING));
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/Utils.java
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diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/Utils.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/Utils.java
deleted file mode 100644
index e81cbf6..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/util/Utils.java
+++ /dev/null
@@ -1,144 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.util;
-
-import static io.github.taverna_extras.component.ui.ComponentConstants.ACTIVITY_URI;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import io.github.taverna_extras.component.api.ComponentFactory;
-import io.github.taverna_extras.component.api.Version;
-import io.github.taverna_extras.component.ui.preference.ComponentPreference;
-import io.github.taverna_extras.component.ui.serviceprovider.ComponentServiceIcon;
-import io.github.taverna_extras.component.ui.serviceprovider.ComponentServiceProvider;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.common.Named;
-import org.apache.taverna.scufl2.api.common.NamedSet;
-import org.apache.taverna.scufl2.api.configurations.Configuration;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
-import org.apache.taverna.workbench.file.FileManager;
-//import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-//import net.sf.taverna.t2.workbench.file.FileManager;
-
-/**
- * @author alanrw
- */
-public class Utils {
- // From http://stackoverflow.com/questions/163360/regular-expresion-to-match-urls-in-java
- public static String URL_PATTERN = "^(https?|ftp|file)://[-a-zA-Z0-9+&@#/%?=~_|!:,.;]*[-a-zA-Z0-9+&@#/%=~_|]";
- public static final String LONG_STRING = "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";
- public static final String SHORT_STRING = "XXX";
-
- private FileManager fileManager;
- private ServiceDescriptionRegistry registry;
- private ComponentFactory factory;
- private ComponentPreference prefs;
- private ComponentServiceIcon icon;
-
- public void setComponentFactory(ComponentFactory factory) {
- this.factory = factory;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setIcon(ComponentServiceIcon icon) {
- this.icon = icon;
- }
-
- public void setPrefs(ComponentPreference prefs) {
- this.prefs = prefs;
- }
-
- public void setRegistry(ServiceDescriptionRegistry registry) {
- this.registry = registry;
- }
-
- public void refreshComponentServiceProvider(Configuration config) {
- ComponentServiceProvider provider = new ComponentServiceProvider(
- factory, prefs, icon, this);
- provider.configure(config);
- registry.removeServiceDescriptionProvider(provider);
- registry.addServiceDescriptionProvider(provider);
- }
-
- public void removeComponentServiceProvider(Configuration config) {
- ComponentServiceProvider provider = new ComponentServiceProvider(
- factory, prefs, icon, this);
- provider.configure(config);
- registry.removeServiceDescriptionProvider(provider);
- }
-
- public boolean dataflowIsComponent(WorkflowBundle d) {
- if (d == null)
- return false;
- Object dataflowSource = fileManager.getDataflowSource(d);
- return dataflowSource instanceof Version.ID;// FIXME Really?
- }
-
- public boolean currentDataflowIsComponent() {
- return dataflowIsComponent(fileManager.getCurrentDataflow());
- }
-
- public static boolean isComponentActivity(Object obj) {
- if (obj == null || !(obj instanceof Activity))
- return false;
- Configuration cfg = ((Activity) obj).getConfiguration();
- return cfg != null && ACTIVITY_URI.equals(cfg.getType());
- }
-
- private static final Pattern SANITIZER_RE = Pattern
- .compile("[^a-zA-Z0-9]+");
- private static final Pattern SUFFIXED_RE = Pattern
- .compile("^(.+)_([0-9]+)$");
-
- /**
- * Pick a name that is unique within the context set. This is done by
- * appending "<tt>_<i>n</i></tt>" as necessary, where <tt><i>n</i></tt> is a
- * number.
- *
- * @param name
- * The suggested name; this is always checked first.
- * @param context
- * The set of things that the name will have to be unique within.
- * @return A name that is definitely not the name of anything in the given
- * set.
- */
- public static String uniqueName(String name, NamedSet<? extends Named> context) {
- String candidate = SANITIZER_RE.matcher(name).replaceAll("_");
- if (context.getByName(candidate) == null)
- return candidate;
- int counter = 0;
- String prefix = candidate;
- Matcher m = SUFFIXED_RE.matcher(candidate);
- if (m.matches()) {
- prefix = m.group(1);
- counter = Integer.parseInt(m.group(2));
- }
- do {
- candidate = prefix + "_" + (++counter);
- } while (context.getByName(candidate) != null);
- return candidate;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivityContextViewFactory.java
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diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivityContextViewFactory.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivityContextViewFactory.java
deleted file mode 100644
index c27278f..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivityContextViewFactory.java
+++ /dev/null
@@ -1,140 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static io.github.taverna_extras.component.api.config.ComponentConfig.URI;
-
-import java.awt.Frame;
-import java.net.MalformedURLException;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Action;
-
-import io.github.taverna_extras.component.api.ComponentFactory;
-import io.github.taverna_extras.component.ui.config.ComponentConfigureAction;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
-import org.apache.taverna.services.ServiceRegistry;
-import org.apache.taverna.workbench.activityicons.ActivityIconManager;
-import org.apache.taverna.workbench.configuration.colour.ColourManager;
-import org.apache.taverna.workbench.edits.EditManager;
-import org.apache.taverna.workbench.file.FileManager;
-import org.apache.taverna.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
-import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-public class ComponentActivityContextViewFactory implements
- ContextualViewFactory<Activity> {
- private ColourManager colourManager;
- private ViewUtil util;
- private ComponentFactory factory;
- private ActivityIconManager aim;
- private ServiceDescriptionRegistry sdr;
- private EditManager em;
- private FileManager fm;
- private ServiceRegistry sr;
-
- public void setComponentFactory(ComponentFactory factory) {
- this.factory = factory;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setViewUtils(ViewUtil util) {
- this.util = util;
- }
-
- public void setIconManager(ActivityIconManager aim) {
- this.aim = aim;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry sdr) {
- this.sdr = sdr;
- }
-
- public void setEditManager(EditManager em) {
- this.em = em;
- }
-
- public void setFileManager(FileManager fm) {
- this.fm = fm;
- }
-
- public void setServiceTypeRegistry(ServiceRegistry sr) {
- this.sr = sr;
- }
-
- @Override
- public boolean canHandle(Object selection) {
- return selection instanceof Activity
- && ((Activity) selection).getType().equals(URI);
- }
-
- @Override
- public List<ContextualView> getViews(Activity selection) {
- return Arrays.<ContextualView>asList(new ComponentActivityContextualView(selection));
- }
-
- @SuppressWarnings("serial")
- private class ComponentActivityContextualView extends
- HTMLBasedActivityContextualView {
- public ComponentActivityContextualView(Activity activity) {
- super(activity, colourManager);
- init();
- }
-
- private void init() {
- }
-
- @Override
- public String getViewTitle() {
- return "Component service";
- }
-
- /**
- * View position hint
- */
- @Override
- public int getPreferredPosition() {
- // We want to be on top
- return 100;
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new ComponentConfigureAction(getActivity(), owner, factory,
- aim, sdr, em, fm, sr);
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- try {
- return util.getRawTablesHtml(getConfigBean());
- } catch (MalformedURLException e) {
- return "<tr><td>malformed URL: <pre>" + e.getMessage()
- + "</pre></td></tr>";
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationContextViewFactory.java
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diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationContextViewFactory.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationContextViewFactory.java
deleted file mode 100644
index fcb6e4a..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationContextViewFactory.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static org.apache.log4j.Logger.getLogger;
-import static io.github.taverna_extras.component.api.config.ComponentConfig.URI;
-
