[21/35] incubator-taverna-common-activities git commit: package names changed to org.apache.taverna.*

[re...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
new file mode 100644
index 0000000..91d0e3b
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetImportHealthCheckerTest.java
@@ -0,0 +1,90 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.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/433612be/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetReadExceptionTest.java
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diff --git a/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetReadExceptionTest.java b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetReadExceptionTest.java
new file mode 100644
index 0000000..cb11067
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetReadExceptionTest.java
@@ -0,0 +1,57 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.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/433612be/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetUtilsTest.java
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diff --git a/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetUtilsTest.java b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetUtilsTest.java
new file mode 100644
index 0000000..4f704a9
--- /dev/null
+++ b/taverna-spreadsheet-import-activity/src/test/java/org/apache/taverna/activities/spreadsheet/SpreadsheetUtilsTest.java
@@ -0,0 +1,97 @@
+/*
+* Licensed to the Apache Software Foundation (ASF) under one
+* or more contributor license agreements. See the NOTICE file
+* distributed with this work for additional information
+* regarding copyright ownership. The ASF licenses this file
+* to you under the Apache License, Version 2.0 (the
+* "License"); you may not use this file except in compliance
+* with the License. You may obtain a copy of the License at
+*
+* http://www.apache.org/licenses/LICENSE-2.0
+*
+* Unless required by applicable law or agreed to in writing,
+* software distributed under the License is distributed on an
+* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+* KIND, either express or implied. See the License for the
+* specific language governing permissions and limitations
+* under the License.
+*/
+
+package org.apache.taverna.activities.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/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java
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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
deleted file mode 100644
index c153722..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/InputPortTypeDescriptorActivity.java
+++ /dev/null
@@ -1,57 +0,0 @@
-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/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java
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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
deleted file mode 100644
index 23a235c..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/OutputPortTypeDescriptorActivity.java
+++ /dev/null
@@ -1,57 +0,0 @@
-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/433612be/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
deleted file mode 100644
index 1e9d1a5..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/T2WSDLSOAPInvoker.java
+++ /dev/null
@@ -1,282 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-
-package net.sf.taverna.t2.activities.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/433612be/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
deleted file mode 100644
index 763cbee..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivity.java
+++ /dev/null
@@ -1,328 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.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/433612be/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
deleted file mode 100644
index 80b0bd5..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityConfigurationBean.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.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/433612be/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
deleted file mode 100644
index 5a41cde..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityDescriptorChecker.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/**
- *
- */
-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/433612be/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
deleted file mode 100644
index eeb7c5a..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityFactory.java
+++ /dev/null
@@ -1,141 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.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;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityHealthChecker.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityHealthChecker.java
deleted file mode 100644
index 0437ff6..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLActivityHealthChecker.java
+++ /dev/null
@@ -1,170 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- *  Modifications to the initial code base are copyright of their
- *  respective authors, or their employers as appropriate.
- *
- *  This program is free software; you can redistribute it and/or
- *  modify it under the terms of the GNU Lesser General Public License
- *  as published by the Free Software Foundation; either version 2.1 of
- *  the License, or (at your option) any later version.
- *
- *  This program is distributed in the hope that it will be useful, but
- *  WITHOUT ANY WARRANTY; without even the implied warranty of
- *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
- *  Lesser General Public License for more details.
