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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:47:03 UTC
[36/50] [abbrv] incubator-taverna-plugin-bioinformatics git commit:
taverna-biomart-activity-ui/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
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diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
new file mode 100644
index 0000000..9891fae
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+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
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+/**
+ *
+ */
+package net.sf.taverna.t2.activities.biomart.servicedescriptions;
+
+import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
+import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
+
+/**
+ * @author alanrw
+ *
+ */
+public class BiomartServiceProviderConfig extends PropertyAnnotated {
+
+ private String url;
+
+ public BiomartServiceProviderConfig() {
+ }
+
+ public BiomartServiceProviderConfig(String url) {
+ this.url = url.trim();
+ }
+
+ @PropertyAnnotation(displayName = "Biomart location", preferred = true)
+ public String getUrl() {
+ return url;
+ }
+
+ public void setUrl(String url) {
+ this.url = url.trim();
+ }
+
+ public String toString() {
+ return getUrl();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
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diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
new file mode 100644
index 0000000..87a2294
--- /dev/null
+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
@@ -0,0 +1,117 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.biomart.views;
+
+import java.awt.Frame;
+import java.io.IOException;
+import java.io.StringReader;
+
+import javax.swing.Action;
+
+import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
+
+import org.biomart.martservice.MartQuery;
+import org.biomart.martservice.MartServiceXMLHandler;
+import org.biomart.martservice.query.Attribute;
+import org.biomart.martservice.query.Filter;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class BiomartActivityContextualView extends HTMLBasedActivityContextualView {
+
+ private final EditManager editManager;
+ private final FileManager fileManager;
+ private final ActivityIconManager activityIconManager;
+ private final ApplicationConfiguration applicationConfiguration;
+ private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private final ServiceRegistry serviceRegistry;
+
+ public BiomartActivityContextualView(Activity activity, EditManager editManager,
+ FileManager fileManager, ActivityIconManager activityIconManager,
+ ColourManager colourManager, ApplicationConfiguration applicationConfiguration,
+ ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+ super(activity, colourManager);
+ this.editManager = editManager;
+ this.fileManager = fileManager;
+ this.activityIconManager = activityIconManager;
+ this.applicationConfiguration = applicationConfiguration;
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ this.serviceRegistry = serviceRegistry;
+ }
+
+ @Override
+ protected String getRawTableRowsHtml() {
+ String queryText = getConfigBean().getJson().get("martQuery").textValue();
+ Element martQuery = null;
+ try {
+ martQuery = new SAXBuilder().build(new StringReader(queryText)).getRootElement();
+ } catch (JDOMException | IOException e) {
+ }
+ MartQuery q = MartServiceXMLHandler.elementToMartQuery(martQuery, null);
+ String html = "<tr><td>URL</td><td>" + q.getMartService().getLocation() + "</td></tr>";
+ html += "<tr><td>Location</td><td>"
+ + q.getMartDataset().getMartURLLocation().getDisplayName() + "</td></tr>";
+ boolean firstFilter = true;
+ for (Filter filter : q.getQuery().getFilters()) {
+ html += firstFilter ? "<tr><td>Filter</td><td>" : "<tr><td></td></td>";
+ firstFilter = false;
+ html += filter.getName() + "</td></tr>";
+ }
+ boolean firstAttribute = true;
+ for (Attribute attribute : q.getQuery().getAttributes()) {
+ html += firstAttribute ? "<tr><td>Attribute</td><td>" : "<tr><td></td><td>";
+ firstAttribute = false;
+ html += attribute.getName() + "</td></tr>";
+ }
+ html += "<tr><td>Dataset</td><td>" + q.getMartDataset().getDisplayName() + "</td></tr>";
+ return html;
+ }
+
+ @Override
+ public String getViewTitle() {
+ return "Biomart service";
+ }
+
+ @Override
+ public Action getConfigureAction(Frame owner) {
+ return new BiomartActivityConfigurationAction(getActivity(), owner, editManager,
+ fileManager, activityIconManager, applicationConfiguration,
+ serviceDescriptionRegistry, serviceRegistry);
+ }
+
+ @Override
+ public int getPreferredPosition() {
+ return 100;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
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diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
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+++ b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
@@ -0,0 +1,86 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.biomart.views;
+
+import java.util.Arrays;
+import java.util.List;
+
+import net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceDescription;
+import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
+import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.file.FileManager;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
+import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+import uk.org.taverna.commons.services.ServiceRegistry;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import uk.org.taverna.scufl2.api.activity.Activity;
+
+public class BiomartActivityViewFactory implements ContextualViewFactory<Activity> {
+
+ private EditManager editManager;
+ private FileManager fileManager;
+ private ActivityIconManager activityIconManager;
+ private ColourManager colourManager;
+ private ApplicationConfiguration applicationConfiguration;
+ private ServiceDescriptionRegistry serviceDescriptionRegistry;
+ private ServiceRegistry serviceRegistry;
+
+ public boolean canHandle(Object object) {
+ return object instanceof Activity && ((Activity) object).getType().equals(BiomartServiceDescription.ACTIVITY_TYPE);
+ }
+
+ public List<ContextualView> getViews(Activity activity) {
+ return Arrays.asList(new ContextualView[] { new BiomartActivityContextualView(activity,
+ editManager, fileManager, activityIconManager, colourManager,
+ applicationConfiguration, serviceDescriptionRegistry, serviceRegistry) });
+ }
+
+ public void setEditManager(EditManager editManager) {
+ this.editManager = editManager;
+ }
+
+ public void setFileManager(FileManager fileManager) {
+ this.fileManager = fileManager;
+ }
+
+ public void setActivityIconManager(ActivityIconManager activityIconManager) {
+ this.activityIconManager = activityIconManager;
+ }
+
+ public void setColourManager(ColourManager colourManager) {
+ this.colourManager = colourManager;
+ }
+
+ public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
+ this.applicationConfiguration = applicationConfiguration;
+ }
+
+ public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+ this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+ }
+