-import java.net.MalformedURLException;
-import java.util.Arrays;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import io.github.taverna_extras.component.api.ComponentException;
-import io.github.taverna_extras.component.api.ComponentFactory;
-import io.github.taverna_extras.component.api.profile.Profile;
-import io.github.taverna_extras.component.ui.ComponentActivityConfigurationBean;
-import io.github.taverna_extras.component.ui.annotation.AbstractSemanticAnnotationContextualView;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.core.Workflow;
-import org.apache.taverna.scufl2.api.port.InputActivityPort;
-import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.OutputActivityPort;
-import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.Port;
-import org.apache.taverna.workbench.file.FileManager;
-import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
-import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-public class ComponentActivitySemanticAnnotationContextViewFactory implements
- ContextualViewFactory<Object> {
- public static final String VIEW_TITLE = "Inherited Semantic Annotations";
- private static final Logger logger = getLogger(ComponentActivitySemanticAnnotationContextViewFactory.class);
-
- private FileManager fm;
- private ComponentFactory factory;
-
- public void setFileManager(FileManager fm) {
- this.fm = fm;
- }
-
- public void setComponentFactory(ComponentFactory factory) {
- this.factory = factory;
- }
-
- @Override
- public boolean canHandle(Object selection) {
- return getContainingComponentActivity(selection) != null;
- }
-
- public Activity getContainingComponentActivity(Object selection) {
- if (selection instanceof Activity) {
- Activity a = (Activity) selection;
- if (a.getType().equals(URI))
- return a;
- }
- if (selection instanceof InputActivityPort
- || selection instanceof OutputActivityPort)
- return getContainingComponentActivity(((OutputActivityPort) selection)
- .getParent());
- return null;
- }
-
- @Override
- public List<ContextualView> getViews(Object selection) {
- return Arrays
- .<ContextualView> asList(new SemanticAnnotationCV(
- selection));
- }
-
- @SuppressWarnings("serial")
- private class SemanticAnnotationCV extends
- AbstractSemanticAnnotationContextualView {
- private Profile componentProfile;
-
- public SemanticAnnotationCV(Object selection) {
- super(fm, false);
- Activity componentActivity = getContainingComponentActivity(selection);
- try {
- ComponentActivityConfigurationBean configuration = new ComponentActivityConfigurationBean(
- componentActivity.getConfiguration(), factory);
- setAnnotatedThing(selection, configuration.getVersion()
- .getImplementation().getMainWorkflow());
- componentProfile = configuration.getComponent().getFamily()
- .getComponentProfile();
- setProfile(selection);
- super.initialise();
- } catch (ComponentException e) {
- logger.error("problem querying registry", e);
- } catch (MalformedURLException e) {
- logger.error("malformed URL in component description", e);
- }
- }
-
- private void setAnnotatedThing(Object selection,
- Workflow underlyingDataflow) {
- if (selection instanceof Activity) {
- setAnnotated(underlyingDataflow);
- } else if (selection instanceof InputActivityPort) {
- String name = ((Port) selection).getName();
- for (InputWorkflowPort dip : underlyingDataflow.getInputPorts())
- if (dip.getName().equals(name)) {
- setAnnotated(dip);
- break;
- }
- } else if (selection instanceof OutputActivityPort) {
- String name = ((Port) selection).getName();
- for (OutputWorkflowPort dop : underlyingDataflow
- .getOutputPorts())
- if (dop.getName().equals(name)) {
- setAnnotated(dop);
- break;
- }
- }
- }
-
- private void setProfile(Object selection) throws ComponentException {
- if (componentProfile == null)
- return;
- if (selection instanceof Activity) {
- setSemanticAnnotationProfiles(componentProfile
- .getSemanticAnnotations());
- } else if (selection instanceof InputActivityPort) {
- setSemanticAnnotationProfiles(componentProfile
- .getInputSemanticAnnotationProfiles());
- } else if (selection instanceof OutputActivityPort) {
- setSemanticAnnotationProfiles(componentProfile
- .getOutputSemanticAnnotationProfiles());
- }
- }
-
- @Override
- public String getViewTitle() {
- return VIEW_TITLE;
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationPanel.java
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diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationPanel.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationPanel.java
deleted file mode 100644
index d3580a8..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentActivitySemanticAnnotationPanel.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static java.awt.Color.GRAY;
-import static java.awt.Color.WHITE;
-import static java.awt.GridBagConstraints.BOTH;
-import static java.awt.GridBagConstraints.EAST;
-import static java.awt.GridBagConstraints.HORIZONTAL;
-import static java.awt.GridBagConstraints.SOUTHEAST;
-import static java.lang.String.format;
-import static io.github.taverna_extras.component.ui.annotation.SemanticAnnotationUtils.getDisplayName;
-import static io.github.taverna_extras.component.ui.annotation.SemanticAnnotationUtils.getObjectName;
-
-import java.awt.Component;
-import java.awt.Graphics;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.Insets;
-import java.util.Set;
-
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JTextArea;
-import javax.swing.border.AbstractBorder;
-import javax.swing.border.EmptyBorder;
-
-import io.github.taverna_extras.component.api.profile.SemanticAnnotationProfile;
-
-import org.apache.jena.ontology.OntProperty;
-import org.apache.jena.rdf.model.Statement;
-
-public class ComponentActivitySemanticAnnotationPanel extends JPanel {
- private static final long serialVersionUID = 3599768150252711758L;
- private static final String ANNTYPE_MSG = "Annotation type : %s";
- private static final String NONE_MSG = "No semantic annotations";
- private SemanticAnnotationProfile profile;
- private final Set<Statement> statements;
-
- public ComponentActivitySemanticAnnotationPanel(
- SemanticAnnotationProfile profile, Set<Statement> statements) {
- this.profile = profile;
- this.statements = statements;
- initialize();
- }
-
- private void initialize() {
- setLayout(new GridBagLayout());
- setBorder(new AbstractBorder() {
- private static final long serialVersionUID = -5921448975807056953L;
-
- @Override
- public void paintBorder(Component c, Graphics g, int x, int y,
- int width, int height) {
- g.setColor(GRAY);
- g.drawLine(x, y + height - 1, x + width - 1, y + height - 1);
- }
- });
-
- GridBagConstraints c = new GridBagConstraints();
- c.anchor = SOUTHEAST;
- c.fill = BOTH;
- c.weightx = 1;
- c.gridx = 0;
-
- OntProperty predicate = profile.getPredicate();
- c.gridwidth = 2;
- JLabel label = new JLabel(format(ANNTYPE_MSG, getDisplayName(predicate)));
- label.setBorder(new EmptyBorder(5, 5, 5, 5));
- label.setBackground(WHITE);
- label.setOpaque(true);
- add(label, c);
-
- c.insets = new Insets(5, 7, 0, 0);
- c.anchor = EAST;
- c.fill = HORIZONTAL;
- if (statements.isEmpty()) {
- c.gridwidth = 2;
- // c.weightx = 1;
- // c.gridy++;
- add(new JLabel(NONE_MSG), c);
- } else {
- c.gridwidth = 1;
- for (Statement statement : statements) {
- c.gridx = 0;
- c.weightx = 1;
- JTextArea value = new JTextArea(getObjectName(statement));
- value.setBackground(WHITE);
- value.setOpaque(true);
- value.setBorder(new EmptyBorder(2, 4, 2, 4));
- add(value, c);
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextViewFactory.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextViewFactory.java
deleted file mode 100644
index 938a32e..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextViewFactory.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static io.github.taverna_extras.component.api.config.ComponentConfig.URI;
-
-import java.util.Arrays;
-import java.util.List;
-
-import io.github.taverna_extras.component.api.Version;
-
-import org.apache.taverna.scufl2.api.activity.Activity;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.workbench.file.FileManager;
-import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
-import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-public class ComponentContextViewFactory implements
- ContextualViewFactory<WorkflowBundle> {
- private FileManager fileManager;
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- @Override
- public boolean canHandle(Object selection) {
- if (selection instanceof WorkflowBundle) {
- Object dataflowSource = fileManager
- .getDataflowSource((WorkflowBundle) selection);
- //FIXME Is this right?
