[26/35] 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-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityFactory.java
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diff --git a/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityFactory.java b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityFactory.java
new file mode 100644
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--- /dev/null
+++ b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityFactory.java
@@ -0,0 +1,164 @@
+/*
+* 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.rest;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.taverna.activities.rest.URISignatureHandler.URISignatureParsingException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+import net.sf.taverna.t2.workflowmodel.Edits;
+import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
+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 org.apache.http.client.CredentialsProvider;
+import org.apache.log4j.Logger;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+/**
+ * An {@link ActivityFactory} for creating <code>RESTActivity</code>.
+ *
+ * @author David Withers
+ */
+public class RESTActivityFactory implements ActivityFactory {
+
+	private static Logger logger = Logger.getLogger(RESTActivityFactory.class);
+
+	private CredentialsProvider credentialsProvider;
+	private Edits edits;
+
+	@Override
+	public RESTActivity createActivity() {
+                RESTActivity activity = new RESTActivity(credentialsProvider);
+                activity.setEdits(edits);
+		return activity; 
+	}
+
+	@Override
+	public URI getActivityType() {
+		return URI.create(RESTActivity.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) {
+		credentialsProvider = new RESTActivityCredentialsProvider(credentialManager);
+	}
+
+	@Override
+	public Set<ActivityInputPort> getInputPorts(JsonNode configuration)
+			throws ActivityConfigurationException {
+		Set<ActivityInputPort> activityInputPorts = new HashSet<>();
+		RESTActivityConfigurationBean configBean = new RESTActivityConfigurationBean(configuration);
+		// ---- CREATE INPUTS ----
+
+		// all input ports are dynamic and depend on the configuration
+		// of the particular instance of the REST activity
+
+		// POST and PUT operations send data, so an input for the message body
+		// is required
+		if (RESTActivity.hasMessageBodyInputPort(configBean.getHttpMethod())) {
+			// the input message will be just an XML string for now
+			activityInputPorts.add(edits.createActivityInputPort(RESTActivity.IN_BODY, 0, true, null, configBean.getOutgoingDataFormat()
+					.getDataFormat()));
+		}
+
+		// now process the URL signature - extract all placeholders and create
+		// an input port for each
+		List<String> placeholders = URISignatureHandler
+				.extractPlaceholders(configBean.getUrlSignature());
+		String acceptsHeaderValue = configBean.getAcceptsHeaderValue();
+		if (acceptsHeaderValue != null && !acceptsHeaderValue.isEmpty()) {
+			try {
+			List<String> acceptsPlaceHolders = URISignatureHandler
+				.extractPlaceholders(acceptsHeaderValue);
+			acceptsPlaceHolders.removeAll(placeholders);
+			placeholders.addAll(acceptsPlaceHolders);
+			}
+			catch (URISignatureParsingException e) {
+				logger.error(e);
+			}
+		}
+		for (ArrayList<String> httpHeaderNameValuePair : configBean.getOtherHTTPHeaders()) {
+			try {
+				List<String> headerPlaceHolders = URISignatureHandler
+				.extractPlaceholders(httpHeaderNameValuePair.get(1));
+				headerPlaceHolders.removeAll(placeholders);
+				placeholders.addAll(headerPlaceHolders);
+			}
+			catch (URISignatureParsingException e) {
+				logger.error(e);
+			}
+		}
+		for (String placeholder : placeholders) {
+			// these inputs will have a dynamic name each;
+			// the data type is string as they are the values to be
+			// substituted into the URL signature at the execution time
+			activityInputPorts.add(edits.createActivityInputPort(placeholder, 0, true, null, String.class));
+		}
+		return activityInputPorts;
+	}
+
+	@Override
+	public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration)
+			throws ActivityConfigurationException {
+		Set<ActivityOutputPort> activityOutputPorts = new HashSet<>();
+		RESTActivityConfigurationBean configBean = new RESTActivityConfigurationBean(configuration);
+		// ---- CREATE OUTPUTS ----
+		// all outputs are of depth 0 - i.e. just a single value on each;
+
+		// output ports for Response Body and Status are static - they don't
