[18/28] incubator-taverna-common-activities git commit: Revert "temporarily empty repository"

[st...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportActivityTest.java b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportActivityTest.java
new file mode 100644
index 0000000..2cd2a2a
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportActivityTest.java
@@ -0,0 +1,186 @@
+/*******************************************************************************
+ * Copyright (C) 2009 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.spreadsheet;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
+import net.sf.taverna.t2.workflowmodel.EditException;
+import net.sf.taverna.t2.workflowmodel.Edits;
+import net.sf.taverna.t2.workflowmodel.Port;
+import net.sf.taverna.t2.workflowmodel.impl.EditsImpl;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * Unit tests for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivityTest}.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportActivityTest {
+
+	private SpreadsheetImportActivity activity;
+	private SpreadsheetImportActivityFactory activityFactory;
+	private Edits edits;
+	private ObjectNode configuration;
+
+	@Before
+	public void setUp() throws Exception {
+		activity = new SpreadsheetImportActivity();
+		activityFactory = new SpreadsheetImportActivityFactory();
+		edits = new EditsImpl();
+		activityFactory.setEdits(edits);
+		configuration = JsonNodeFactory.instance.objectNode();
+		configuration.put("columnRange", configuration.objectNode().put("start", 0).put("end", 1));
+		configuration.put("rowRange", configuration.objectNode().put("start", 0).put("end", -1));
+		configuration.put("emptyCellValue", "");
+		configuration.put("allRows", true);
+		configuration.put("excludeFirstRow", false);
+		configuration.put("ignoreBlankRows", false);
+		configuration.put("emptyCellPolicy", "EMPTY_STRING");
+		configuration.put("outputFormat", "PORT_PER_COLUMN");
+		configuration.put("csvDelimiter", ",");
+	}
+
+	@Test
+	public void testSpreadsheetImportActivity() {
+		assertNotNull(activity);
+		assertNull(activity.getConfiguration());
+	}
+
+	@Test
+	public void testConfigureSpreadsheetImportConfiguration() throws Exception {
+		assertEquals(0, activity.getInputPorts().size());
+		assertEquals(0, activity.getOutputPorts().size());
+		configuration.put("columnRange", configuration.objectNode().put("start", 0).put("end", 10));
+		ArrayNode columnNames = configuration.arrayNode();
+		columnNames.addObject().put("column", "C").put("port", "test");
+		configuration.put("columnNames", columnNames);
+		activity.configure(configuration);
+		for (ActivityInputPort activityInputPort : activityFactory.getInputPorts(configuration)) {
+			edits.getAddActivityInputPortEdit(activity, activityInputPort).doEdit();
+		}
+		for (ActivityOutputPort activityOutputPort : activityFactory.getOutputPorts(configuration)) {
+			edits.getAddActivityOutputPortEdit(activity, activityOutputPort).doEdit();
+		}
+		assertEquals(configuration, activity.getConfiguration());
+		assertEquals(1, activity.getInputPorts().size());
+		Set<ActivityOutputPort> outputPorts = activity.getOutputPorts();
+		int[] rangeValues = SpreadsheetUtils.getRange(configuration.get("columnRange")).getRangeValues();
+		assertEquals(rangeValues.length, outputPorts.size());
+		for (int i = 0; i < rangeValues.length; i++) {
+			String portName = SpreadsheetUtils.getPortName(rangeValues[i], configuration);
+			Port port = null;
+			for (Port outputPort : outputPorts) {
+				if (outputPort.getName().equals(portName)) {
+					port = outputPort;
+					break;
+				}
+			}
+			assertNotNull(port);
+			outputPorts.remove(port);
+		}
+		assertEquals(0, outputPorts.size());
+
+		configuration.put("outputFormat", SpreadsheetOutputFormat.SINGLE_PORT.name());
+		activity.configure(configuration);
+		assertEquals(1, activityFactory.getOutputPorts(configuration).size());
+	}
+
+	@Test
+	public void testGetConfiguration() throws ActivityConfigurationException {
+		assertNull(activity.getConfiguration());
+		activity.configure(configuration);
+		assertNotNull(activity.getConfiguration());
+		assertEquals(configuration, activity.getConfiguration());
+	}
+
+	@Test
+	public void testExecuteAsynchMapOfStringT2ReferenceAsynchronousActivityCallback() throws Exception {
+		configuration.put("columnRange", configuration.objectNode().put("start", 0).put("end", 3));
+		activity.configure(configuration);
+		for (ActivityInputPort activityInputPort : activityFactory.getInputPorts(configuration)) {
+			edits.getAddActivityInputPortEdit(activity, activityInputPort).doEdit();
+		}
+		for (ActivityOutputPort activityOutputPort : activityFactory.getOutputPorts(configuration)) {
+			edits.getAddActivityOutputPortEdit(activity, activityOutputPort).doEdit();
+		}
+		Map<String, Class<?>> outputs = new HashMap<String, Class<?>>();
+		outputs.put("A", String.class);
+		outputs.put("B", String.class);
+		outputs.put("C", String.class);
+		outputs.put("D", String.class);
+		Map<String, Object> results = ActivityInvoker.invokeAsyncActivity(activity, Collections.singletonMap("fileurl",
+				(Object) "src/test/resources/test-spreadsheet.xls"), outputs);
+		assertEquals(4, results.size());
+		assertTrue(results.get("A") instanceof List<?>);
+		assertEquals(15, ((List<?>) results.get("A")).size());
+		results = ActivityInvoker.invokeAsyncActivity(activity, Collections.singletonMap("fileurl",
+				(Object) "src/test/resources/test-spreadsheet.ods"), outputs);
+		assertEquals(4, results.size());
+		assertTrue(results.get("A") instanceof List<?>);
+		assertEquals(15, ((List<?>) results.get("A")).size());
+		results = ActivityInvoker.invokeAsyncActivity(activity, Collections.singletonMap("fileurl",
+				(Object) "src/test/resources/test-spreadsheet.csv"), outputs);
+		assertEquals(4, results.size());
+		assertTrue(results.get("A") instanceof List<?>);
+		assertEquals(15, ((List<?>) results.get("A")).size());
+
+		// CSV output
+		configuration.put("outputFormat", SpreadsheetOutputFormat.SINGLE_PORT.name());
+		activity.configure(configuration);
+		outputs = new HashMap<String, Class<?>>();
+		outputs.put("output", String.class);
+		results = ActivityInvoker.invokeAsyncActivity(activity, Collections.singletonMap("fileurl",
+				(Object) "src/test/resources/test-spreadsheet.xls"), outputs);
+		assertEquals(1, results.size());
+		assertTrue(results.get("output") instanceof String);
+		assertEquals(15, ((String) results.get("output")).split(System.getProperty("line.separator")).length);
+
+		// TSV output
+		configuration.put("csvDelimiter", "\t");
+		activity.configure(configuration);
+		results = ActivityInvoker.invokeAsyncActivity(activity, Collections.singletonMap("fileurl",
+				(Object) "src/test/resources/test-spreadsheet.csv"), outputs);
+		assertEquals(1, results.size());
+		assertTrue(results.get("output") instanceof String);
+		assertEquals(15, ((String) results.get("output")).split(System.getProperty("line.separator")).length);
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportConfigurationTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportConfigurationTest.java b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportConfigurationTest.java
new file mode 100644
index 0000000..918f6f7
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportConfigurationTest.java
@@ -0,0 +1,265 @@
+/*******************************************************************************
+ * Copyright (C) 2009 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.spreadsheet;
+
+import static org.junit.Assert.*;
+
+import java.util.Collections;
+
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * Unit tests for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration}.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportConfigurationTest {
+
+	private SpreadsheetImportConfiguration configuration;
+	
+	@Before
+	public void setUp() throws Exception {
+		configuration = new SpreadsheetImportConfiguration();
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#SpreadsheetImportConfiguration()}.