- return dataflowSource instanceof Version.ID;
- }
- return selection instanceof Activity
- && ((Activity) selection).getType().equals(URI);
- }
-
- @Override
- public List<ContextualView> getViews(WorkflowBundle selection) {
- Object dataflowSource = fileManager.getDataflowSource(selection);
- return Arrays.<ContextualView> asList(new ComponentContextualView(
- (Version.ID) dataflowSource));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextualView.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextualView.java
deleted file mode 100644
index c763d06..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ComponentContextualView.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static java.lang.String.format;
-
-import java.awt.Color;
-
-import javax.swing.JComponent;
-import javax.swing.JEditorPane;
-
-import io.github.taverna_extras.component.api.Version;
-import org.apache.taverna.lang.ui.HtmlUtils;
-import org.apache.taverna.workbench.configuration.colour.ColourManager;
-import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
-
-@SuppressWarnings("serial")
-public class ComponentContextualView extends ContextualView {
- private JEditorPane editorPane;
- private final Version.ID component;
- ColourManager colourManager;//FIXME beaninject
- ViewUtil viewUtils;//FIXME beaninject;
-
- public ComponentContextualView(Version.ID component) {
- this.component = component;
- initView();
- }
-
- @Override
- public JComponent getMainFrame() {
- editorPane = HtmlUtils.createEditorPane(buildHtml());
- return HtmlUtils.panelForHtml(editorPane);
- }
-
- private String buildHtml() {
- StringBuilder html = new StringBuilder(HtmlUtils.getHtmlHead(getBackgroundColour()));
- html.append(HtmlUtils.buildTableOpeningTag());
- viewUtils.getRawTablesHtml(component, html);
- return html.append("</table></body></html>").toString();
- }
-
- public String getBackgroundColour() {
- Color colour = colourManager.getPreferredColour(
- "io.github.taverna_extras.component.registry.Component");
- return format("#%1$2x%2$2x%3$2x", colour.getRed(), colour.getGreen(),
- colour.getBlue());
- }
-
- @Override
- public int getPreferredPosition() {
- return 50;
- }
-
- private static int MAX_LENGTH = 50;
-
- private String limitName(String fullName) {
- if (fullName.length() > MAX_LENGTH)
- return fullName.substring(0, MAX_LENGTH - 3) + "...";
- return fullName;
- }
-
- @Override
- public String getViewTitle() {
- return "Component " + limitName(component.getComponentName());
- }
-
- @Override
- public void refreshView() {
- editorPane.setText(buildHtml());
- repaint();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ViewUtil.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ViewUtil.java b/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ViewUtil.java
deleted file mode 100644
index 5764f6c..0000000
--- a/taverna-component-activity-ui/src/main/java/org/apache/taverna/component/ui/view/ViewUtil.java
+++ /dev/null
@@ -1,178 +0,0 @@
-/*
-* 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 io.github.taverna_extras.component.ui.view;
-
-import static java.lang.String.format;
-import static org.apache.log4j.Logger.getLogger;
-
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import io.github.taverna_extras.component.api.Component;
-import io.github.taverna_extras.component.api.ComponentFactory;
-import io.github.taverna_extras.component.api.Family;
-import io.github.taverna_extras.component.api.Version;
-import io.github.taverna_extras.component.ui.ComponentActivityConfigurationBean;
-
-import org.apache.taverna.scufl2.api.configurations.Configuration;
-import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
-import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
-
-/**
- * @author alanrw
- */
-public class ViewUtil {
- private static Logger logger = getLogger(ViewUtil.class);
-
- private static final String VERSION_DESCRIPTION_LABEL = "Component version description";
- private static final String COMPONENT_DESCRIPTION_LABEL = "Component description";
- private static final String FAMILY_DESCRIPTION_LABEL = "Family description";
-
- private static final String plainFormat = "<tr><td><b>%1$s</b></td><td nowrap=\"wrap\" style=\"width:100px;\">%2$s</td></tr>";
- private static final String headerFormat = "<tr><th>%1$s</th><th>%2$s</th></tr>";
- private static final String rowFormat = "<tr><td><b>%1$s</b></td><td>%2$s</td></tr>";
- private static final String rowLinkFormat = "<tr><td><b>%1$s</b></td><td><a href=\"%3$s\">%2$s</a></td></tr>";
- private static final String descriptionFormat = "<tr><td colspan=\"2\"><b>%1$s</b></td></tr><tr><td colspan=\"2\" nowrap=\"wrap\" style=\"width:100px;\">%2$s</td></tr>";
-
- private ComponentFactory factory;//FIXME beaninject
-
- public void setComponentFactory(ComponentFactory factory) {
- this.factory = factory;
- }
-
- public String getRawTablesHtml(Version.ID id) {
- StringBuilder html = new StringBuilder();
- getRawTablesHtml(id, html);
- return html.toString();
- }
-
- public String getRawTablesHtml(Configuration config) throws MalformedURLException {
- StringBuilder html = new StringBuilder();
- getRawTablesHtml(
- new ComponentActivityConfigurationBean(
- config.getJsonAsObjectNode(), factory), html);
- return html.toString();
- }
-
- public void getRawTablesHtml(Version.ID id, StringBuilder html) {
- URL registryBase = id.getRegistryBase();
- String registryLink = null;
- if (registryBase.getProtocol().startsWith("http"))
- registryLink = registryBase.toExternalForm();
- /*
- * \u200b is a zero-width space, so the HTML renderer can know to break
- * lines.