+		// depend on the configuration of the activity;
+		activityOutputPorts.add(edits.createActivityOutputPort(RESTActivity.OUT_RESPONSE_BODY, 0, 0));
+		activityOutputPorts.add(edits.createActivityOutputPort(RESTActivity.OUT_STATUS, 0, 0));
+		if (configBean.getShowActualUrlPort()) {
+			activityOutputPorts.add(edits.createActivityOutputPort(RESTActivity.OUT_COMPLETE_URL, 0, 0));
+			}
+			if (configBean.getShowResponseHeadersPort()) {
+				activityOutputPorts.add(edits.createActivityOutputPort(RESTActivity.OUT_RESPONSE_HEADERS, 1, 1));
+			}
+		// Redirection port may be hidden/shown
+		if (configBean.getShowRedirectionOutputPort()) {
+			activityOutputPorts.add(edits.createActivityOutputPort(RESTActivity.OUT_REDIRECTION, 0, 0));
+		}
+		return activityOutputPorts;
+	}
+
+	public void setEdits(Edits edits) {
+		this.edits = edits;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthCheck.java
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diff --git a/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthCheck.java b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthCheck.java
new file mode 100644
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+++ b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthCheck.java
@@ -0,0 +1,51 @@
+/*
+* 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.rest;
+
+import net.sf.taverna.t2.visit.VisitKind;
+import net.sf.taverna.t2.visit.Visitor;
+
+/**
+ * A <code>RESTActivityHealthCheck</code> is a kind of visit that determines
+ * if the corresponding REST activity in a workflow will work during a workflow run.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class RESTActivityHealthCheck extends VisitKind {
+
+	// The following values indicate the type of results that can be associated
+	// with a VisitReport generated by a health-checking visitor.
+
+	public static final int CORRECTLY_CONFIGURED = 0;
+	public static final int GENERAL_CONFIG_PROBLEM = 10;
+
+	@Override
+	public Class<? extends Visitor<?>> getVisitorClass() {
+		return RESTActivityHealthChecker.class;
+	}
+
+	private static class Singleton {
+		private static RESTActivityHealthCheck instance = new RESTActivityHealthCheck();
+	}
+
+	public static RESTActivityHealthCheck getInstance() {
+		return Singleton.instance;
+	}
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthChecker.java
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diff --git a/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthChecker.java b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthChecker.java
new file mode 100644
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+++ b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/RESTActivityHealthChecker.java
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+/*
+* 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.rest;
+
+import java.util.ArrayList;
+import java.util.List;
+
+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.HealthChecker;
+
+/**
+ * A {@link HealthChecker} for a {@link RESTActivity}.
+ *
+ * @author Sergejs Aleksejevs
+ */
+public class RESTActivityHealthChecker implements HealthChecker<RESTActivity> {
+	@Override
+	public boolean canVisit(Object subject) {
+		return (subject instanceof RESTActivity);
+	}
+
+	@Override
+	public VisitReport visit(RESTActivity activity, List<Object> ancestors) {
+		// collection of validation reports that this health checker will create
+		List<VisitReport> reports = new ArrayList<VisitReport>();
+
+		RESTActivityConfigurationBean configBean = activity.getConfigurationBean();
+		if (configBean.isValid()) {
+			reports.add(new VisitReport(RESTActivityHealthCheck.getInstance(), activity,
+					"REST Activity is configured correctly",
+					RESTActivityHealthCheck.CORRECTLY_CONFIGURED, Status.OK));
+		} else {
+			reports.add(new VisitReport(RESTActivityHealthCheck.getInstance(), activity,
+					"REST Activity - bad configuration",
+					RESTActivityHealthCheck.GENERAL_CONFIG_PROBLEM, Status.SEVERE));
+		}
+
+		// (possibly other types of reports could be added later)
+
+		// collection all reports together
+		Status worstStatus = VisitReport.getWorstStatus(reports);
+		VisitReport report = new VisitReport(RESTActivityHealthCheck.getInstance(), activity,
+				"REST Activity Report", HealthCheck.NO_PROBLEM, worstStatus, reports);
+
+		return report;
+	}
+
+	/**
+	 * Health check for the REST activity only involves
+	 * verifying details in the configuration bean -
+	 * that is quick.