+	 */
+	@Test
+	public void testSpreadsheetImportConfiguration() {
+		assertNotNull(configuration);
+		assertEquals(new Range(0, 1), configuration.getColumnRange());
+		assertEquals(new Range(0, -1), configuration.getRowRange());
+		assertEquals("", configuration.getEmptyCellValue());
+		assertEquals(SpreadsheetEmptyCellPolicy.EMPTY_STRING, configuration.getEmptyCellPolicy());
+		assertEquals(SpreadsheetOutputFormat.PORT_PER_COLUMN, configuration.getOutputFormat());
+		assertEquals(Collections.EMPTY_MAP, configuration.getColumnNames());
+		assertEquals(true, configuration.isAllRows());
+		assertEquals(false, configuration.isExcludeFirstRow());
+		assertEquals(false, configuration.isIgnoreBlankRows());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#SpreadsheetImportConfiguration(net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration)}.
+	 */
+	@Test
+	public void testSpreadsheetImportConfigurationSpreadsheetImportConfiguration() {
+		configuration.setColumnRange(new Range(3, 22));
+		configuration.setColumnRange(new Range(2, 53));
+		configuration.setAllRows(false);
+		configuration.setExcludeFirstRow(true);
+		configuration.setIgnoreBlankRows(true);
+		configuration.setEmptyCellPolicy(SpreadsheetEmptyCellPolicy.GENERATE_ERROR);
+		configuration.setEmptyCellValue("NO VALUE");
+		configuration.setColumnNames(Collections.singletonMap("D", "delta"));
+		configuration.setOutputFormat(SpreadsheetOutputFormat.SINGLE_PORT);
+		configuration.setCsvDelimiter(" ");
+		SpreadsheetImportConfiguration newConfiguration = new SpreadsheetImportConfiguration(configuration);
+		assertEquals(configuration, newConfiguration);
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#getEmptyCellValue()}.
+	 */
+	@Test
+	public void testGetEmptyCellValue() {
+		assertEquals("", configuration.getEmptyCellValue());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setEmptyCellValue(java.lang.String)}.
+	 */
+	@Test
+	public void testSetEmptyCellValue() {
+		configuration.setEmptyCellValue("XXXX");
+		assertEquals("XXXX", configuration.getEmptyCellValue());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#getColumnRange()}.
+	 */
+	@Test
+	public void testGetColumnRange() {
+		assertEquals(new Range(0, 1), configuration.getColumnRange());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setColumnRange(net.sf.taverna.t2.activities.spreadsheet.Range)}.
+	 */
+	@Test
+	public void testSetColumnRange() {
+		configuration.setColumnRange(new Range(5, 89));
+		assertEquals(new Range(5, 89), configuration.getColumnRange());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#getRowRange()}.
+	 */
+	@Test
+	public void testGetRowRange() {
+		assertEquals(new Range(0, -1), configuration.getRowRange());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setRowRange(net.sf.taverna.t2.activities.spreadsheet.Range)}.
+	 */
+	@Test
+	public void testSetRowRange() {
+		configuration.setRowRange(new Range(41, 67));
+		assertEquals(new Range(41, 67), configuration.getRowRange());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#getColumnNames()}.
+	 */
+	@Test
+	public void testGetColumnNames() {
+		assertEquals(Collections.EMPTY_MAP, configuration.getColumnNames());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setColumnNames(java.util.Map)}.
+	 */
+	@Test
+	public void testSetColumnNames() {
+		configuration.setColumnNames(Collections.singletonMap("A", "alpha"));
+		assertEquals(Collections.singletonMap("A", "alpha"), configuration.getColumnNames());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#isAllRows()}.
+	 */
+	@Test
+	public void testIsAllRows() {
+		assertEquals(true, configuration.isAllRows());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setAllRows(boolean)}.
+	 */
+	@Test
+	public void testSetAllRows() {
+		configuration.setAllRows(false);
+		assertEquals(false, configuration.isAllRows());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#isExcludeFirstRow()}.
+	 */
+	@Test
+	public void testIsExcludeFirstRow() {
+		assertEquals(false, configuration.isExcludeFirstRow());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setExcludeFirstRow(boolean)}.
+	 */
+	@Test
+	public void testSetExcludeFirstRow() {
+		configuration.setExcludeFirstRow(true);
+		assertEquals(true, configuration.isExcludeFirstRow());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#isIgnoreBlankRows()}.
+	 */
+	@Test
+	public void testIsIgnoreBlankRows() {
+		assertEquals(false, configuration.isIgnoreBlankRows());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setIgnoreBlankRows(boolean)}.
+	 */
+	@Test
+	public void testSetIgnoreBlankRows() {
+		configuration.setIgnoreBlankRows(true);
+		assertEquals(true, configuration.isIgnoreBlankRows());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#getEmptyCellPolicy()}.
+	 */
+	@Test
+	public void testGetEmptyCellPolicy() {
+		assertEquals(SpreadsheetEmptyCellPolicy.EMPTY_STRING, configuration.getEmptyCellPolicy());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#setEmptyCellPolicy(net.sf.taverna.t2.activities.spreadsheet.SpreadsheetEmptyCellPolicy)}.
+	 */
+	@Test
+	public void testSetEmptyCellPolicy() {
+		configuration.setEmptyCellPolicy(SpreadsheetEmptyCellPolicy.GENERATE_ERROR);
+		assertEquals(SpreadsheetEmptyCellPolicy.GENERATE_ERROR, configuration.getEmptyCellPolicy());
+		configuration.setEmptyCellPolicy(SpreadsheetEmptyCellPolicy.USER_DEFINED);
+		assertEquals(SpreadsheetEmptyCellPolicy.USER_DEFINED, configuration.getEmptyCellPolicy());
+		configuration.setEmptyCellPolicy(SpreadsheetEmptyCellPolicy.EMPTY_STRING);
+		assertEquals(SpreadsheetEmptyCellPolicy.EMPTY_STRING, configuration.getEmptyCellPolicy());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#equals(java.lang.Object)}.
+	 */
+	@Test
+	public void testEqualsObject() {
+		assertTrue(configuration.equals(configuration));
+		assertTrue(configuration.equals(new SpreadsheetImportConfiguration()));
+		assertFalse(configuration.equals(null));
+		configuration.setEmptyCellValue("NIL");
+		assertFalse(configuration.equals(new SpreadsheetImportConfiguration()));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportConfiguration#hashCode()}.
+	 */
+	@Test
+	public void testHashCode() {
+		assertEquals(configuration.hashCode(), configuration.hashCode());
+		assertEquals(configuration.hashCode(), new SpreadsheetImportConfiguration().hashCode());
+	}
+
+	@Test
+	public void testGetOutputFormat() {
+		assertEquals(SpreadsheetOutputFormat.PORT_PER_COLUMN, configuration.getOutputFormat());
+	}
+
+	@Test
+	public void testSetOutputFormat() {
+		configuration.setOutputFormat(SpreadsheetOutputFormat.PORT_PER_COLUMN);
+		assertEquals(SpreadsheetOutputFormat.PORT_PER_COLUMN, configuration.getOutputFormat());
+		configuration.setOutputFormat(SpreadsheetOutputFormat.SINGLE_PORT);
+		assertEquals(SpreadsheetOutputFormat.SINGLE_PORT, configuration.getOutputFormat());
+	}
+
+	@Test
+	public void testGetCsvDelimiter() {
+		assertEquals(",", configuration.getCsvDelimiter());
+	}
+
+	@Test
+	public void testSetCsvDelimiter() {
+		configuration.setCsvDelimiter("'");
+		assertEquals("'", configuration.getCsvDelimiter());
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
new file mode 100644
index 0000000..dbf6711
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
@@ -0,0 +1,91 @@
+/*******************************************************************************
+ * Copyright (C) 2009 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.spreadsheet;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+
+import net.sf.taverna.t2.visit.VisitReport.Status;
+import net.sf.taverna.t2.workflowmodel.impl.EditsImpl;
+
+import org.junit.Before;
+import org.junit.Test;
+
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * Unit tests for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportHealthChecker}.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetImportHealthCheckerTest {
+
+	private SpreadsheetImportHealthChecker healthChecker;
+
+	private SpreadsheetImportActivity activity;
+	private ArrayList ancestors;
+
+	@Before
+	public void setUp() throws Exception {
+		EditsImpl ei = new EditsImpl();
+		healthChecker = new SpreadsheetImportHealthChecker();
+		activity = new SpreadsheetImportActivity();
+		activity.setEdits(new EditsImpl());
+		ancestors = new ArrayList();
+		ancestors.add(ei.createProcessor("fred"));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportHealthChecker#canHandle(java.lang.Object)}.