- */
- String registryName = registryBase.toString().replaceAll("/", "\u200b/");
- appendRow(html, "Component registry base", registryName, registryLink);
-
- String familyName = id.getFamilyName();
- appendRow(html, "Component family", familyName, null);
- try {
- Family family = factory.getFamily(registryBase, familyName);
- if (family != null)
- appendDescriptionHtml(html, FAMILY_DESCRIPTION_LABEL,
- family.getDescription());
- } catch (Exception e) {
- logger.error("failed to get component family description", e);
- }
-
- String componentName = id.getComponentName();
- String helpLink = null;
- try {
- URL helpURL = factory.getVersion(id).getHelpURL();
- if (helpURL != null)
- helpLink = helpURL.toExternalForm();
- } catch (Exception e) {
- logger.error(e);
- }
-
- appendRow(html, "Component name", componentName, helpLink);
- try {
- Component component = factory.getComponent(registryBase,
- familyName, componentName);
- if (component != null)
- appendDescriptionHtml(html, COMPONENT_DESCRIPTION_LABEL,
- component.getDescription());
- } catch (Exception e) {
- logger.error("failed to get component description", e);
- }
-
- Integer componentVersion = id.getComponentVersion();
-
- if (componentVersion == null)
- appendRow(html, "Component version", "N/A", helpLink);
- else {
- appendRow(html, "Component version", componentVersion, helpLink);
- try {
- Version version = factory.getVersion(registryBase,
- familyName, componentName, componentVersion);
- if (version != null) {
- appendDescriptionHtml(html, VERSION_DESCRIPTION_LABEL,
- version.getDescription());
- WorkflowBundle impl = version.getImplementation();
- Set<InputWorkflowPort> inputs = impl.getMainWorkflow().getInputPorts();
- if (!inputs.isEmpty()) {
- appendHeaderRow(html, "Input Port Name", "Depth");
- for (InputWorkflowPort input : inputs)
- appendPlainRow(html, input.getName(), input.getDepth());
- }
- Set<OutputWorkflowPort> outputs = impl.getMainWorkflow().getOutputPorts();
- if (!outputs.isEmpty()) {
- appendHeaderRow(html, "Output Port Name", "Depth");
- for (OutputWorkflowPort output : outputs) {
- //FIXME get depth of output ports!
- appendPlainRow(html, output.getName(), -1 /*output.getDepth()*/);
- }
- }
- }
- } catch (Exception e) {
- logger.error("failed to get component version description", e);
- }
- }
- }
-
- private static void appendRow(StringBuilder html, Object label,
- Object value, String link) {
- if (link == null)
- html.append(format(rowFormat, label, value));
- else
- html.append(format(rowLinkFormat, label, value, link));
- }
-
- private static void appendHeaderRow(StringBuilder html, Object label1,
- Object label2) {
- html.append(format(headerFormat, label1, label2));
- }
-
- private static void appendPlainRow(StringBuilder html, Object value1,
- Object value2) {
- html.append(format(plainFormat, value1, value2));
- }
-
- private static void appendDescriptionHtml(StringBuilder html,
- String header, String description) {
- if ((description != null) && !description.isEmpty())
- html.append(format(descriptionFormat, header, description));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivity.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivity.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivity.java
new file mode 100644
index 0000000..9619297
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivity.java
@@ -0,0 +1,167 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import static org.apache.log4j.Logger.getLogger;
+
+import java.net.MalformedURLException;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.profile.ExceptionHandling;
+import io.github.taverna_extras.component.registry.ComponentImplementationCache;
+import io.github.taverna_extras.component.registry.ComponentUtil;
+import io.github.taverna_extras.component.utils.AnnotationUtils;
+import io.github.taverna_extras.component.utils.SystemUtils;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import org.apache.taverna.activities.dataflow.DataflowActivity;
+import org.apache.taverna.annotation.annotationbeans.SemanticAnnotation;
+import org.apache.taverna.invocation.InvocationContext;
+import org.apache.taverna.invocation.impl.InvocationContextImpl;
+import org.apache.taverna.platform.execution.api.InvalidWorkflowException;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.workflowmodel.Dataflow;
+import org.apache.taverna.workflowmodel.EditException;
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback;
+import org.apache.taverna.workflowmodel.utils.AnnotationTools;
+
+public class ComponentActivity extends
+ AbstractAsynchronousActivity<JsonNode> {
+ public static final String URI = "http://ns.taverna.org.uk/2010/activity/component";
+ private Logger logger = getLogger(ComponentActivity.class);
+
+ private ComponentUtil util;
+ private ComponentImplementationCache cache;
+ private volatile DataflowActivity componentRealization;
+ private JsonNode json;
+ private ComponentActivityConfigurationBean bean;
+ private SystemUtils system;
+ private AnnotationUtils annUtils;
+ private ComponentExceptionFactory cef;
+
+ private Dataflow realizingDataflow = null;
+
+ ComponentActivity(ComponentUtil util, ComponentImplementationCache cache,
+ Edits edits, SystemUtils system, AnnotationUtils annUtils, ComponentExceptionFactory exnFactory) {
+ this.util = util;
+ this.cache = cache;
+ this.system = system;
+ this.annUtils = annUtils;
+ setEdits(edits);
+ this.componentRealization = new DataflowActivity();
+ this.cef = exnFactory;
+ }
+
+ @Override
+ public void configure(JsonNode json) throws ActivityConfigurationException {
+ this.json = json;
+ try {
+ bean = new ComponentActivityConfigurationBean(json, util, cache);
+ } catch (MalformedURLException e) {
+ throw new ActivityConfigurationException(
+ "failed to understand configuration", e);
+ }
+ try {
+ configurePorts(bean.getPorts());
+ } catch (ComponentException e) {
+ throw new ActivityConfigurationException(
+ "failed to get component realization", e);
+ }
+ }
+
+ @Override
+ public void executeAsynch(Map<String, T2Reference> inputs,
+ AsynchronousActivityCallback callback) {
+ try {
+ ExceptionHandling exceptionHandling = bean.getExceptionHandling();
+ // InvocationContextImpl newContext = copyInvocationContext(callback);
+
+ getComponentRealization().executeAsynch(inputs, new ProxyCallback(
+ callback, callback.getContext(), exceptionHandling, cef));
+ } catch (ActivityConfigurationException e) {
+ callback.fail("Unable to execute component", e);
+ }
+ }
+
+ @SuppressWarnings("unused")
+ private InvocationContextImpl copyInvocationContext(
+ AsynchronousActivityCallback callback) {
+ InvocationContext originalContext = callback.getContext();
+ ReferenceService rs = originalContext.getReferenceService();
+ InvocationContextImpl newContext = new InvocationContextImpl(rs, null);
+ // for (Object o : originalContext.getEntities(Object.class)) {
+ // newContext.addEntity(o);
+ // }
+ return newContext;
+ }
+
+ @Override
+ public JsonNode getConfiguration() {
+ return json;
+ }
+
+ ComponentActivityConfigurationBean getConfigBean() {
+ return bean;
+ }
+
+ private DataflowActivity getComponentRealization()
+ throws ActivityConfigurationException {
+ synchronized (componentRealization) {
+ try {
+ if (componentRealization.getNestedDataflow() == null) {
+ if (realizingDataflow == null)
+ realizingDataflow = system.compile(util
+ .getVersion(bean).getImplementation());
+ componentRealization.setNestedDataflow(realizingDataflow);
+ copyAnnotations();
+ }
+ } catch (ComponentException e) {
+ logger.error("unable to read workflow", e);
+ throw new ActivityConfigurationException(
+ "unable to read workflow", e);
+ } catch (InvalidWorkflowException e) {
+ logger.error("unable to compile workflow", e);
+ throw new ActivityConfigurationException(
+ "unable to compile workflow", e);
+ }
+ }
+
+ return componentRealization;
+ }
+
+ private void copyAnnotations() {
+ // FIXME Completely wrong way of doing this!