+	 */
+	@Override
+	public boolean isTimeConsuming() {
+		return false;
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/URISignatureHandler.java
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diff --git a/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/URISignatureHandler.java b/taverna-rest-activity/src/main/java/org/apache/taverna/activities/rest/URISignatureHandler.java
new file mode 100644
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@@ -0,0 +1,431 @@
+/*
+* 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.rest;
+
+import java.io.UnsupportedEncodingException;
+import java.text.Normalizer;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+
+/**
+ * This class deals with URI signatures - essentially, strings that represent
+ * some resource's URI with zero or more placeholders. URI signatures are known
+ * at workflow definition time and represent the pattern of the complete URIs
+ * that will be used at workflow run time.
+ * 
+ * An example of the URI signature is:
+ * http://sysmo-db.org/sops/{sop_id}/experimental_conditions
+ * /{cond_id}?condition_unit={unit}
+ * 
+ * Placeholders "{sop_id}", "{cond_id}" and "{unit}" will be replaced by the
+ * real values prior to using the URI for a real request.
+ * 
+ * This class is concerned with validation of URI signatures, extraction of
+ * placeholders and substituting placeholders to generate complete URIs.
+ * 
+ * @author Sergejs Aleksejevs
+ */
+public class URISignatureHandler {
+	
+	private static Logger logger = Logger.getLogger(URISignatureHandler.class);
+	
+
+	public static final char PLACEHOLDER_START_SYMBOL = '{';
+	public static final char PLACEHOLDER_END_SYMBOL = '}';
+
+	/**
+	 * Extracts placeholders of the given URI signature with their positions in
+	 * the signature in the order of their occurrence.
+	 * 
+	 * Extraction is done in a robust way with signature validity checks being
+	 * carried out simultaneously. This makes sure that even with no explicit
+	 * validation (see {@link URISignatureHandler#isValid(String)}) no
+	 * unexpected faults occur.
+	 * 
+	 * @param uriSignature
+	 *            The URI signature to process.
+	 * @return A map of placeholders as they are encountered (from start to end)
+	 *         in the URI signature and their start positions. Keys of the map
+	 *         are the "titles" of the placeholders without opening and closing
+	 *         placeholder symbols; values are the URI signature string indices,
+	 *         where the title of the corresponding placeholder starts in the
+	 *         string.
+	 */
+	public static LinkedHashMap<String, Integer> extractPlaceholdersWithPositions(
+			String uriSignature) {
+		// no signature - nothing to process
+		if (uriSignature == null || uriSignature.isEmpty())
+			throw new URISignatureParsingException(
+					"URI signature is null or empty - nothing to process.");
+
+		LinkedHashMap<String, Integer> foundPlaceholdersWithPositions = new LinkedHashMap<>();
+
+		int nestingLevel = 0;
+		int startSymbolIdx = -1;
+
+		// go through the signature character by character trying to extract
+		// placeholders
+		for (int i = 0; i < uriSignature.length(); i++) {
+			switch (uriSignature.charAt(i)) {
+			case PLACEHOLDER_START_SYMBOL:
+				if (++nestingLevel != 1)
+					throw new URISignatureParsingException(
+							"Malformed URL: at least two parameter placeholder opening\n" +
+									"symbols follow each other without being closed appropriately\n" +
+							"(possibly the signature contains nested placeholders).");
+				startSymbolIdx = i;
+				break;
+
+			case PLACEHOLDER_END_SYMBOL:
+				if (--nestingLevel < 0)
+					throw new URISignatureParsingException(
+							"Malformed URL: parameter placeholder closing symbol found before the opening one.");
+				if (nestingLevel == 0) {
+					// correctly opened and closed placeholder found; check if
+					// it is a "fresh" one
+					String placeholderCandidate = uriSignature.substring(
+							startSymbolIdx + 1, i);
+					if (!foundPlaceholdersWithPositions
+							.containsKey(placeholderCandidate)) {
+						foundPlaceholdersWithPositions.put(
+								placeholderCandidate, startSymbolIdx + 1);
+					} else {
+						throw new URISignatureParsingException(
+								"Malformed URL: duplicate parameter placeholder \""
+										+ placeholderCandidate + "\" found.");
+					}
+				}
+				break;
+
+			default:
+				continue;
+			}
+		}
+
+		// the final check - make sure that after traversing the string, we are
+		// not "inside" one of the placeholders (e.g. this could happen if a
+		// placeholder
+		// opening symbol was found, but the closing one never occurred after
+		// that)
+		if (nestingLevel > 0)
+			throw new URISignatureParsingException(
+					"Malformed URL: parameter placeholder opening symbol found,\n"
+							+ "but the closing one has not been encountered.");
+
+		return foundPlaceholdersWithPositions;
+	}
+
+	/**
+	 * Works identical to
+	 * {@link URISignatureHandler#extractPlaceholdersWithPositions(String)}
+	 * except for returning only the list of placeholder titles - without
+	 * positions.