+	 */
+	@Test
+	public void testCanHandle() {
+		assertTrue(healthChecker.canVisit(activity));
+		assertFalse(healthChecker.canVisit(null));
+		assertFalse(healthChecker.canVisit(""));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportHealthChecker#checkHealth(net.sf.taverna.t2.activities.spreadsheet.SpreadsheetImportActivity)}.
+	 * @throws Exception
+	 */
+	@Test
+	public void testCheckHealth() throws Exception {
+		assertEquals(Status.SEVERE, healthChecker.visit(activity, ancestors).getStatus());
+		ObjectNode configuration = JsonNodeFactory.instance.objectNode();
+		configuration.put("columnRange", configuration.objectNode().put("start", 0).put("end", 1));
+		configuration.put("rowRange", configuration.objectNode().put("start", 0).put("end", -1));
+		configuration.put("emptyCellValue", "");
+		configuration.put("allRows", true);
+		configuration.put("excludeFirstRow", false);
+		configuration.put("ignoreBlankRows", false);
+		configuration.put("emptyCellPolicy", "EMPTY_STRING");
+		configuration.put("outputFormat", "PORT_PER_COLUMN");
+		configuration.put("csvDelimiter", ",");
+		activity.configure(configuration);
+		assertEquals(Status.OK, healthChecker.visit(activity, ancestors).getStatus());
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetReadExceptionTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetReadExceptionTest.java b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetReadExceptionTest.java
new file mode 100644
index 0000000..ef3445f
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetReadExceptionTest.java
@@ -0,0 +1,38 @@
+package net.sf.taverna.t2.activities.spreadsheet;
+
+import static org.junit.Assert.*;
+
+import org.junit.Test;
+
+public class SpreadsheetReadExceptionTest {
+
+	@Test
+	public void testSpreadsheetReadException() {
+		SpreadsheetReadException spreadsheetReadException = new SpreadsheetReadException();
+		assertNull(spreadsheetReadException.getMessage());
+		assertNull(spreadsheetReadException.getCause());
+	}
+
+	@Test
+	public void testSpreadsheetReadExceptionString() {
+		SpreadsheetReadException spreadsheetReadException = new SpreadsheetReadException("test exception");
+		assertEquals("test exception", spreadsheetReadException.getMessage());
+		assertNull(spreadsheetReadException.getCause());
+	}
+
+	@Test
+	public void testSpreadsheetReadExceptionThrowable() {
+		Exception exception = new Exception();
+		SpreadsheetReadException spreadsheetReadException = new SpreadsheetReadException(exception);
+		assertEquals(exception, spreadsheetReadException.getCause());
+	}
+
+	@Test
+	public void testSpreadsheetReadExceptionStringThrowable() {
+		Exception exception = new Exception();
+		SpreadsheetReadException spreadsheetReadException = new SpreadsheetReadException("test exception", exception);
+		assertEquals("test exception", spreadsheetReadException.getMessage());
+		assertEquals(exception, spreadsheetReadException.getCause());
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetUtilsTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetUtilsTest.java b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetUtilsTest.java
new file mode 100644
index 0000000..1c3a8f5
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/net/sf/taverna/t2/activities/spreadsheet/SpreadsheetUtilsTest.java
@@ -0,0 +1,98 @@
+/*******************************************************************************
+ * Copyright (C) 2009 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.spreadsheet;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+/**
+ * Unit tests for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils}.
+ *
+ * @author David Withers
+ */
+public class SpreadsheetUtilsTest {
+
+	@Test
+	public void testSpreadsheetUtils() {
+		assertNotNull(new SpreadsheetUtils());
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils#getColumnIndex(java.lang.String)}.
+	 */
+	@Test
+	public void testGetColumnIndex() {
+		assertEquals(0, SpreadsheetUtils.getColumnIndex("A"));
+		assertEquals(4, SpreadsheetUtils.getColumnIndex("E"));
+		assertEquals(25, SpreadsheetUtils.getColumnIndex("Z"));
+		assertEquals(26, SpreadsheetUtils.getColumnIndex("AA"));
+		assertEquals(457833, SpreadsheetUtils.getColumnIndex("ZAFZ"));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils#getColumnLabel(int)}.
+	 */
+	@Test
+	public void testGetColumnLabel() {
+		assertEquals("A", SpreadsheetUtils.getColumnLabel(0));
+		assertEquals("E", SpreadsheetUtils.getColumnLabel(4));
+		assertEquals("Z", SpreadsheetUtils.getColumnLabel(25));
+		assertEquals("AA", SpreadsheetUtils.getColumnLabel(26));
+		assertEquals("ZAFZ", SpreadsheetUtils.getColumnLabel(457833));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils#getPortName(java.lang.String, java.util.Map)}.
+	 */
+	@Test
+	public void testGetPortNameStringMapOfStringString() {
+		assertEquals("A", SpreadsheetUtils.getPortName("A", null));
+		assertEquals("AABR", SpreadsheetUtils.getPortName("AABR", null));
+		ObjectNode configuration = JsonNodeFactory.instance.objectNode();
+		ArrayNode columnNames = configuration.arrayNode();
+		columnNames.addObject().put("column", "B").put("port", "beta");
+		configuration.put("columnNames", columnNames);
+		assertEquals("beta", SpreadsheetUtils.getPortName("B", configuration));
+		assertEquals("T", SpreadsheetUtils.getPortName("T", configuration));
+	}
+
+	/**
+	 * Test method for {@link net.sf.taverna.t2.activities.spreadsheet.SpreadsheetUtils#getPortName(int, java.util.Map)}.