+ try {
+ //annUtils.getAnnotation(subject, uriForAnnotation)
+ String annotationValue = AnnotationTools.getAnnotationString(realizingDataflow,
+ SemanticAnnotation.class, null);
+ if (annotationValue != null)
+ AnnotationTools.setAnnotationString(this, SemanticAnnotation.class,
+ annotationValue, getEdits()).doEdit();
+ } catch (EditException e) {
+ logger.error("failed to set annotation string", e);
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityConfigurationBean.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityConfigurationBean.java
new file mode 100644
index 0000000..6819b3f
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityConfigurationBean.java
@@ -0,0 +1,168 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import static org.apache.log4j.Logger.getLogger;
+import static io.github.taverna_extras.component.api.config.ComponentPropertyNames.COMPONENT_NAME;
+import static io.github.taverna_extras.component.api.config.ComponentPropertyNames.COMPONENT_VERSION;
+import static io.github.taverna_extras.component.api.config.ComponentPropertyNames.FAMILY_NAME;
+import static io.github.taverna_extras.component.api.config.ComponentPropertyNames.REGISTRY_BASE;
+
+import java.io.Serializable;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+//import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
+//import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+//import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.Version;
+import io.github.taverna_extras.component.api.profile.ExceptionHandling;
+import io.github.taverna_extras.component.registry.ComponentImplementationCache;
+import io.github.taverna_extras.component.registry.ComponentUtil;
+import io.github.taverna_extras.component.registry.ComponentVersionIdentification;
+
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
+import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+
+/**
+ * Component activity configuration bean.
+ */
+public class ComponentActivityConfigurationBean extends
+ ComponentVersionIdentification implements Serializable {
+ public static final String ERROR_CHANNEL = "error_channel";
+ public static final List<String> ignorableNames = Arrays
+ .asList(ERROR_CHANNEL);
+ private static final long serialVersionUID = 5774901665863468058L;
+ private static final Logger logger = getLogger(ComponentActivity.class);
+
+ private transient ActivityPortsDefinitionBean ports = null;
+ private transient ExceptionHandling eh;
+ private transient ComponentUtil util;
+ private transient ComponentImplementationCache cache;
+
+ public ComponentActivityConfigurationBean(Version.ID toBeCopied,
+ ComponentUtil util, ComponentImplementationCache cache) {
+ super(toBeCopied);
+ this.util = util;
+ this.cache = cache;
+ try {
+ getPorts();
+ } catch (io.github.taverna_extras.component.api.ComponentException e) {
+ logger.error("failed to get component realization", e);
+ }
+ }
+
+ public ComponentActivityConfigurationBean(JsonNode json,
+ ComponentUtil util, ComponentImplementationCache cache) throws MalformedURLException {
+ super(getUrl(json), getFamily(json), getComponent(json),
+ getVersion(json));
+ this.util = util;
+ this.cache = cache;
+ }
+
+ private static URL getUrl(JsonNode json) throws MalformedURLException {
+ return new URL(json.get(REGISTRY_BASE).textValue());
+ }
+
+ private static String getFamily(JsonNode json) {
+ return json.get(FAMILY_NAME).textValue();
+ }
+
+ private static String getComponent(JsonNode json) {
+ return json.get(COMPONENT_NAME).textValue();
+ }
+
+ private static Integer getVersion(JsonNode json) {
+ JsonNode node = json.get(COMPONENT_VERSION);
+ if (node == null || !node.isInt())
+ return null;
+ return node.intValue();
+ }
+
+ private ActivityPortsDefinitionBean getPortsDefinition(WorkflowBundle w) {
+ ActivityPortsDefinitionBean result = new ActivityPortsDefinitionBean();
+ List<ActivityInputPortDefinitionBean> inputs = result
+ .getInputPortDefinitions();
+ List<ActivityOutputPortDefinitionBean> outputs = result
+ .getOutputPortDefinitions();
+
+ for (InputWorkflowPort iwp : w.getMainWorkflow().getInputPorts())
+ inputs.add(makeInputDefinition(iwp));
+ // FIXME: Get the ValidatorState (so we can get getPortResolvedDepth()
+ ValidatorState vs = ... ;
+ for (OutputWorkflowPort owp : w.getMainWorkflow().getOutputPorts())
+ outputs.add(makeOutputDefinition(vs.getPortResolvedDepth(owp), owp.getName()));
+
+ try {
+ eh = util.getFamily(getRegistryBase(), getFamilyName())
+ .getComponentProfile().getExceptionHandling();
+ if (eh != null)
+ outputs.add(makeOutputDefinition(1, ERROR_CHANNEL));
+ } catch (io.github.taverna_extras.component.api.ComponentException e) {
+ logger.error("failed to get exception handling for family", e);
+ }
+ return result;
+ }
+
+ private ActivityInputPortDefinitionBean makeInputDefinition(
+ InputWorkflowPort dip) {
+ ActivityInputPortDefinitionBean activityInputPortDefinitionBean = new ActivityInputPortDefinitionBean();
+ activityInputPortDefinitionBean.setHandledReferenceSchemes(null);
+ activityInputPortDefinitionBean.setMimeTypes((List<String>) null);
+ activityInputPortDefinitionBean.setTranslatedElementType(String.class);
+ activityInputPortDefinitionBean.setAllowsLiteralValues(true);
+ activityInputPortDefinitionBean.setDepth(dip.getDepth());
+ activityInputPortDefinitionBean.setName(dip.getName());
+ return activityInputPortDefinitionBean;
+ }
+
+ private ActivityOutputPortDefinitionBean makeOutputDefinition(int depth,
+ String name) {
+ ActivityOutputPortDefinitionBean activityOutputPortDefinitionBean = new ActivityOutputPortDefinitionBean();