+	 * 
+	 * @param uriSignature
+	 *            The URI signature to process.
+	 * @return List of the placeholder titles in the order of their occurrence
+	 *         in the provided URI signature.
+	 */
+	public static List<String> extractPlaceholders(String uriSignature) {
+		return new ArrayList<>(extractPlaceholdersWithPositions(uriSignature)
+				.keySet());
+	}
+
+	/**
+	 * This method performs explicit validation of the URI signature. If the
+	 * validation succeeds, the method terminates quietly; in case of any
+	 * identified problems a {@link URISignatureParsingException} is thrown.
+	 * 
+	 * @param uriSignature
+	 *            The URI signature to validate.
+	 * @throws URISignatureParsingException
+	 */
+	public static void validate(String uriSignature)
+			throws URISignatureParsingException {
+		// this method essentially needs to do exactly the same thing
+		// as the method to extract the placeholders with their corresponding
+		// positions; all necessary validation is already performed there -
+		// hence the trick is simply to call that method (discarding its
+		// output),
+		// while keeping track of any exceptions that may be generated by the
+		// called method;
+		//
+		// for this simply call the placeholder extraction method - any
+		// exceptions
+		// will be forwarded up the method call stack; in case of success, the
+		// method
+		// will terminate quietly
+		extractPlaceholdersWithPositions(uriSignature);
+	}
+	
+	 /**
+	  * Check if the URL string contains "unsafe" characters, i.e. characters 
+	  * that need URL-encoding.
+	  * From RFC 1738: "...Only alphanumerics [0-9a-zA-Z], the special 
+	  * characters "$-_.+!*'()," (not including the quotes) and reserved 
+	  * characters used for their reserved purposes may be 
+	  * used unencoded within a URL." 
+	  * Reserved characters are: ";/?:@&=" ..." and "%" used for escaping.
+	 */
+	public static void checkForUnsafeCharacters(String candidateURLSignature) throws URISignatureParsingException{
+		String allowedURLCharactersString = new String("abcdefghijklmnopqrstuvwxyz0123456789$-_.+!*'(),;/?:@&=%");
+		char[] allowedURLCharactersArray = allowedURLCharactersString.toCharArray();
+		List<Character> allowedURLCharactersList = new ArrayList<Character>();
+		    for (char value : allowedURLCharactersArray)
+		    	allowedURLCharactersList.add(new Character(value));
+
+		int index = 0;
+		String unsafeCharactersDetected = "";
+		while (index < candidateURLSignature.length()){
+			char character = candidateURLSignature.charAt(index);
+			if (character == '{') { // a start of a parameter
+				// This is a paramater name - ignore until we find the closing '}'
+				index++;
+				while(character != '}' && index < candidateURLSignature.length()){
+					character = candidateURLSignature.charAt(index);
+					index++;
+				}
+			} else if (!allowedURLCharactersList.contains(Character
+					.valueOf(Character.toLowerCase(character)))) {
+				// We found an unsafe character in the URL - add to the list of unsafe characters
+				unsafeCharactersDetected += "'" + character + "', ";
+				index++;
+			} else {
+				index++;
+			}
+		}
+		String message = "";
+		unsafeCharactersDetected = unsafeCharactersDetected.trim();
+		if (unsafeCharactersDetected.endsWith(",")){ // remove the last ","
+			unsafeCharactersDetected = unsafeCharactersDetected.substring(0, unsafeCharactersDetected.lastIndexOf(','));
+		}
+		if  (!unsafeCharactersDetected.equals("")){
+			message += "REST service's URL contains unsafe characters that need\nto be URL-encoded or the service will most probably fail:\n"+ unsafeCharactersDetected;	
+			throw new URISignatureParsingException(message);
+		}
+	}
+
+
+	/**
+	 * Tests whether the provided URI signature is valid or not.