+	 */
+	@Test
+	public void testGetPortNameIntMapOfStringString() {
+		assertEquals("A", SpreadsheetUtils.getPortName(0, null));
+		assertEquals("AA", SpreadsheetUtils.getPortName(26, null));
+		ObjectNode configuration = JsonNodeFactory.instance.objectNode();
+		ArrayNode columnNames = configuration.arrayNode();
+		columnNames.addObject().put("column", "D").put("port", "delta");
+		configuration.put("columnNames", columnNames);
+		assertEquals("delta", SpreadsheetUtils.getPortName(3, configuration));
+		assertEquals("AB", SpreadsheetUtils.getPortName(27, configuration));
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.csv
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.csv b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.csv
new file mode 100644
index 0000000..bbbc3f3
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.csv
@@ -0,0 +1 @@
+A,5,C,1
A,5,C,1
TRUE,15/06/09,,2
X,X,X,X
X,X,X,X




y,y,y,y
y,y,y,y
y,y,y,y
y,y,y,y
y,y,y,y
y,y,y,y
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.ods
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.ods b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.ods
new file mode 100644
index 0000000..e4dbd98
Binary files /dev/null and b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.ods differ

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xls
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xls b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xls
new file mode 100644
index 0000000..12a2536
Binary files /dev/null and b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xls differ

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xlsx
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xlsx b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xlsx
new file mode 100644
index 0000000..2accc38
Binary files /dev/null and b/taverna-spreadsheet-import-activity/src/test/resources/test-spreadsheet.xlsx differ

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/pom.xml b/taverna-wsdl-activity/pom.xml
new file mode 100644
index 0000000..d92b618
--- /dev/null
+++ b/taverna-wsdl-activity/pom.xml
@@ -0,0 +1,118 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<parent>
+		<groupId>org.apache.taverna.commonactivities</groupId>
+		<artifactId>taverna-common-activities</artifactId>
+		<version>2.1.0-incubating-SNAPSHOT</version>
+	</parent>
+	<artifactId>taverna-wsdl-activity</artifactId>
+	<packaging>bundle</packaging>
+	<name>Apache Taverna WSDL Activity</name>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.felix</groupId>
+				<artifactId>maven-bundle-plugin</artifactId>
+				<extensions>true</extensions>
+				<configuration>
+					<instructions>
+						<!-- Use the java version instead of xmlcommons for javax.* packages -->
+						<Import-Package>javax.xml.namespace;version="0.0.0",javax.xml.parsers;version="0.0.0",org.w3c.dom;version="0.0.0",org.xml.sax;version="0.0.0",*</Import-Package>
+					</instructions>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.apache.taverna.engine</groupId>
+			<artifactId>taverna-workflowmodel-api</artifactId>
+			<version>${taverna.engine.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.taverna.engine</groupId>
+			<artifactId>taverna-reference-api</artifactId>
+			<version>${taverna.engine.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>${project.parent.groupId}</groupId>
+			<artifactId>taverna-wsdl-generic</artifactId>
+			<version>${project.parent.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.taverna.engine</groupId>
+			<artifactId>taverna-credential-manager</artifactId>
+			<version>${taverna.engine.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.jdom</groupId>
+			<artifactId>com.springsource.org.jdom</artifactId>
+			<version>${jdom.version}</version>
+		</dependency>
+<!--
+		<dependency>
+			<groupId>org.apache.ws</groupId>
+			<artifactId>com.springsource.org.apache.ws.security</artifactId>
+			<version>${ws.security.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.xml</groupId>
+			<artifactId>com.springsource.org.apache.xml.security</artifactId>
+			<version>${xml.security.version}</version>
+		</dependency>
+-->
+<!--
+<dependency>
+  <groupId>org.apache.axis</groupId>
+  <artifactId>com.springsource.org.apache.axis</artifactId>
+  <version>1.4.0</version>
+</dependency>
+-->
+<dependency>
+  <groupId>org.apache.ws.security</groupId>
+  <artifactId>wss4j</artifactId>
+  <version>${wss4j.version}</version> 
+  <!-- NOTE: wss4j 1.6 removes org.apache.ws.axis.security.WSDoAllSender 
+       Do we still need this? I can't see how it's used.. -->
+</dependency>
+<dependency>
+  <groupId>org.apache.santuario</groupId>
+  <artifactId>xmlsec</artifactId>
+  <version>${santuario.xmlsec.version}</version>
+</dependency>
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>${log4j.version}</version>
+		</dependency>
+
+		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+			<version>2.2.2</version>
+		</dependency>
+
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>${junit.version}</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.apache.taverna.engine</groupId>
+			<artifactId>taverna-activity-test-utils</artifactId>
+			<version>${taverna.engine.version}</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.taverna.engine</groupId>
+			<artifactId>taverna-workflowmodel-impl</artifactId>
+			<version>${taverna.engine.version}</version>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+</project>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java
new file mode 100644
index 0000000..c153722
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java
@@ -0,0 +1,57 @@
+package net.sf.taverna.t2.activities.wsdl;
+
+import java.io.IOException;
+import java.util.Map;
+
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLInputSplitterActivity;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+/**
+ * Interface for an activity such as {@link WSDLActivity} and
+ * {@link XMLInputSplitterActivity} that can provide {@link TypeDescriptor}s for
+ * its inputs.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ * @param <ActivityBeanType> The configuration bean type of the activity
+ */
+public interface InputPortTypeDescriptorActivity {
+
+	/**
+	 * Provides access to the TypeDescriptor for a given input port name.
+	 * <br>
+	 * This TypeDescriptor represents the Type defined in the schema for this Activities
+	 * WSDL.
+	 *
+	 * @param portName
+	 * @return the TypeDescriptor, or null if the portName is not recognised.
+	 * @throws UnknownOperationException if the operation this Activity is associated with doesn't exist.
+	 * @throws IOException
+	 *
+	 * @see TypeDescriptor
+	 * @see #getTypeDescriptorsForInputPorts()
+	 * @see #getTypeDescriptorForOutputPort(String)
+	 */
+	public abstract TypeDescriptor getTypeDescriptorForInputPort(String portName)
+			throws UnknownOperationException, IOException;
+
+	/**
+	 * Return TypeDescriptor for a all input ports.
+	 * <p>
+	 * This TypeDescriptor represents the Type defined in the schema for this Activities
+	 * WSDL.
+	 *
+	 * @param portName
+	 * @return A {@link Map} from portname to {@link TypeDescriptor}
+	 * @throws UnknownOperationException if the operation this Activity is associated with doesn't exist.
+	 * @throws IOException If the WSDL or some of its dependencies could not be read
+	 *
+	 * @see TypeDescriptor
+	 * @see #getTypeDescriptorForInputPort(String)
+	 * @see #getTypeDescriptorsForOutputPorts()
+	 */
+	public abstract Map<String, TypeDescriptor> getTypeDescriptorsForInputPorts()
+			throws UnknownOperationException, IOException;
+
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java
new file mode 100644
index 0000000..23a235c
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java
@@ -0,0 +1,57 @@
+package net.sf.taverna.t2.activities.wsdl;
+
+import java.io.IOException;
+import java.util.Map;
+
+import net.sf.taverna.t2.activities.wsdl.xmlsplitter.XMLOutputSplitterActivity;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+/**
+ * Interface for an activity such as {@link WSDLActivity} and
+ * {@link XMLOutputSplitterActivity} that can provide {@link TypeDescriptor}s for
+ * it's outputs.
+ *
+ * @author Stian Soiland-Reyes
+ *
+ * @param <ActivityBeanType> The configuration bean type of the activity
+ */
+public interface OutputPortTypeDescriptorActivity {
+
+	/**
+	 * Provides access to the TypeDescriptor for a given output port name.
+	 * <br>
+	 * This TypeDescriptor represents the Type defined in the schema for this Activities
+	 * WSDL.
+	 *
+	 * @param portName
+	 * @return the TypeDescriptor, or null if the portName is not recognised.
+	 * @throws UnknownOperationException if the operation this Activity is associated with doesn't exist.
+	 * @throws IOException
+	 *
+	 * @see TypeDescriptor
+	 * @see #getTypeDescriptorsForOutputPorts()
+	 * @see #getTypeDescriptorForInputPort(String)
+	 */
+	public abstract TypeDescriptor getTypeDescriptorForOutputPort(
+			String portName) throws UnknownOperationException, IOException;
+
+	/**
+	 * Return TypeDescriptor for a all output ports.
+	 * <p>
+	 * This TypeDescriptor represents the Type defined in the schema for this Activities
+	 * WSDL.
+	 *
+	 * @param portName
+	 * @return A {@link Map} from portname to {@link TypeDescriptor}
+	 * @throws UnknownOperationException if the operation this Activity is associated with doesn't exist.
+	 * @throws IOException If the WSDL or some of its dependencies could not be read
+	 *
+	 * @see TypeDescriptor
+	 * @see #getTypeDescriptorForOutputPort(String)
+	 * @see #getTypeDescriptorsForInputPorts()
+	 */
+	public abstract Map<String, TypeDescriptor> getTypeDescriptorsForOutputPorts()
+			throws UnknownOperationException, IOException;
+
+}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/T2WSDLSOAPInvoker.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/T2WSDLSOAPInvoker.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/T2WSDLSOAPInvoker.java
new file mode 100644
index 0000000..1e9d1a5
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/T2WSDLSOAPInvoker.java
@@ -0,0 +1,282 @@
+/*******************************************************************************
+ * 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.wsdl;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import net.sf.taverna.t2.activities.wsdl.security.SecurityProfiles;
+import net.sf.taverna.t2.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.security.credentialmanager.UsernamePassword;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+import net.sf.taverna.wsdl.soap.WSDLSOAPInvoker;
+
+import org.apache.axis.AxisProperties;
+import org.apache.axis.EngineConfiguration;
+import org.apache.axis.MessageContext;
+import org.apache.axis.client.Call;
+import org.apache.axis.configuration.XMLStringProvider;
+import org.apache.axis.message.SOAPHeaderElement;
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.Namespace;
+import org.jdom.input.SAXBuilder;
+import org.jdom.output.DOMOutputter;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * Invokes SOAP based Web Services from T2.