+ activityOutputPortDefinitionBean.setMimeTypes(new ArrayList<String>());
+ activityOutputPortDefinitionBean.setDepth(depth);
+ activityOutputPortDefinitionBean.setGranularDepth(depth);
+ activityOutputPortDefinitionBean.setName(name);
+ return activityOutputPortDefinitionBean;
+ }
+
+ /**
+ * @return the ports
+ */
+ public ActivityPortsDefinitionBean getPorts() throws io.github.taverna_extras.component.api.ComponentException{
+ if (ports == null)
+ ports = getPortsDefinition(cache.getImplementation(this));
+ return ports;
+ }
+
+ public ExceptionHandling getExceptionHandling() {
+ return eh;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityFactory.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityFactory.java
new file mode 100644
index 0000000..c90ea1a
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityFactory.java
@@ -0,0 +1,142 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.api.Version.ID;
+import io.github.taverna_extras.component.registry.ComponentImplementationCache;
+import io.github.taverna_extras.component.registry.ComponentUtil;
+import io.github.taverna_extras.component.utils.AnnotationUtils;
+import io.github.taverna_extras.component.utils.SystemUtils;
+import org.springframework.beans.factory.annotation.Required;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+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 org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+
+public class ComponentActivityFactory extends ComponentExceptionFactory
+ implements ActivityFactory {
+ private ComponentUtil util;
+ private ComponentImplementationCache cache;
+ private Edits edits;
+ private SystemUtils system;
+ private AnnotationUtils annUtils;
+
+ @Override
+ public ComponentActivity createActivity() {
+ return new ComponentActivity(util, cache, edits, system, annUtils, this);
+ }
+
+ @Override
+ public URI getActivityType() {
+ return URI.create(ComponentActivity.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)
+ throws ActivityConfigurationException {
+ try {
+ Set<ActivityInputPort> activityInputPorts = new HashSet<>();
+ for (ActivityInputPortDefinitionBean ipd : createConfiguration(
+ configuration).getPorts().getInputPortDefinitions())
+ activityInputPorts.add(edits.createActivityInputPort(
+ ipd.getName(), ipd.getDepth(), true, null,
+ ipd.getTranslatedElementType()));
+ return activityInputPorts;
+ } catch (MalformedURLException | ComponentException | RuntimeException e) {
+ throw new ActivityConfigurationException(
+ "failed to get implementation for configuration of inputs",
+ e);
+ }
+ }
+
+ @Override
+ public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration)
+ throws ActivityConfigurationException {
+ try {
+ Set<ActivityOutputPort> activityOutputPorts = new HashSet<>();
+ for (ActivityOutputPortDefinitionBean opd : createConfiguration(
+ configuration).getPorts().getOutputPortDefinitions())
+ activityOutputPorts.add(edits.createActivityOutputPort(
+ opd.getName(), opd.getDepth(), opd.getGranularDepth()));
+ return activityOutputPorts;
+ } catch (MalformedURLException | ComponentException | RuntimeException e) {
+ throw new ActivityConfigurationException(
+ "failed to get implementation for configuration of outputs",
+ e);
+ }
+ }
+
+ public ComponentActivityConfigurationBean createConfiguration(ID id) {
+ return new ComponentActivityConfigurationBean(id, util, cache);
+ }
+
+ public ComponentActivityConfigurationBean createConfiguration(JsonNode json)
+ throws MalformedURLException {
+ return new ComponentActivityConfigurationBean(json, util, cache);
+ }
+
+ @Required
+ public void setComponentUtil(ComponentUtil util) {
+ this.util = util;
+ }
+
+ @Required
+ public void setDataflowCache(ComponentImplementationCache cache) {
+ this.cache = cache;
+ }
+
+ @Required
+ public void setEdits(Edits edits) {
+ this.edits = edits;
+ }
+
+ @Required
+ public void setSystemUtil(SystemUtils system) {
+ this.system = system;
+ }
+
+ @Required
+ public void setAnnotationUtils(AnnotationUtils annUtils) {
+ this.annUtils = annUtils;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityLocalChecker.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityLocalChecker.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityLocalChecker.java
new file mode 100644
index 0000000..d874241
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityLocalChecker.java
@@ -0,0 +1,69 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import static io.github.taverna_extras.component.activity.ComponentHealthCheck.NON_SHAREABLE;
+
+import java.util.List;
+import org.apache.taverna.visit.VisitKind;
+import org.apache.taverna.visit.VisitReport;
+import static org.apache.taverna.visit.VisitReport.Status.WARNING;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+
+/**
+ * Component health checker
+ *
+ */
+public class ComponentActivityLocalChecker implements
+ HealthChecker<ComponentActivity> {
+ private static final VisitKind visitKind = ComponentHealthCheck
+ .getInstance();
+
+ @Override
+ public boolean canVisit(Object o) {
+ /*
+ * Return True if we can visit the object. We could do deeper (but not
+ * time consuming) checks here, for instance if the health checker only
+ * deals with ComponentActivity where a certain configuration option is
+ * enabled.
+ */
+ return o instanceof ComponentActivity;
+ }
+
+ @Override
+ public boolean isTimeConsuming() {
+ /*
+ * Return true if the health checker does a network lookup or similar
+ * time consuming checks, in which case it would only be performed when
+ * using File->Validate workflow or File->Run.