- *
- *  You should have received a copy of the GNU Lesser General Public
- *  License along with this program; if not, write to the Free Software
- *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.wsdl;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.wsdl.WSDLException;
-import javax.xml.parsers.ParserConfigurationException;
-
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-import net.sf.taverna.wsdl.parser.UnknownOperationException;
-import net.sf.taverna.wsdl.parser.WSDLParser;
-
-import org.xml.sax.SAXException;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class WSDLActivityHealthChecker extends RemoteHealthChecker {
-
-	private Activity<?> activity;
-
-	public boolean canVisit(Object subject) {
-		if (subject == null) {
-			return false;
-		}
-		if (subject instanceof WSDLActivity) {
-			return true;
-		}
-		if (subject instanceof DisabledActivity) {
-			return (((DisabledActivity) subject).getActivity() instanceof WSDLActivity);
-		}
-		return false;
-	}
-
-	public VisitReport visit(Object o, List<Object> ancestors) {
-		List<VisitReport> reports = new ArrayList<VisitReport>();
-		activity = (Activity<?>) o;
-		String endpoint = null;
-
-		WSDLParser parser;
-		try {
-			JsonNode configuration = null;
-			if (activity instanceof WSDLActivity) {
-				configuration = ((WSDLActivity)activity).getConfiguration();
-			} else if (activity instanceof DisabledActivity) {
-				configuration = (JsonNode) ((DisabledActivity) activity).getActivityConfiguration();
-			}
-			endpoint = configuration.get("operation").get("wsdl").asText();
-			VisitReport wsdlEndpointReport = RemoteHealthChecker.contactEndpoint(activity, endpoint);
-			reports.add(wsdlEndpointReport);
-			if (!wsdlEndpointReport.getStatus().equals(Status.SEVERE)) {
-			    parser = new WSDLParser(endpoint);
-
-			    String operationName = configuration.get("operation").get("name").asText();
-			    try {
-                reports.add(testStyleAndUse(endpoint,
-							    parser,
-							    operationName));
-				reports.add(testEndpoint(parser, operationName));
-			    } catch (UnknownOperationException e) {
-				VisitReport vr = new VisitReport(HealthCheck.getInstance(), activity,
-							 "Operation not found", HealthCheck.UNKNOWN_OPERATION,
-							 Status.SEVERE);
-				vr.setProperty("operationName", operationName);
-				vr.setProperty("endpoint", endpoint);
-				reports.add(vr);
-			    }
-			}
-
-		} catch (ParserConfigurationException e) {
-			VisitReport vr = new VisitReport(HealthCheck.getInstance(), activity, "Invalid WSDL", HealthCheck.BAD_WSDL, Status.SEVERE);
-			vr.setProperty("exception", e);
-			vr.setProperty("endpoint", endpoint);
-			reports.add(vr);
-		} catch (WSDLException e) {
-			VisitReport vr = new VisitReport(HealthCheck.getInstance(), activity, "Invalid WSDL", HealthCheck.BAD_WSDL, Status.SEVERE);
-			vr.setProperty("exception", e);
-			vr.setProperty("endpoint", endpoint);
-			reports.add(vr);
-		} catch (IOException e) {
-			VisitReport vr = new VisitReport(HealthCheck.getInstance(), activity, "Read problem", HealthCheck.IO_PROBLEM, Status.SEVERE);
-			vr.setProperty("exception", e);
-			vr.setProperty("endpoint", endpoint);
-			reports.add(vr);
-		} catch (SAXException e) {
-			VisitReport vr = new VisitReport(HealthCheck.getInstance(), activity, "Invalid WSDL", HealthCheck.BAD_WSDL, Status.SEVERE);
-			vr.setProperty("exception", e);
-			vr.setProperty("endpoint", endpoint);
-			reports.add(vr);
-		}
-
-		Status status = VisitReport.getWorstStatus(reports);
-		VisitReport report = new VisitReport(HealthCheck.getInstance(), activity, "WSDL Activity report", HealthCheck.NO_PROBLEM,
-				status, reports);
-
-		return report;
-	}
-	
-	public static boolean checkStyleAndUse(String style, String use) {
-		return !(style.equalsIgnoreCase("rpc") && use.equalsIgnoreCase("literal"));
-	}
-
-	private VisitReport testStyleAndUse(String endpoint, WSDLParser parser, String operationName) throws
-                UnknownOperationException {
-		VisitReport report;
-		String style = parser.getStyle().toLowerCase();
-		String use = "?";
-		use = parser.getUse(operationName).toLowerCase();
-		if (!checkStyleAndUse(style, use)) {
-		    report = new VisitReport(HealthCheck.getInstance(), activity,
-					     "Unsupported style", HealthCheck.UNSUPPORTED_STYLE,
-					     Status.SEVERE);
-		    report.setProperty("use", use);
-		    report.setProperty("style", style);