+ *
+ * Subclasses WSDLSOAPInvoker used for invoking Web Services from Taverna 1.x
+ * and extends it to provide support for invoking secure Web services.
+ *
+ * @author Stuart Owen
+ * @author Alex Nenadic
+ * @author Stian Soiland-Reyes
+ *
+ */
+public class T2WSDLSOAPInvoker extends WSDLSOAPInvoker {
+
+	private static final String REFERENCE_PROPERTIES = "ReferenceProperties";
+	private static final String ENDPOINT_REFERENCE = "EndpointReference";
+	private static Logger logger = Logger.getLogger(T2WSDLSOAPInvoker.class);
+	private static final Namespace wsaNS = Namespace.getNamespace("wsa",
+			"http://schemas.xmlsoap.org/ws/2004/03/addressing");
+
+	private String wsrfEndpointReference = null;
+
+	private CredentialManager credentialManager;
+
+	public T2WSDLSOAPInvoker(WSDLParser parser, String operationName,
+			List<String> outputNames, CredentialManager credentialManager) {
+		super(parser, operationName, outputNames);
+		this.credentialManager = credentialManager;
+	}
+
+	public T2WSDLSOAPInvoker(WSDLParser parser, String operationName,
+			List<String> outputNames, String wsrfEndpointReference, CredentialManager credentialManager) {
+		this(parser, operationName, outputNames, credentialManager);
+		this.wsrfEndpointReference = wsrfEndpointReference;
+	}
+
+	@SuppressWarnings("unchecked")
+	protected void addEndpointReferenceHeaders(
+			List<SOAPHeaderElement> soapHeaders) {
+		// Extract elements
+		// Add WSA-stuff
+		// Add elements
+
+		Document wsrfDoc;
+		try {
+			wsrfDoc = parseWsrfEndpointReference(wsrfEndpointReference);
+		} catch (JDOMException e) {
+			logger.warn("Could not parse endpoint reference, ignoring:\n"
+					+ wsrfEndpointReference, e);
+			return;
+		} catch (IOException e) {
+			logger.error("Could not read endpoint reference, ignoring:\n"
+					+ wsrfEndpointReference, e);
+			return;
+		}
+
+		Element endpointRefElem = null;
+		Element wsrfRoot = wsrfDoc.getRootElement();
+		if (wsrfRoot.getNamespace().equals(wsaNS)
+				&& wsrfRoot.getName().equals(ENDPOINT_REFERENCE)) {
+			endpointRefElem = wsrfRoot;
+		} else {
+			// Only look for child if the parent is not an EPR
+			Element childEndpoint = wsrfRoot
+					.getChild(ENDPOINT_REFERENCE, wsaNS);
+			if (childEndpoint != null) {
+				// Support wrapped endpoint reference for backward compatibility
+				// and convenience (T2-677)
+				endpointRefElem = childEndpoint;
+			} else {
+				logger
+						.warn("Unexpected element name for endpoint reference, but inserting anyway: "
+								+ wsrfRoot.getQualifiedName());
+				endpointRefElem = wsrfRoot;
+			}
+		}
+
+		Element refPropsElem = endpointRefElem.getChild(REFERENCE_PROPERTIES,
+				wsaNS);
+		if (refPropsElem == null) {
+			logger.warn("Could not find " + REFERENCE_PROPERTIES);
+			return;
+		}
+
+		List<Element> refProps = refPropsElem.getChildren();
+		// Make a copy of the list as it would be modified by
+		// prop.detach();
+		for (Element prop : new ArrayList<Element>(refProps)) {
+			DOMOutputter domOutputter = new DOMOutputter();
+			SOAPHeaderElement soapElem;
+			prop.detach();
+			try {
+				org.w3c.dom.Document domDoc = domOutputter.output(new Document(
+						prop));
+				soapElem = new SOAPHeaderElement(domDoc.getDocumentElement());
+			} catch (JDOMException e) {
+				logger.warn(
+						"Could not translate wsrf element to DOM:\n" + prop, e);
+				continue;
+			}
+			soapElem.setMustUnderstand(false);
+			soapElem.setActor(null);
+			soapHeaders.add(soapElem);
+		}
+
+		// soapHeaders.add(new SOAPHeaderElement((Element) wsrfDoc
+		// .getDocumentElement()));
+	}
+
+	protected void configureSecurity(Call call, JsonNode bean) throws Exception {
+
+		// If security settings require WS-Security - configure the axis call
+		// with appropriate properties
+		URI securityProfile = new URI(bean.get("securityProfile").textValue());
+		if (securityProfile
+				.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD)
+				|| securityProfile
+						.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD)
+				|| securityProfile
+						.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)
+				|| securityProfile
+						.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) {
+			
+			UsernamePassword usernamePassword = getUsernameAndPasswordForService(bean, false);
+			call.setProperty(Call.USERNAME_PROPERTY, usernamePassword.getUsername());
+			call.setProperty(Call.PASSWORD_PROPERTY, usernamePassword.getPasswordAsString());
+			usernamePassword.resetPassword();
+		} else if (securityProfile.equals(SecurityProfiles.HTTP_BASIC_AUTHN)){
+			// Basic HTTP AuthN - set HTTP headers
+			// pathrecursion allowed
+			UsernamePassword usernamePassword = getUsernameAndPasswordForService(bean, true);
+			MessageContext context = call.getMessageContext();
+			context.setUsername(usernamePassword.getUsername());
+			context.setPassword(usernamePassword.getPasswordAsString());
+			usernamePassword.resetPassword();
+		} else {
+			logger.error("Unknown security profile " + securityProfile);
+		}
+	}
+
+	/**
+	 * Get username and password from Credential Manager or ask user to supply
+	 * one. Username is the first element of the returned array, and the
+	 * password is the second.