+ */
+ return false;
+ }
+
+ @Override
+ public VisitReport visit(ComponentActivity activity, List<Object> ancestry) {
+ if (!activity.getConfigBean().getRegistryBase().getProtocol()
+ .startsWith("http"))
+ return new VisitReport(visitKind, activity,
+ "Local component makes workflow non-shareable",
+ NON_SHAREABLE, WARNING);
+ return null;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityUpgradeChecker.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityUpgradeChecker.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityUpgradeChecker.java
new file mode 100644
index 0000000..4d45b60
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentActivityUpgradeChecker.java
@@ -0,0 +1,83 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import static org.apache.log4j.Logger.getLogger;
+import static io.github.taverna_extras.component.activity.ComponentHealthCheck.OUT_OF_DATE;
+
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.ComponentException;
+import io.github.taverna_extras.component.registry.ComponentUtil;
+import org.apache.taverna.visit.VisitKind;
+import org.apache.taverna.visit.VisitReport;
+import static org.apache.taverna.visit.VisitReport.Status.WARNING;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+import org.springframework.beans.factory.annotation.Required;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ComponentActivityUpgradeChecker implements
+ HealthChecker<ComponentActivity> {
+ private static final String OUTDATED_MSG = "Component out of date";
+ private static final VisitKind visitKind = ComponentHealthCheck
+ .getInstance();
+ private static Logger logger = getLogger(ComponentActivityUpgradeChecker.class);
+ private ComponentUtil utils;
+
+ @Required
+ public void setComponentUtil(ComponentUtil util) {
+ this.utils = util;
+ }
+
+ @Override
+ public boolean canVisit(Object o) {
+ return o instanceof ComponentActivity;
+ }
+
+ @Override
+ public boolean isTimeConsuming() {
+ return false;
+ }
+
+ @Override
+ public VisitReport visit(ComponentActivity activity, List<Object> ancestry) {
+ ComponentActivityConfigurationBean config = activity.getConfigBean();
+ int versionNumber = config.getComponentVersion();
+ int latestVersion = 0;
+
+ try {
+ latestVersion = utils
+ .getComponent(config.getRegistryBase(),
+ config.getFamilyName(), config.getComponentName())
+ .getComponentVersionMap().lastKey();
+ } catch (ComponentException e) {
+ logger.error("failed to get component description", e);
+ }
+
+ if (latestVersion > versionNumber)
+ return new VisitReport(visitKind, activity, OUTDATED_MSG,
+ OUT_OF_DATE, WARNING);
+ return null;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentExceptionFactory.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentExceptionFactory.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentExceptionFactory.java
new file mode 100644
index 0000000..243fe84
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentExceptionFactory.java
@@ -0,0 +1,38 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+class ComponentExceptionFactory {
+ private static final String UNEXPECTED_ID = "http://ns.taverna.org.uk/2012/component/unexpected";
+
+ ComponentExceptionFactory() {
+ }
+
+ public ComponentImplementationException createComponentException(
+ String exceptionId, String message) {
+ ComponentImplementationException result = new ComponentImplementationException(message);
+ result.setExceptionId(exceptionId);
+ return result;
+ }
+
+ public ComponentImplementationException createUnexpectedComponentException(
+ String message) {
+ return createComponentException(UNEXPECTED_ID, message);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentHealthCheck.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentHealthCheck.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentHealthCheck.java
new file mode 100644
index 0000000..0381de1
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentHealthCheck.java
@@ -0,0 +1,42 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import org.apache.taverna.visit.VisitKind;
+import org.apache.taverna.visit.Visitor;
+
+public class ComponentHealthCheck extends VisitKind {
+ public static final int NO_PROBLEM = 0;
+ public static final int OUT_OF_DATE = 10;
+ public static final int NON_SHAREABLE = 20;
+ public static final int FAILS_PROFILE = 30;
+
+ @Override
+ public Class<? extends Visitor<?>> getVisitorClass() {
+ return ComponentActivityUpgradeChecker.class;
+ }
+
+ private static class Singleton {
+ private static ComponentHealthCheck instance = new ComponentHealthCheck();
+ }
+
+ public static ComponentHealthCheck getInstance() {
+ return Singleton.instance;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentImplementationException.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentImplementationException.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentImplementationException.java
new file mode 100644
index 0000000..7ef77f7
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ComponentImplementationException.java
@@ -0,0 +1,37 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+public class ComponentImplementationException extends Exception {
+ public ComponentImplementationException(String string) {
+ super(string);
+ this.setStackTrace(new StackTraceElement[] {});
+ }
+
+ private static final long serialVersionUID = -3844030382222698090L;
+ private String exceptionId;
+
+ public void setExceptionId(String exceptionId) {
+ this.exceptionId = exceptionId;
+ }
+
+ public String getExceptionId() {
+ return exceptionId;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ProxyCallback.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ProxyCallback.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ProxyCallback.java
new file mode 100644
index 0000000..3a04af3
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/ProxyCallback.java
@@ -0,0 +1,264 @@
+package io.github.taverna_extras.component.activity;
+/*
+ * 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.
+ */
+
+import static org.apache.log4j.Logger.getLogger;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import javax.xml.ws.Holder;
+
+import org.apache.log4j.Logger;
+import io.github.taverna_extras.component.api.profile.ExceptionHandling;
+import io.github.taverna_extras.component.api.profile.ExceptionReplacement;
+import io.github.taverna_extras.component.api.profile.HandleException;
+import org.apache.taverna.invocation.InvocationContext;
+import org.apache.taverna.reference.ErrorDocument;
+import org.apache.taverna.reference.ErrorDocumentService;
+import org.apache.taverna.reference.IdentifiedList;
+import org.apache.taverna.reference.ListService;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.T2Reference;
+import static org.apache.taverna.reference.T2ReferenceType.ErrorDocument;
+import static org.apache.taverna.reference.T2ReferenceType.IdentifiedList;
+import static org.apache.taverna.reference.T2ReferenceType.ReferenceSet;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback;
+import org.apache.taverna.workflowmodel.processor.dispatch.events.DispatchErrorType;
+
+/**
+ * @author alanrw
+ *
+ */
+public class ProxyCallback implements AsynchronousActivityCallback {
+ private static final Logger logger = getLogger(ProxyCallback.class);
+
+ private final ComponentExceptionFactory cef;
+ private final AsynchronousActivityCallback proxiedCallback;
+ private final ReferenceService references;
+ private final InvocationContext context;
+ private final ExceptionHandling exceptionHandling;
+ private final ListService lists;
+ private final ErrorDocumentService errors;
+
+ /**
+ * @param proxiedCallback
+ * @param invocationContext
+ * @param exceptionHandling
+ * @param exnFactory
+ */
+ ProxyCallback(AsynchronousActivityCallback proxiedCallback,
+ InvocationContext invocationContext,
+ ExceptionHandling exceptionHandling,
+ ComponentExceptionFactory exnFactory) {
+ this.proxiedCallback = proxiedCallback;
+ this.exceptionHandling = exceptionHandling;
+ context = invocationContext;
+ references = context.getReferenceService();