-		    report.setProperty("endpoint", endpoint);
-		} else {
-		    report = new VisitReport(HealthCheck.getInstance(), activity, style + "/"
-					     + use + " is OK", HealthCheck.NO_PROBLEM, Status.OK);
-		}
-		return report;
-	}
-
-	private VisitReport testEndpoint(WSDLParser parser, String operationName) {
-		List<VisitReport> reports = new ArrayList<VisitReport>();
-		List<String> endpoints = parser
-				.getOperationEndpointLocations(operationName);
-		for (String endpoint : endpoints) {
-			reports.add(RemoteHealthChecker.contactEndpoint(activity, endpoint));
-		}
-
-		Status status = VisitReport.getWorstStatus(reports);
-		if (reports.size()==1) {
-			return reports.get(0);
-		}
-		else if (reports.size()==0) {
-		    VisitReport report = new VisitReport(HealthCheck.getInstance(), activity, "Service could not be located.", HealthCheck.NO_ENDPOINTS, Status.SEVERE);
-		    report.setProperty("operationName", operationName);
-		    return report;
-		}
-		else {
-			return new VisitReport(HealthCheck.getInstance(), activity, "Endpoint tests",  HealthCheck.NO_PROBLEM, status, reports);
-		}
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLOperationConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLOperationConfigurationBean.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLOperationConfigurationBean.java
deleted file mode 100644
index ac012ae..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/WSDLOperationConfigurationBean.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 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;
-
-/**
- * Configuration for a WSDL operation.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = WSDLActivity.URI + "/operation")
-public class WSDLOperationConfigurationBean {
-
-	private URI wsdl;
-	private String operationName;
-
-	public URI getWsdl() {
-		return wsdl;
-	}
-
-	@ConfigurationProperty(name = "wsdl", label = "WSDL URL", description = "The location of the WSDL definition for the web service")
-	public void setWsdl(URI wsdl) {
-		this.wsdl = wsdl;
-	}
-
-	public String getOperationName() {
-		return operationName;
-	}
-
-	@ConfigurationProperty(name = "name", label = "Operation Name", description = "The name of the WSDL operation")
-	public void setOperationName(String operationName) {
-		this.operationName = operationName;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/package.html
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/package.html b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/package.html
deleted file mode 100644
index e38a14e..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/package.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<body>
-Contains the activity classes required to interact with a WSDL based web-service.
-</body>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SSLUtilities.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SSLUtilities.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SSLUtilities.java
deleted file mode 100644
index 69033bb..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SSLUtilities.java
+++ /dev/null
@@ -1,151 +0,0 @@
-package net.sf.taverna.t2.activities.wsdl.security;
-
-import java.security.GeneralSecurityException;
-import java.security.SecureRandom;
-import java.security.cert.X509Certificate;
-import javax.net.ssl.HostnameVerifier;
-import javax.net.ssl.HttpsURLConnection;
-import javax.net.ssl.SSLContext;
-import javax.net.ssl.SSLSocketFactory;
-import javax.net.ssl.TrustManager;
-import javax.net.ssl.X509TrustManager;
-
-/**
- * This class provide various static methods that relax X509 certificate and 
- * hostname verification while using the SSL over the HTTP protocol.
- * <p>
- * Call:
- * SSLUtilities.trustAllHostnames() to turn off the default hostname verification on HTTPS connection;
- * SSLUtilities.trustAllHttpsCertificates() to turn off the default certificate validation on HTTPS connection.
- * SSLUtilities.stopTrustingAllHttpsCertificates() to stop trusting all hosts' certificates and go back to default Java settings.
- *
- * @author    Francis Labrie
- */
-public final class SSLUtilities {
-
-  /**
-   * Hostname verifier.
-   */
-  private static HostnameVerifier hostnameVerifier;
-  /**
-   * Thrust managers.
-   */
-  private static TrustManager[] trustManagers;
-
-  /**
-   * Set the default Hostname Verifier to an instance of a fake class that 
-   * trust all hostnames.
