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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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; + } +}