+	 * 
+	 * @param uriSignature
+	 *            URI signature to check for validity.
+	 * @return <code>true</code> if the URI signature is valid;
+	 *         <code>false</code> otherwise.
+	 */
+	public static boolean isValid(String uriSignature) {
+		try {
+			// no exceptions are generated by validate(), the validation has
+			// succeeded
+			validate(uriSignature);
+			return (true);
+		} catch (URISignatureParsingException e) {
+			return false;
+		}
+	}
+
+	/**
+	 * Substitutes real values for all placeholders encountered in the URI
+	 * signature and produces a complete URI that can be used directly.
+	 * 
+	 * @param uriSignature
+	 *            The URI signature to use as a basis.
+	 * @param parameters
+	 *            Map of {name,value} pairs for all placeholders in the
+	 *            signature. These values will be used to replace the
+	 *            placeholders in the signature.
+	 * @param escapeParameters
+	 *            Whether to URL-escape paramaters before placing them in the
+	 *            final URL.
+	 * @return A complete URI with all placeholders replaced by the provided
+	 *         values.
+	 * @throws URISignatureParsingException
+	 *             Thrown if there is a problem with the provided URI signature
+	 *             (e.g. null, empty, ill-formed, etc).
+	 * @throws URIGenerationFromSignatureException
+	 *             Thrown if there is a problem with the provided parameter map
+	 *             (e.g. null, empty, not containing enough values for some of
+	 *             the placeholders found in <code>uriSignature</code>.
+	 */
+	public static String generateCompleteURI(String uriSignature,
+			Map<String, String> specifiedParameters, boolean escapeParameters)
+			throws URISignatureParsingException,
+			URIGenerationFromSignatureException {
+		StringBuilder completeURI = new StringBuilder(uriSignature);
+
+		// no need to make any checks on the uriSignature - it is
+		// already handled by extractPlaceholdersWithPositions() --
+		// if something goes wrong a runtime exception will be thrown
+		// during placeholder extraction
+		LinkedHashMap<String, Integer> placeholdersWithPositions = extractPlaceholdersWithPositions(uriSignature);
+
+		// check that the URI signature contains some placeholders
+		if (placeholdersWithPositions.keySet().size() > 0) {
+			Map<String, String> parameters;
+			// some work will actually have to be done to replace placeholders
+			// with real values;
+			// check that the parameter map contains some values
+			if (specifiedParameters == null || specifiedParameters.isEmpty()) {
+				parameters = Collections.emptyMap();
+			} else {
+				parameters = specifiedParameters;
+			}
+
+			// the 'placeholders' linked list is guaranteed to be in the order
+			// of occurrence of placeholders in the URI signature;
+			// this will allow to traverse the URI signature and replace the
+			// placeholders in the reverse order --
+			// this way it is possible to use the indices of placeholders that
+			// were already found during their extraction to
+			// improve performance
+			LinkedList<String> placeholders = new LinkedList<String>(
+					placeholdersWithPositions.keySet());
+			Collections.reverse(placeholders);
+			Iterator<String> placeholdersIterator = placeholders.iterator();