+	 */
+	protected UsernamePassword getUsernameAndPasswordForService(
+			JsonNode bean, boolean usePathRecursion) throws CMException {
+
+		// Try to get username and password for this service from Credential
+		// Manager (which should pop up UI if needed)
+		URI serviceUri = URI.create(bean.get("operation").get("wsdl").textValue());
+		UsernamePassword username_password = credentialManager.getUsernameAndPasswordForService(serviceUri, usePathRecursion, null);
+		if (username_password == null) {
+			throw new CMException("No username/password provided for service " + serviceUri);
+		}
+		return username_password;
+	}
+
+	@Override
+	protected List<SOAPHeaderElement> makeSoapHeaders() {
+		List<SOAPHeaderElement> soapHeaders = new ArrayList<SOAPHeaderElement>(
+				super.makeSoapHeaders());
+		if (wsrfEndpointReference != null && getParser().isWsrfService()) {
+			addEndpointReferenceHeaders(soapHeaders);
+		}
+		return soapHeaders;
+	}
+
+	protected org.jdom.Document parseWsrfEndpointReference(
+			String wsrfEndpointReference) throws JDOMException, IOException {
+		SAXBuilder builder = new SAXBuilder();
+		return builder.build(new StringReader(wsrfEndpointReference));
+	}
+
+	public Map<String, Object> invoke(Map<String, Object> inputMap,
+			JsonNode bean) throws Exception {
+
+		EngineConfiguration wssEngineConfiguration = null;
+		if (bean.has("securityProfile")) {
+			URI securityProfile = new URI(bean.get("securityProfile").textValue());
+
+			// If security settings require WS-Security and not just e.g. Basic HTTP
+			// AuthN - configure the axis engine from the appropriate config strings
+			if (securityProfile
+					.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD)) {
+				wssEngineConfiguration = new XMLStringProvider(
+						SecurityProfiles.WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD_CONFIG);
+			} else if (securityProfile
+					.equals(SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD)) {
+				wssEngineConfiguration = new XMLStringProvider(
+						SecurityProfiles.WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD_CONFIG);
+			} else if (securityProfile
+					.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD)) {
+				wssEngineConfiguration = new XMLStringProvider(
+						SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTETPASSWORD_CONFIG);
+			} else if (securityProfile
+					.equals(SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD)) {
+				wssEngineConfiguration = new XMLStringProvider(
+						SecurityProfiles.WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD_CONFIG);
+			}
+		}
+
+		// This does not work
+//		ClassUtils.setClassLoader("net.sf.taverna.t2.activities.wsdl.security.TavernaAxisCustomSSLSocketFactory",TavernaAxisCustomSSLSocketFactory.class.getClassLoader());
+
+		// Setting Axis property only works when we also set the Thread's classloader as below
+		// (we do it from the net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invoke.requestRun())
+//		Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
+		if (AxisProperties.getProperty("axis.socketSecureFactory")== null || !AxisProperties.getProperty("axis.socketSecureFactory").equals("net.sf.taverna.t2.activities.wsdl.security.TavernaAxisCustomSSLSocketFactory")){
+			AxisProperties.setProperty("axis.socketSecureFactory", "net.sf.taverna.t2.activities.wsdl.security.TavernaAxisCustomSSLSocketFactory");
+			logger.info("Setting axis.socketSecureFactory property to " + AxisProperties.getProperty("axis.socketSecureFactory"));
+		}
+
+		// This also does not work
+		//AxisProperties.setClassDefault(SecureSocketFactory.class, "net.sf.taverna.t2.activities.wsdl.security.TavernaAxisCustomSSLSocketFactory");
+
+		Call call = super.getCall(wssEngineConfiguration);
+		
+		// Now that we have an axis Call object, configure any additional
+		// security properties on it (or its message context or its Transport
+		// handler),
+		// such as WS-Security UsernameToken or HTTP Basic AuthN
+		if (bean.has("securityProfile")) {
+			configureSecurity(call, bean);
+		}
+
+		return invoke(inputMap, call);
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivity.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivity.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivity.java
new file mode 100644
index 0000000..763cbee
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivity.java
@@ -0,0 +1,328 @@
+/*******************************************************************************
+ * 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.wsdl;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.SocketTimeoutException;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.reference.ReferenceService;
+import net.sf.taverna.t2.reference.ReferenceServiceException;
+import net.sf.taverna.t2.reference.T2Reference;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.workflowmodel.OutputPort;
+import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
+import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+
+import org.apache.log4j.Logger;
+import org.xml.sax.SAXException;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * An asynchronous Activity that is concerned with WSDL based web-services.
+ * <p>
+ * The activity is configured according to the WSDL location and the operation.<br>
+ * The ports are defined dynamically according to the WSDL specification, and in
+ * addition an output<br>
+ * port <em>attachmentList</em> is added to represent any attachements that are
+ * returned by the webservice.
+ * </p>
+ *
+ * @author Stuart Owen
+ * @author Stian Soiland-Reyes
+ */
+public class WSDLActivity extends
+		AbstractAsynchronousActivity<JsonNode> implements
+		InputPortTypeDescriptorActivity, OutputPortTypeDescriptorActivity {
+
+	public static final String URI = "http://ns.taverna.org.uk/2010/activity/wsdl";
+
+	public static final String ENDPOINT_REFERENCE = "EndpointReference";
+	private JsonNode configurationBean;
+	private WSDLParser parser;
+//	private Map<String, Integer> outputDepth = new HashMap<String, Integer>();
+	private boolean isWsrfService = false;
+//	private String endpointReferenceInputPortName;
+	private CredentialManager credentialManager;
+
+	public WSDLActivity(CredentialManager credentialManager) {
+		this.credentialManager = credentialManager;
+	}
+
+	public boolean isWsrfService() {
+		return isWsrfService;
+	}
+
+	private static Logger logger = Logger.getLogger(WSDLActivity.class);
+
+	/**
+	 * Configures the activity according to the information passed by the
+	 * configuration bean.<br>
+	 * During this process the WSDL is parsed to determine the input and output
+	 * ports.
+	 *
+	 * @param bean
+	 *            the {@link WSDLActivityConfigurationBean} configuration bean
+	 */
+	@Override
+	public void configure(JsonNode bean)
+			throws ActivityConfigurationException {
+		this.configurationBean = bean;
+		try {
+			parseWSDL();
+		} catch (Exception ex) {
+			throw new ActivityConfigurationException(
+					"Unable to parse the WSDL " + bean.get("operation").get("wsdl").textValue(), ex);
+		}
+	}
+
+	@Override
+	public JsonNode getConfiguration() {
+		return configurationBean;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @seenet.sf.taverna.t2.activities.wsdl.InputPortTypeDescriptorActivity#
+	 * getTypeDescriptorForInputPort(java.lang.String)
+	 */
+	public TypeDescriptor getTypeDescriptorForInputPort(String portName)
+			throws UnknownOperationException, IOException {
+		List<TypeDescriptor> inputDescriptors = parser
+				.getOperationInputParameters(configurationBean.get("operation").get("name").textValue());
+		TypeDescriptor result = null;
+		for (TypeDescriptor descriptor : inputDescriptors) {
+			if (descriptor.getName().equals(portName)) {
+				result = descriptor;
+				break;
+			}
+		}
+		return result;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @seenet.sf.taverna.t2.activities.wsdl.InputPortTypeDescriptorActivity#
+	 * getTypeDescriptorsForInputPorts()
+	 */
+	public Map<String, TypeDescriptor> getTypeDescriptorsForInputPorts()
+			throws UnknownOperationException, IOException {
+		Map<String, TypeDescriptor> descriptors = new HashMap<String, TypeDescriptor>();
+		List<TypeDescriptor> inputDescriptors = parser
+				.getOperationInputParameters(configurationBean.get("operation").get("name").textValue());
+		for (TypeDescriptor descriptor : inputDescriptors) {
+			descriptors.put(descriptor.getName(), descriptor);
+		}
+		return descriptors;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @seenet.sf.taverna.t2.activities.wsdl.OutputPortTypeDescriptorActivity#
+	 * getTypeDescriptorForOutputPort(java.lang.String)
+	 */
+	public TypeDescriptor getTypeDescriptorForOutputPort(String portName)
+			throws UnknownOperationException, IOException {
+		TypeDescriptor result = null;
+		List<TypeDescriptor> outputDescriptors = parser
+				.getOperationOutputParameters(configurationBean.get("operation").get("name").textValue());
+		for (TypeDescriptor descriptor : outputDescriptors) {
+			if (descriptor.getName().equals(portName)) {
+				result = descriptor;
+				break;
+			}
+		}
+		return result;
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @seenet.sf.taverna.t2.activities.wsdl.OutputPortTypeDescriptorActivity#
+	 * getTypeDescriptorsForOutputPorts()
+	 */
+	public Map<String, TypeDescriptor> getTypeDescriptorsForOutputPorts()
+			throws UnknownOperationException, IOException {
+		Map<String, TypeDescriptor> descriptors = new HashMap<String, TypeDescriptor>();
+		List<TypeDescriptor> inputDescriptors = parser
+				.getOperationOutputParameters(configurationBean.get("operation").get("name").textValue());
+		for (TypeDescriptor descriptor : inputDescriptors) {
+			descriptors.put(descriptor.getName(), descriptor);
+		}
+		return descriptors;
+	}
+
+	private void parseWSDL() throws ParserConfigurationException,
+			WSDLException, IOException, SAXException, UnknownOperationException {
+		String wsdlLocation = configurationBean.get("operation").get("wsdl").textValue();
+		URLConnection connection = null;
+		try {
+			URL wsdlURL = new URL(wsdlLocation);
+			connection = wsdlURL.openConnection();
+			connection.setConnectTimeout(RemoteHealthChecker.getTimeoutInSeconds() * 1000);
+			connection.connect();
+		} catch (MalformedURLException e) {
+			throw new IOException("Malformed URL", e);
+		} catch (SocketTimeoutException e) {
+			throw new IOException("Timeout", e);
+		} catch (IOException e) {
+			throw e;
+		} finally {
+			if ((connection != null) && (connection.getInputStream() != null)) {
+				connection.getInputStream().close();
+			}
+		}
+		parser = new WSDLParser(wsdlLocation);
+		isWsrfService = parser.isWsrfService();
+	}
+
+	@Override
+	public void executeAsynch(final Map<String, T2Reference> data,
+			final AsynchronousActivityCallback callback) {
+
+		callback.requestRun(new Runnable() {
+
+			public void run() {
+
+				ReferenceService referenceService = callback.getContext()
+						.getReferenceService();
+
+				Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
+				Map<String, Object> invokerInputMap = new HashMap<String, Object>();
+				String endpointReferenceInputPortName = getEndpointReferenceInputPortName();
+
+				try {
+					String endpointReference = null;
+					for (String key : data.keySet()) {
+						Object renderIdentifier = referenceService
+								.renderIdentifier(data.get(key), String.class,
+										callback.getContext());
+						if (isWsrfService()
+								&& key.equals(endpointReferenceInputPortName)) {
+							endpointReference = (String) renderIdentifier;
+						} else {
+							invokerInputMap.put(key, renderIdentifier);
+						}
+					}
+					List<String> outputNames = new ArrayList<String>();
+					for (OutputPort port : getOutputPorts()) {
+						outputNames.add(port.getName());
+					}
+
+					T2WSDLSOAPInvoker invoker = new T2WSDLSOAPInvoker(parser,
+							configurationBean.get("operation").get("name").textValue(), outputNames,
+							endpointReference, credentialManager);
+
+					Map<String, Object> invokerOutputMap = invoker.invoke(
+							invokerInputMap, configurationBean);
+					
+					for (String outputName : invokerOutputMap.keySet()) {
+					    Object value = invokerOutputMap.get(outputName);
+						
+						if (value != null) {
+							Integer depth = getOutputPortDepth(outputName);
+							if (depth != null) {
+								outputData.put(outputName, referenceService
+										.register(value, depth, true, callback
+												.getContext()));
+							} else {
+								logger.info("Skipping unknown output port :"
+												+ outputName);
+//								// TODO what should the depth be in this case?