-   */
-  public static void trustAllHostnames() {
-      // Create a trust manager that does not validate certificate chains
-      if(hostnameVerifier == null) {
-          hostnameVerifier = new FakeHostnameVerifier();
-      } // if
-        // Install the all-trusting host name verifier:
-      HttpsURLConnection.setDefaultHostnameVerifier(hostnameVerifier);
-  } // _trustAllHttpsCertificates
-  
-  /**
-   * Set the default X509 Trust Manager to an instance of a fake class that 
-   * trust all certificates, even the self-signed ones.
-   */
-  public static void trustAllHttpsCertificates() {
-      SSLContext context;
-      
-      // Create a trust manager that does not validate certificate chains
-      if(trustManagers == null) {
-          trustManagers = new TrustManager[] {new FakeX509TrustManager()};
-      } // if
-      // Install the all-trusting trust manager:
-      try {
-      context = SSLContext.getInstance("SSL");
-      context.init(null, trustManagers, new SecureRandom());
-      } catch(GeneralSecurityException gse) {
-          throw new IllegalStateException(gse.getMessage());
-      } // catch
-      HttpsURLConnection.setDefaultSSLSocketFactory(context.
-          getSocketFactory());
-  } // _trustAllHttpsCertificates
-  
-  /**
-   * This class implements a fake hostname verificator, trusting any host 
-   * name.
-   *
-   * @author    Francis Labrie
-   */
-  public static class FakeHostnameVerifier implements HostnameVerifier {
-      
-      /**
-       * Always return true, indicating that the host name is 
-       * an acceptable match with the server's authentication scheme.
-       *
-       * @param hostname        the host name.
-       * @param session         the SSL session used on the connection to 
-       * host.
-       * @return                the true boolean value 
-       * indicating the host name is trusted.
-       */
-      public boolean verify(String hostname, 
-          javax.net.ssl.SSLSession session) {
-          return(true);
-      } // verify
-  } // FakeHostnameVerifier
-
-  /**
-   * This class allow any X509 certificates to be used to authenticate the 
-   * remote side of a secure socket, including self-signed certificates.
-   *
-   * @author    Francis Labrie
-   */
-  public static class FakeX509TrustManager implements X509TrustManager {
-
-      /**
-       * Empty array of certificate authority certificates.
-       */
-      private static final X509Certificate[] _AcceptedIssuers = 
-          new X509Certificate[] {};
-
-      /**
-       * Always trust for client SSL chain peer certificate 
-       * chain with any authType authentication types.
-       *
-       * @param chain           the peer certificate chain.
-       * @param authType        the authentication type based on the client 
-       * certificate.
-       */
-      public void checkClientTrusted(X509Certificate[] chain, 
-          String authType) {
-      } // checkClientTrusted
-      
-      /**
-       * Always trust for server SSL chain peer certificate 
-       * chain with any authType exchange algorithm types.
-       *
-       * @param chain           the peer certificate chain.
-       * @param authType        the key exchange algorithm used.
-       */
-      public void checkServerTrusted(X509Certificate[] chain, 
-          String authType) {
-      } // checkServerTrusted
-      
-      /**
-       * Return an empty array of certificate authority certificates which 
-       * are trusted for authenticating peers.
-       *
-       * @return                a empty array of issuer certificates.
-       */
-      public X509Certificate[] getAcceptedIssuers() {
-          return(_AcceptedIssuers);
-      } // getAcceptedIssuers
-  } // FakeX509TrustManager
-  
-  /**
-   * Stop trusting all certificates and go back to the default settings.
-   * 
-   * @author Alex Nenadic
-   */
-  public static void stopTrustingAllHttpsCertificates(){
-      HttpsURLConnection.setDefaultSSLSocketFactory((SSLSocketFactory) SSLSocketFactory.getDefault());
-  }
-} // SSLUtilities
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SecurityProfiles.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SecurityProfiles.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SecurityProfiles.java
deleted file mode 100644
index aa8084b..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/SecurityProfiles.java
+++ /dev/null
@@ -1,130 +0,0 @@
-package net.sf.taverna.t2.activities.wsdl.security;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.activities.wsdl.WSDLActivity;
-
-/**
- * Various security profiles for Web services.