+
+			while (placeholdersIterator.hasNext()) {
+				String placeholder = placeholdersIterator.next();
+				int placeholderStartPos = placeholdersWithPositions
+						.get(placeholder) - 1;
+				int placeholderEndPos = placeholderStartPos
+						+ placeholder.length() + 2;
+				if (parameters.containsKey(placeholder)) {
+					if (escapeParameters) {
+						completeURI.replace(placeholderStartPos,
+								placeholderEndPos, urlEncodeQuery(parameters
+										.get(placeholder)));
+					} else {
+						completeURI.replace(placeholderStartPos,
+								placeholderEndPos, parameters.get(placeholder));
+					}
+				} else {
+					int qnPos = completeURI.lastIndexOf("?", placeholderStartPos);
+ 					int ampPos = completeURI.lastIndexOf("&", placeholderStartPos);
+ 					int slashPos = completeURI.lastIndexOf("/", placeholderStartPos);
+ 					int startParamPos = Math.max(qnPos, ampPos);
+					if (startParamPos > -1 && startParamPos > slashPos) {
+ 						// We found an optional parameter, so delete all of it
+ 						if (qnPos > ampPos) {
+ 							// It might be the first or only parameter so delete carefully
+ 							if (placeholderEndPos >= (completeURI.length() - 1)) {
+ 								// No parameters
+ 								completeURI.replace(startParamPos, placeholderEndPos, "");
+ 							} else {
+ 								// Remove the & from the following parameter, not the ? that starts
+ 								completeURI.replace(startParamPos + 1, placeholderEndPos + 1, "");
+ 							}
+						} else {
+ 							// Just delete the optional parameter in total
+							completeURI.replace(startParamPos, placeholderEndPos, "");
+ 						}
+ 					} else {
+ 						throw new URIGenerationFromSignatureException(
+ 								"Parameter map does not contain a key/value for \""
+ 										+ placeholder + "\" mandatory placeholder");
+ 					}
+				}
+			}
+		}
+		/*
+		 * else { NO PLACEHOLDERS, SO NOTHING TO REPLACE WITH REAL VALUES - JUST
+		 * RETURN THE ORIGINAL 'uriSignature' }
+		 */
+
+		return (completeURI.toString());
+	}
+
+	/**
+	 * Exceptions of this type may be thrown when errors occur during URI
+	 * signature parsing - these will often indicate the reason for failure
+	 * (e.g. missing URI signature, nested placeholders, ill-formed signature,
+	 * etc).
+	 * 
+	 * @author Sergejs Aleksejevs
+	 */
+	@SuppressWarnings("serial")
+	public static class URISignatureParsingException extends
+			IllegalArgumentException {
+		public URISignatureParsingException() {
+		}
+
+		public URISignatureParsingException(String message) {
+			super(message);
+		}
+	}
+
+	/**
+	 * Exceptions of this type may be thrown during generation of a complete URI
+	 * from the provided signature and parameter hash. These may occur because
+	 * of wrong parameters, etc.
+	 * 
+	 * @author Sergejs Aleksejevs
+	 */
+	@SuppressWarnings("serial")
+	public static class URIGenerationFromSignatureException extends
+			RuntimeException {
+		public URIGenerationFromSignatureException() {
+		}
+
+		public URIGenerationFromSignatureException(String message) {
+			super(message);
+		}
+	}
+
+	/**
+	 * Prepares the string to serve as a part of url query to the server.
+	 * 
+	 * @param query
+	 *            The string that needs URL encoding.
+	 * @return URL encoded string that can be inserted into the request URL.