+ lists = references.getListService();
+ errors = references.getErrorDocumentService();
+ cef = exnFactory;
+ }
+
+ @Override
+ public InvocationContext getContext() {
+ return context;
+ }
+
+ @Override
+ public void requestRun(Runnable runMe) {
+ proxiedCallback.requestRun(runMe);
+ }
+
+ @Override
+ public void receiveResult(Map<String, T2Reference> data, int[] index) {
+ if (exceptionHandling == null) {
+ proxiedCallback.receiveResult(data, index);
+ return;
+ }
+
+ List<T2Reference> exceptions = new ArrayList<>();
+ Map<String, T2Reference> replacement = new HashMap<>();
+ for (Entry<String, T2Reference> entry : data.entrySet())
+ replacement.put(entry.getKey(),
+ considerReference(entry.getValue(), exceptions));
+ replacement.put("error_channel",
+ references.register(exceptions, 1, true, context));
+ proxiedCallback.receiveResult(replacement, index);
+ }
+
+ private T2Reference considerReference(T2Reference value,
+ List<T2Reference> exceptions) {
+ if (!value.containsErrors())
+ return value;
+ else if (!value.getReferenceType().equals(IdentifiedList))
+ return replaceErrors(value, value.getDepth(), exceptions);
+ else if (exceptionHandling.failLists())
+ return replaceErrors(findFirstFailure(value), value.getDepth(),
+ exceptions);
+
+ List<T2Reference> replacementList = new ArrayList<>();
+ for (T2Reference subValue : lists.getList(value))
+ replacementList.add(considerReference(subValue, exceptions));
+ return references.register(replacementList, value.getDepth(), true,
+ context);
+ }
+
+ private T2Reference findFirstFailure(T2Reference value) {
+ IdentifiedList<T2Reference> originalList = lists.getList(value);
+ for (T2Reference subValue : originalList) {
+ if (subValue.getReferenceType().equals(ErrorDocument))
+ return subValue;
+ if (subValue.getReferenceType().equals(IdentifiedList))
+ if (subValue.containsErrors())
+ return findFirstFailure(subValue);
+ // No need to consider value
+ }
+ return null;
+ }
+
+ private T2Reference replaceErrors(T2Reference value, int depth,
+ List<T2Reference> exceptions) {
+ ErrorDocument doc = errors.getError(value);
+
+ Holder<HandleException> handleException = new Holder<>();
+ Set<ErrorDocument> toConsider = new HashSet<>();
+ Set<ErrorDocument> considered = new HashSet<>();
+ toConsider.add(doc);
+
+ while (!toConsider.isEmpty())
+ try {
+ ErrorDocument nudoc = remapException(toConsider, considered,
+ handleException);
+ if (nudoc != null) {
+ doc = nudoc;
+ break;
+ }
+ } catch (Exception e) {
+ logger.error("failed to locate exception mapping", e);
+ }
+
+ String exceptionMessage = doc.getExceptionMessage();
+ // An exception that is not mentioned
+ if (handleException.value == null) {
+ ComponentImplementationException newException = cef
+ .createUnexpectedComponentException(exceptionMessage);
+ T2Reference replacement = errors.registerError(exceptionMessage,
+ newException, depth, context).getId();
+ exceptions.add(errors.registerError(exceptionMessage, newException,
+ 0, context).getId());
+ return replacement;
+ }
+
+ if (handleException.value.pruneStack())
+ doc.getStackTraceStrings().clear();
+
+ ExceptionReplacement exnReplacement = handleException.value
+ .getReplacement();
+ if (exnReplacement == null) {
+ T2Reference replacement = references.register(doc, depth, true,
+ context);
+ exceptions.add(references.register(doc, 0, true, context));
+ return replacement;
+ }
+
+ ComponentImplementationException newException = cef
+ .createComponentException(exnReplacement.getReplacementId(),
+ exnReplacement.getReplacementMessage());
+ T2Reference replacement = errors.registerError(
+ exnReplacement.getReplacementMessage(), newException, depth,
+ context).getId();
+ exceptions.add(errors.registerError(
+ exnReplacement.getReplacementMessage(), newException, 0,
+ context).getId());
+ return replacement;
+ }
+
+ private ErrorDocument remapException(Set<ErrorDocument> toConsider,
+ Set<ErrorDocument> considered,
+ Holder<HandleException> handleException) {
+ ErrorDocument found = null;
+ ErrorDocument errorDoc = toConsider.iterator().next();
+
+ considered.add(errorDoc);
+ toConsider.remove(errorDoc);
+ String exceptionMessage = errorDoc.getExceptionMessage();
+ for (HandleException he : exceptionHandling.getHandleExceptions()) {
+ if (!he.matches(exceptionMessage))
+ continue;
+ handleException.value = he;
+ found = errorDoc;
+ }
+ if (!errorDoc.getErrorReferences().isEmpty())
+ for (T2Reference subRef : errorDoc.getErrorReferences())
+ for (T2Reference newErrorRef : getErrors(subRef)) {
+ ErrorDocument subDoc = errors.getError(newErrorRef);
+ if (subDoc == null)
+ logger.error("Error document contains references to non-existent sub-errors");
+ else if (!considered.contains(subDoc))
+ toConsider.add(subDoc);
+ }
+ return found;
+ }
+
+ private Set<T2Reference> getErrors(T2Reference ref) {
+ Set<T2Reference> result = new HashSet<>();
+ if (ref.getReferenceType().equals(ReferenceSet)) {
+ // nothing
+ } else if (ref.getReferenceType().equals(IdentifiedList)) {
+ IdentifiedList<T2Reference> originalList = lists.getList(ref);
+ for (T2Reference subValue : originalList)
+ if (subValue.containsErrors())
+ result.addAll(getErrors(subValue));
+ } else
+ result.add(ref);
+ return result;
+ }
+
+ @Override
+ public void receiveCompletion(int[] completionIndex) {
+ proxiedCallback.receiveCompletion(completionIndex);
+ }
+
+ @Override
+ public void fail(String message, Throwable t, DispatchErrorType errorType) {
+ proxiedCallback.fail(message, t, errorType);
+ }
+
+ @Override
+ public void fail(String message, Throwable t) {
+ proxiedCallback.fail(message, t);
+ }
+
+ @Override
+ public void fail(String message) {
+ proxiedCallback.fail(message);
+ }
+
+ @Override
+ public String getParentProcessIdentifier() {
+ // return "";
+ return proxiedCallback.getParentProcessIdentifier();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/package-info.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/package-info.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/package-info.java
new file mode 100644
index 0000000..086a49b
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/activity/package-info.java
@@ -0,0 +1,19 @@
+/*
+ * 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 io.github.taverna_extras.component.activity;
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-component/blob/b7b61e71/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ActivityProfileImpl.java
----------------------------------------------------------------------
diff --git a/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ActivityProfileImpl.java b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ActivityProfileImpl.java
new file mode 100644
index 0000000..a948cd4
--- /dev/null
+++ b/taverna-component-activity/src/main/java/io/github/taverna_extras/component/profile/ActivityProfileImpl.java
@@ -0,0 +1,53 @@
+package io.github.taverna_extras.component.profile;
+/*
+ * 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.
+ */
+
+import java.util.ArrayList;
+import java.util.List;
+
+import io.github.taverna_extras.component.api.profile.ActivityProfile;
+import io.github.taverna_extras.component.api.profile.SemanticAnnotationProfile;
+
+import io.github.taverna_extras.component.api.profile.doc.Activity;
+import io.github.taverna_extras.component.api.profile.doc.SemanticAnnotation;
+
+/**
+ * Specifies the semantic annotations that an activity must have.
+ *
+ * @author David Withers
+ */
+public class ActivityProfileImpl implements ActivityProfile {
+ private final ComponentProfileImpl componentProfile;
+ private final Activity activity;
+
+ public ActivityProfileImpl(ComponentProfileImpl componentProfile,
+ Activity activity) {
+ this.componentProfile = componentProfile;
+ this.activity = activity;
+ }
+
+ @Override
+ public List<SemanticAnnotationProfile> getSemanticAnnotations() {
+ List<SemanticAnnotationProfile> saProfiles = new ArrayList<>();
+ for (SemanticAnnotation annotation : activity.getSemanticAnnotation())
+ saProfiles.add(new SemanticAnnotationProfileImpl(componentProfile,
+ annotation));
+ return saProfiles;
+ }
+}