- *
- * @author Alex Nenadic
- *
- */
-public class SecurityProfiles {
-
-	public static URI SECURITY = URI.create(WSDLActivity.URI).resolve("wsdl/security");
-
-	/**
-	  * Security profile for Web services that require
-	 * UsernameToken authentication with plaintext password.
-	 * Such services should typically be invoked over HTTPS.
-	 */
-	public static final URI WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD = SECURITY.resolve("#WSSecurityUsernameTokenPlainTextPassword");
-	/**
-	 * XML string for configuring Axis engine with wss4j handlers to handle setting security
-	 * headers on the SOAP message for profile WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD.
-	 */
-	public static final String WSSECURITY_USERNAMETOKEN_PLAINTEXTPASSWORD_CONFIG = "<deployment xmlns=\"http://xml.apache.org/axis/wsdd/\" xmlns:java=\"http://xml.apache.org/axis/wsdd/providers/java\">" +
-	"<globalConfiguration>" +
-	"<requestFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllSender\">" +
-	"<parameter name=\"action\" value=\"UsernameToken\"/>" +
-	"<parameter name=\"passwordType\" value=\"PasswordText\"/>" +
-	"</handler>"+
-	"</requestFlow>" +
-	"</globalConfiguration>" +
-	"<transport name=\"http\" pivot=\"java:org.apache.axis.transport.http.HTTPSender\"/>"+
-	"</deployment>";
-
-	 /**
-	  * Security profile for Web services that require
-	 * UsernameToken authentication with digest password.
-	 * Such services would typically be invoked over HTTPS.
-	 */
-	public static final URI WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD = SECURITY.resolve("#WSSecurityUsernameTokenDigestPassword");
-	/**
-	 * XML string for configuring Axis engine with wss4j handlers to handle setting security
-	 * headers on the SOAP message for profile WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD.
-	 */
-	public static final String WSSECURITY_USERNAMETOKEN_DIGESTPASSWORD_CONFIG = "<deployment xmlns=\"http://xml.apache.org/axis/wsdd/\" xmlns:java=\"http://xml.apache.org/axis/wsdd/providers/java\">" +
-	"<globalConfiguration>" +
-	"<requestFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllSender\">" +
-	"<parameter name=\"action\" value=\"UsernameToken\"/>" +
-	"<parameter name=\"passwordType\" value=\"PasswordDigest\"/>" +
-	"</handler>"+
-	"</requestFlow>" +
-	"</globalConfiguration>" +
-	"<transport name=\"http\" pivot=\"java:org.apache.axis.transport.http.HTTPSender\"/>"+
-	"</deployment>";
-
-	 /**
-	  * Security profile for Web services that require a timestamp SOAP header
-	  * to be sent in addition to UsernameToken authentication with plaintext password.
-	 * Such services should typically be invoked over HTTPS.
-	 */
-	public static final URI WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTEXTPASSWORD = SECURITY.resolve("#WSSecurityTimestampUsernameTokenPlainTextPassword");
-	/**
-	 * XML string for configuring Axis engine with wss4j handlers to handle setting security
-	 * headers on the SOAP message for profile WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD.
-	 */
-	public static final String WSSECURITY_TIMESTAMP_USERNAMETOKEN_PLAINTETPASSWORD_CONFIG = "<deployment xmlns=\"http://xml.apache.org/axis/wsdd/\" xmlns:java=\"http://xml.apache.org/axis/wsdd/providers/java\">" +
-	"<globalConfiguration>" +
-	"<requestFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllSender\">" +
-	"<parameter name=\"action\" value=\"Timestamp UsernameToken\"/>" +
-	"<parameter name=\"passwordType\" value=\"PasswordText\"/>" +
-	"</handler>"+
-	"</requestFlow>" +
-	"<responseFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllReceiver\">" +
-	"<parameter name=\"action\" value=\"Timestamp\"/>" +
-	"</handler>"+
-	"</responseFlow>" +
-	"</globalConfiguration>" +
-	"<transport name=\"http\" pivot=\"java:org.apache.axis.transport.http.HTTPSender\"/>"+
-	"</deployment>";
-
-	 /**
-	  * Security profile for Web services that require a timestamp SOAP header
-	  * to be sent in addition to UsernameToken authentication with digest password.