+//								outputData.put(outputName, referenceService
+//										.register(value, 0, true, callback
+//												.getContext()));
+							}
+						}
+					}
+					callback.receiveResult(outputData, new int[0]);
+				} catch (ReferenceServiceException e) {
+					logger.error("Error finding the input data for "
+							+ getConfiguration().get("operation"), e);
+					callback.fail("Unable to find input data", e);
+					return;
+				} catch (Exception e) {
+					logger.error("Error invoking WSDL service "
+							+ getConfiguration().get("operation"), e);
+					callback.fail(
+							"An error occurred invoking the WSDL service", e);
+					return;
+				}
+
+			}
+
+		});
+
+	}
+
+	private Integer getOutputPortDepth(String portName) {
+		for (ActivityOutputPort outputPort : getOutputPorts()) {
+			if (outputPort.getName().equals(portName)) {
+				return outputPort.getDepth();
+			}
+		}
+		return null;
+	}
+
+	private String getEndpointReferenceInputPortName() {
+		String endpointReferenceInputPortName = null;
+		if (parser.isWsrfService()) {
+			Set<String> inputPorts = new HashSet<>();
+			try {
+				List<TypeDescriptor> inputDescriptors = parser.getOperationInputParameters(configurationBean
+						.get("operation").get("name").textValue());
+				for (TypeDescriptor descriptor : inputDescriptors) {
+					inputPorts.add(descriptor.getName());
+				}
+			} catch (UnknownOperationException | IOException e) {
+			}
+			// Make sure the port name is unique
+			endpointReferenceInputPortName = WSDLActivity.ENDPOINT_REFERENCE;
+			int counter = 0;
+			while (inputPorts.contains(endpointReferenceInputPortName)) {
+				endpointReferenceInputPortName = WSDLActivity.ENDPOINT_REFERENCE + counter++;
+			}
+		}
+		return endpointReferenceInputPortName;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityConfigurationBean.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityConfigurationBean.java
new file mode 100644
index 0000000..80b0bd5
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityConfigurationBean.java
@@ -0,0 +1,82 @@
+/*******************************************************************************
+ * 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.wsdl;
+
+import java.net.URI;
+
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * A standard Java Bean that provides the details required to configure a WSDLActivity.
+ * <p>
+ * This contains details about the WSDL and the Operation that the WSDLActivity is intended to invoke.
+ * </p>
+ * @author Stuart Owen
+ */
+@ConfigurationBean(uri = WSDLActivity.URI + "#Config")
+public class WSDLActivityConfigurationBean {
+    private WSDLOperationConfigurationBean operation;
+    private URI securityProfile;
+
+    // In the case service requires username and password for authentication,
+    // but do not serialise these variables to file
+    //transient private String username;
+    //transient private String password;
+
+    /** Creates a new instance of WSDLActivityConfigurationBean */
+    public WSDLActivityConfigurationBean() {
+    }
+
+    public WSDLOperationConfigurationBean getOperation() {
+        return operation;
+    }
+
+	@ConfigurationProperty(name = "operation", label = "WSDL Operation", description = "The WSDL operation")
+    public void setOperation(WSDLOperationConfigurationBean operation) {
+        this.operation = operation;
+    }
+
+	public URI getSecurityProfile() {
+		return securityProfile;
+	}
+
+	@ConfigurationProperty(name = "securityProfile", label = "Security Profile", description = "WS-Security settings required by the web service", required = false)
+	public void setSecurityProfile(URI securityProfile) {
+		this.securityProfile = securityProfile;
+	}
+
+//	public void setUsername(String username) {
+//		this.username = username;
+//	}
+//
+//	public String getUsername() {
+//		return username;
+//	}
+//
+//	public void setPassword(String password) {
+//		this.password = password;
+//	}
+//
+//	public String getPassword() {
+//		return password;
+//	}
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityDescriptorChecker.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityDescriptorChecker.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityDescriptorChecker.java
new file mode 100644
index 0000000..5a41cde
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityDescriptorChecker.java
@@ -0,0 +1,147 @@
+/**
+ *
+ */
+package net.sf.taverna.t2.activities.wsdl;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import net.sf.taverna.t2.visit.VisitReport;
+import net.sf.taverna.t2.visit.VisitReport.Status;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.Datalink;
+import net.sf.taverna.t2.workflowmodel.Merge;
+import net.sf.taverna.t2.workflowmodel.MergeInputPort;
+import net.sf.taverna.t2.workflowmodel.MergeOutputPort;
+import net.sf.taverna.t2.workflowmodel.MergePort;
+import net.sf.taverna.t2.workflowmodel.Port;
+import net.sf.taverna.t2.workflowmodel.Processor;
+import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
+import net.sf.taverna.t2.workflowmodel.ProcessorPort;
+import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
+import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+import net.sf.taverna.t2.workflowmodel.utils.Tools;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+import org.apache.log4j.Logger;
+
+/**
+ * @author alanrw
+ *
+ */
+public final class WSDLActivityDescriptorChecker implements HealthChecker<InputPortTypeDescriptorActivity> {
+
+	private static Logger logger = Logger.getLogger(WSDLActivityDescriptorChecker.class);
+
+	public boolean canVisit(Object o) {
+		return ((o != null) && (o instanceof InputPortTypeDescriptorActivity));
+	}
+
+	public boolean isTimeConsuming() {
+		return false;
+	}
+
+	public VisitReport visit(InputPortTypeDescriptorActivity o,
+			List<Object> ancestry) {
+		List<VisitReport> reports = new ArrayList<VisitReport>();
+		try {
+			Map<String, TypeDescriptor> typeMap = o.getTypeDescriptorsForInputPorts();
+			Processor p = (Processor) VisitReport.findAncestor(ancestry, Processor.class);
+			Dataflow d = (Dataflow) VisitReport.findAncestor(ancestry, Dataflow.class);
+
+
+			for (Entry<String, TypeDescriptor> entry : typeMap.entrySet()) {
+				TypeDescriptor descriptor = entry.getValue();
+				if (!descriptor.getMimeType().contains("'text/xml'")) {
+					continue;
+				}
+				if (!((descriptor instanceof ArrayTypeDescriptor) || (descriptor instanceof ComplexTypeDescriptor))) {
+					continue;
+				}
+				// Find the processor port, if any that corresponds to the activity port
+				ActivityInputPort aip = Tools.getActivityInputPort((Activity<?>) o, entry.getKey());
+				if (aip == null) {
+					continue;
+				}
+				ProcessorInputPort pip = Tools.getProcessorInputPort(p, (Activity<?>) o, aip);
+
+				if (pip == null) {
+					continue;
+				}
+
+				for (Datalink dl : d.getLinks()) {
+
+					if (dl.getSink().equals(pip)) {
+						Port source = dl.getSource();
+						Set<VisitReport> subReports = checkSource(source, d, (Activity<?>) o, aip);