+ public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+ this.serviceRegistry = serviceRegistry;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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+net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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+++ b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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+net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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+++ b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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+net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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+++ b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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+net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
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+++ b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:beans="http://www.springframework.org/schema/beans"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi.xsd">
+
+ <service ref="BiomartActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
+
+ <service ref="BiomartServiceProvider">
+ <interfaces>
+ <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
+ <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
+ </interfaces>
+ </service>
+
+ <service ref="BiomartConfigurationMenuAction" auto-export="interfaces" />
+
+ <service ref="BiomartActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+ <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
+ <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
+ <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
+ <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
+ <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry"/>
+ <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
+ <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
+
+</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
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+++ b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
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+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans.xsd">
+
+ <bean id="BiomartActivityIcon" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon" />
+
+ <bean id="BiomartServiceProvider" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider">
+ <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+ </bean>
+
+ <bean id="BiomartConfigurationMenuAction" class="net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+ <bean id="BiomartActivityViewFactory" class="net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory">
+ <property name="editManager" ref="editManager" />
+ <property name="fileManager" ref="fileManager" />
+ <property name="activityIconManager" ref="activityIconManager" />
+ <property name="colourManager" ref="colourManager" />
+ <property name="applicationConfiguration" ref="applicationConfiguration" />
+ <property name="serviceRegistry" ref="serviceRegistry" />
+ </bean>
+
+</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/main/resources/biomart.png
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diff --git a/taverna-biomart-activity-ui/src/main/resources/biomart.png b/taverna-biomart-activity-ui/src/main/resources/biomart.png
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
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diff --git a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
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+++ b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
@@ -0,0 +1,94 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.biomart.views;
+
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+
+import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
+import net.sf.taverna.t2.activities.biomart.views.BiomartActivityContextualView;
+
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.input.SAXBuilder;
+import org.jdom.output.XMLOutputter;
+import org.junit.Before;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.configurations.Configuration;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class TestBiomartActivityContextualView {
+ Activity activity;
+
+ @Before
+ public void setup() throws Exception {
+ activity = new Activity();
+ activity.setParent(new Profile());
+
+ Element el = getQueryElement("biomart-query.xml");
+
+ Configuration configuration = new Configuration();
+ configuration.setType(URI.create("http://ns.taverna.org.uk/2010/activity/biomart").resolve("#Config"));
+ String queryText = new XMLOutputter().outputString(new Document(el));
+ ((ObjectNode) configuration.getJson()).put("martQuery", queryText);
+
+ configuration.setConfigures(activity);
+ }
+
+ @Test @Ignore
+ public void testConfigurationAction() throws Exception {
+ BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
+ assertNotNull("The view should provide a configuration action",view.getConfigureAction(null));
+ assertTrue("The configuration action should be an instance of BiomartActivityConfigurationAction",view.getConfigureAction(null) instanceof BiomartActivityConfigurationAction);
+ }
+
+ private Element getQueryElement(String resourceName) throws Exception {
+ InputStream inStream = TestBiomartActivityContextualView.class
+ .getResourceAsStream("/"+resourceName);
+
+ if (inStream == null)
+ throw new IOException(
+ "Unable to find resource for:"
+ + resourceName);
+ SAXBuilder builder = new SAXBuilder();
+ return builder.build(inStream).detachRootElement();
+ }
+
+ private void run() throws Exception {
+ setup();
+ BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
+ view.setVisible(true);
+ }
+
+ public static void main(String[] args) throws Exception {
+ new TestBiomartActivityContextualView().run();
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/54aa18b5/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
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diff --git a/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml b/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
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index 0000000..0e52a23
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+++ b/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
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+<biomart:MartQuery
+ xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha">
+ <biomart:MartService
+ location="http://www.biomart.org/biomart/martservice" />
+ <biomart:MartDataset displayName="Homo sapiens genes (NCBI36)"
+ name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="10"
+ maximumBatchSize="50000" visible="false" interface="default"
+ modified="2006-11-27 12:49:27">
+ <biomart:MartURLLocation database="ensembl_mart_41" default="1"
+ displayName="ENSEMBL 41 (SANGER)" host="www.biomart.org"
+ includeDatasets="" martUser="" name="ensembl"
+ path="/biomart/martservice" port="80" serverVirtualSchema="default"
+ virtualSchema="default" visible="1" />
+ </biomart:MartDataset>
+ <biomart:Query virtualSchemaName="default" count="0" uniqueRows="0"
+ softwareVersion="0.5" requestId="taverna">
+ <biomart:Dataset name="hsapiens_gene_ensembl">
+ <biomart:Attribute name="coding_gene_flank" />
+ <biomart:Attribute name="gene_stable_id" />
+ <biomart:Filter name="ensembl_gene_id" value="" list="true" />
+ <biomart:Filter name="upstream_flank" value="100" />
+ </biomart:Dataset>
+ </biomart:Query>
+</biomart:MartQuery>
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