-	 * Such services would typically be invoked over HTTPS.
-	 */
-	public static final URI WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD = SECURITY.resolve("#WSSecurityTimestampUsernameTokenDigestPassword");
-	/**
-	 * XML string for configuring Axis engine with wss4j handlers to handle setting security
-	 * headers on the SOAP message for profile WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD.
-	 */
-	public static final String WSSECURITY_TIMESTAMP_USERNAMETOKEN_DIGESTPASSWORD_CONFIG = "<deployment xmlns=\"http://xml.apache.org/axis/wsdd/\" xmlns:java=\"http://xml.apache.org/axis/wsdd/providers/java\">" +
-	"<globalConfiguration>" +
-	"<requestFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllSender\">" +
-	"<parameter name=\"action\" value=\"Timestamp UsernameToken\"/>" +
-	"<parameter name=\"passwordType\" value=\"PasswordDigest\"/>" +
-	"</handler>"+
-	"</requestFlow>" +
-	"<responseFlow>" +
-	"<handler type=\"java:org.apache.ws.axis.security.WSDoAllReceiver\">" +
-	"<parameter name=\"action\" value=\"Timestamp\"/>" +
-	"</handler>"+
-	"</responseFlow>" +
-	"</globalConfiguration>" +
-	"<transport name=\"http\" pivot=\"java:org.apache.axis.transport.http.HTTPSender\"/>"+
-	"</deployment>";
-
-	/**
-	 * Security profile for Web services that require HTTP Basic Authentication.
-	 * There is no WS-Security involved.
-	 * Such services should typically be invoked over HTTPS.
-	 */
-	public static final URI HTTP_BASIC_AUTHN = SECURITY.resolve("#HTTPBasicAuthNPlainTextPassword");
-
-	/**
-	 * Security profile for Web services that require HTTP Digest Authentication.
-	 * There is no WS-Security involved.
-	 * Such services would typically be invoked over HTTPS.
-	 */
-	public static final URI HTTP_DIGEST_AUTHN = SECURITY.resolve("#HTTPDigestAuthN");
-
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/TavernaAxisCustomSSLSocketFactory.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/TavernaAxisCustomSSLSocketFactory.java b/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/TavernaAxisCustomSSLSocketFactory.java
deleted file mode 100644
index 19ecb14..0000000
--- a/taverna-wsdl-activity/src/main/java/net/sf/taverna/t2/activities/wsdl/security/TavernaAxisCustomSSLSocketFactory.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package net.sf.taverna.t2.activities.wsdl.security;
-
-import java.io.IOException;
-import java.net.Socket;
-import java.util.Hashtable;
-
-import javax.net.ssl.SSLContext;
-
-import org.apache.axis.components.net.BooleanHolder;
-import org.apache.axis.components.net.JSSESocketFactory;
-
-public class TavernaAxisCustomSSLSocketFactory extends JSSESocketFactory {
-
-
-	public TavernaAxisCustomSSLSocketFactory(Hashtable attributes) {
-		super(attributes);
-	}
-
-	@Override
-	public Socket create(String host, int port, StringBuffer otherHeaders,
-			BooleanHolder useFullURL) throws Exception {
-		// Make sure we always pick up the default socket factory from SSLContext, which is based on 
-		// Taverna's Keystore and Truststore and gets updated when they get updated (it may have
-		// been updated in the menatime so just refresh it here just in case).
-		initFactory();
-		return super.create(host, port, otherHeaders, useFullURL);
-	}
-	
-	@Override
-	protected void initFactory() throws IOException {
-		try{
-			// Set it to the default one from the SSLContext which is set to use Taverna's Keystore and Truststore
-			sslFactory = SSLContext.getDefault().getSocketFactory();
-		}
-		catch (Exception e) {
-			throw new IOException("Could not get the Taverna's default SSLSocketFactory from SSLContext",e);
-		}
-	}
-	
-}