+						for (VisitReport vr : subReports) {
+						    vr.setProperty("activity", o);
+						    vr.setProperty("sinkPort", pip);
+						}
+						reports.addAll(subReports);
+					}
+				}
+
+			}
+		} catch (UnknownOperationException e) {
+			logger.error("Problem getting type descriptors for activity", e);
+		} catch (IOException e) {
+			logger.error("Problem getting type descriptors for activity", e);
+		} catch (NullPointerException e) {
+			logger.error("Problem getting type desciptors for activity", e);
+		}
+		if (reports.isEmpty()) {
+			return null;
+		}
+		if (reports.size() == 1) {
+			return reports.get(0);
+		}
+		else {
+			return new VisitReport(HealthCheck.getInstance(), o, "Collation", HealthCheck.DEFAULT_VALUE, reports);
+		}
+	}
+
+	private Set<VisitReport> checkSource(Port source, Dataflow d, Activity<?> o, ActivityInputPort aip) {
+		Set<VisitReport> reports = new HashSet<VisitReport>();
+		if (source instanceof ProcessorPort) {
+			ProcessorPort processorPort = (ProcessorPort) source;
+			Processor sourceProcessor = processorPort.getProcessor();
+			Activity<?> sourceActivity = sourceProcessor.getActivityList().get(0);
+			if (!(sourceActivity instanceof InputPortTypeDescriptorActivity)) {
+				VisitReport newReport = new VisitReport(HealthCheck.getInstance(), o, "Source of " + aip.getName(), HealthCheck.DATATYPE_SOURCE, Status.WARNING);
+				newReport.setProperty("sinkPortName", aip.getName());
+				newReport.setProperty("sourceName", sourceProcessor.getLocalName());
+				newReport.setProperty("isProcessorSource", "true");
+				reports.add(newReport);
+			}
+		} else if (source instanceof MergeOutputPort) {
+			Merge merge = ((MergePort) source).getMerge();
+			for (MergeInputPort mip : merge.getInputPorts()) {
+				for (Datalink dl : d.getLinks()) {
+					if (dl.getSink().equals(mip)) {
+						reports.addAll(checkSource(dl.getSource(), d, o, aip));
+					}
+				}
+
+			}
+		} else /* if (source instanceof DataflowInputPort) */  {
+			VisitReport newReport = new VisitReport(HealthCheck.getInstance(), o, "Source of " + aip.getName(), HealthCheck.DATATYPE_SOURCE, Status.WARNING);
+			newReport.setProperty("sinkPortName", aip.getName());
+			newReport.setProperty("sourceName", source.getName());
+			newReport.setProperty("isProcessorSource", "false");
+			reports.add(newReport);
+		}
+		return reports;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/390c286b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityFactory.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityFactory.java
new file mode 100644
index 0000000..eeb7c5a
--- /dev/null
+++ b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityFactory.java
@@ -0,0 +1,141 @@
+/*******************************************************************************
+ * Copyright (C) 2010 The University of Manchester
+ *
+ *  Modifications to the initial code base are copyright of their
+ *  respective authors, or their employers as appropriate.
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public License
+ *  as published by the Free Software Foundation; either version 2.1 of
+ *  the License, or (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful, but
+ *  WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public
+ *  License along with this program; if not, write to the Free Software
+ *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.wsdl;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.workflowmodel.Edits;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+import net.sf.taverna.wsdl.parser.WSDLParser;
+
+import org.apache.log4j.Logger;
+import org.xml.sax.SAXException;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+/**
+ * An {@link ActivityFactory} for creating <code>WSDLActivity</code>.
+ *
+ * @author David Withers
+ */
+public class WSDLActivityFactory implements ActivityFactory {
+
+	private static Logger logger = Logger.getLogger(WSDLActivityFactory.class);
+
+	private CredentialManager credentialManager;
+	private Edits edits;
+
+	@Override
+	public WSDLActivity createActivity() {
+		return new WSDLActivity(credentialManager);
+	}
+
+	@Override
+	public URI getActivityType() {
+		return URI.create(WSDLActivity.URI);
+	}
+
+	@Override
+	public JsonNode getActivityConfigurationSchema() {
+		ObjectMapper objectMapper = new ObjectMapper();
+		try {
+			return objectMapper.readTree(getClass().getResource("/schema.json"));
+		} catch (IOException e) {
+			return objectMapper.createObjectNode();
+		}
+	}
+
+	public void setCredentialManager(CredentialManager credentialManager) {
+		this.credentialManager = credentialManager;
+	}
+
+	@Override
+	public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
+		Map<String, ActivityInputPort> inputPorts = new HashMap<>();
+		try {
+			WSDLParser parser = new WSDLParser(configuration.get("operation").get("wsdl").textValue());
+			List<TypeDescriptor> inputDescriptors = parser.getOperationInputParameters(configuration
+					.get("operation").get("name").textValue());
+			for (TypeDescriptor descriptor : inputDescriptors) {
+				inputPorts.put(descriptor.getName(), edits.createActivityInputPort(
+						descriptor.getName(), descriptor.getDepth(), true, null, String.class));
+			}
+			if (parser.isWsrfService()) {
+				// Make sure the port name is unique
+				String endpointReferenceInputPortName = WSDLActivity.ENDPOINT_REFERENCE;
+				int counter = 0;
+				while (inputPorts.containsKey(endpointReferenceInputPortName)) {
+					endpointReferenceInputPortName = WSDLActivity.ENDPOINT_REFERENCE + counter++;
+				}
+				inputPorts.put(endpointReferenceInputPortName, edits.createActivityInputPort(
+						endpointReferenceInputPortName, 0, true, null, String.class));
+			}
+		} catch (ParserConfigurationException | WSDLException | IOException | SAXException | UnknownOperationException e) {
+			logger.warn(
+					"Unable to parse the WSDL " + configuration.get("operation").get("wsdl").textValue(), e);
+		}
+
+		return new HashSet<>(inputPorts.values());
+	}
+
+	@Override
+	public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
+		Set<ActivityOutputPort> outputPorts = new HashSet<>();
+		try {
+			WSDLParser parser = new WSDLParser(configuration.get("operation").get("wsdl")
+					.textValue());
+			List<TypeDescriptor> outputDescriptors = parser
+					.getOperationOutputParameters(configuration.get("operation").get("name")
+							.textValue());
+			for (TypeDescriptor descriptor : outputDescriptors) {
+				outputPorts.add(edits.createActivityOutputPort(descriptor.getName(),
+						descriptor.getDepth(), descriptor.getDepth()));
+			}
+			// add output for attachment list
+			outputPorts.add(edits.createActivityOutputPort("attachmentList", 1, 1));
+		} catch (ParserConfigurationException | WSDLException | IOException | SAXException | UnknownOperationException e) {
+			logger.warn(
+					"Unable to parse the WSDL " + configuration.get("operation").get("wsdl").textValue(), e);
+		}
+
+		return outputPorts;
+	}
+
+	public void setEdits(Edits edits) {
+		this.edits = edits;
+	}
+
+}