+	 */
+	public static String urlEncodeQuery(String query) {
+		String ns = Normalizer.normalize(query, Normalizer.Form.NFC);
+		byte[] bb = null;
+		try {
+			bb = ns.getBytes("UTF-8");
+		} catch (UnsupportedEncodingException e) {
+			logger.error(e);
+			return query;
+		}
+		
+		StringBuffer sb = new StringBuffer();
+		
+		for (int i = 0; i < bb.length; i++) {
+		    int b = bb[i] & 0xff;
+		    if (!Character.isLetterOrDigit(b) || (b >= 0x80)) {
+		    	sb.append("%");
+		    	sb.append(Integer.toHexString(b).toUpperCase());
+			} else {
+		    	sb.append((char)b);
+		    }
+		}
+		return sb.toString();
+	}
+
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context.xml b/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context.xml
index f1c900e..ee58f29 100644
--- a/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context.xml
+++ b/taverna-rest-activity/src/main/resources/META-INF/spring/rest-activity-context.xml
@@ -3,9 +3,9 @@
 	xsi:schemaLocation="http://www.springframework.org/schema/beans
                       http://www.springframework.org/schema/beans/spring-beans.xsd">
 
-	<bean id="RESTActivityHealthChecker" class="net.sf.taverna.t2.activities.rest.RESTActivityHealthChecker" />
+	<bean id="RESTActivityHealthChecker" class="org.apache.taverna.activities.rest.RESTActivityHealthChecker" />
 
-	<bean id="restActivityFactory" class="net.sf.taverna.t2.activities.rest.RESTActivityFactory">
+	<bean id="restActivityFactory" class="org.apache.taverna.activities.rest.RESTActivityFactory">
 		<property name="credentialManager" ref="credentialManager" />
 		<property name="edits" ref="edits" />
 	</bean>

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ApacheHttpClientUsageTest.java.bak
----------------------------------------------------------------------
diff --git a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ApacheHttpClientUsageTest.java.bak b/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ApacheHttpClientUsageTest.java.bak
deleted file mode 100644
index 518fbc3..0000000
--- a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ApacheHttpClientUsageTest.java.bak
+++ /dev/null
@@ -1,215 +0,0 @@
-package net.sf.taverna.t2.activities.rest;
-
-import java.awt.BorderLayout;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.BufferedReader;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.UnsupportedEncodingException;
-
-import javax.swing.BorderFactory;
-import javax.swing.JButton;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-
-import org.apache.commons.codec.binary.Base64;
-import org.apache.http.HttpEntity;
-import org.apache.http.HttpHost;
-import org.apache.http.HttpResponse;
-import org.apache.http.client.HttpClient;
-import org.apache.http.client.methods.HttpDelete;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.client.methods.HttpPost;
-import org.apache.http.client.methods.HttpPut;
-import org.apache.http.client.methods.HttpRequestBase;
-import org.apache.http.client.methods.HttpUriRequest;
-import org.apache.http.entity.StringEntity;
-import org.apache.http.impl.client.DefaultHttpClient;
-import org.apache.http.protocol.BasicHttpContext;
-import org.apache.http.protocol.ExecutionContext;
-import org.apache.http.protocol.HttpContext;
-
-/**
- * 
- * @author Sergejs Aleksejevs
- */
-public class ApacheHttpClientUsageTest extends JFrame implements ActionListener
-{
-  private JComboBox cbHttpMethod;
-  private JTextField tfAddressBar;
-  private JButton bGo;
-  private JTextArea taResponse;
-  private JScrollPane spResponse;
-  
-  
-  /**
-   * Constructor is solely involved in the UI initialisation.
-   */
-  public ApacheHttpClientUsageTest()
-  {
-    Container contentPane = this.getContentPane();
-    contentPane.setLayout(new BorderLayout(5,5));
-    
-    bGo = new JButton("GO!");
-    bGo.addActionListener(this);
-    bGo.setDefaultCapable(true);
-    this.getRootPane().setDefaultButton(bGo);
-    
-    tfAddressBar = new JTextField(50);
-    tfAddressBar.setPreferredSize(new Dimension(0,bGo.getPreferredSize().height));
-    tfAddressBar.setText("http://test.biocatalogue.org/");
-    
-    JPanel jpAddressBar = new JPanel();
-    jpAddressBar.add(tfAddressBar);
-    jpAddressBar.add(bGo);
-    
-    cbHttpMethod = new JComboBox(RESTActivity.HTTP_METHOD.values());
-    cbHttpMethod.setBorder(BorderFactory.createCompoundBorder(
-        BorderFactory.createEmptyBorder(5, 5, 5, 5),
-        cbHttpMethod.getBorder()));
-    
-    JPanel jpAllNavigation = new JPanel(new BorderLayout());
-    jpAllNavigation.add(jpAddressBar, BorderLayout.NORTH);
-    jpAllNavigation.add(cbHttpMethod, BorderLayout.CENTER);
-    
-    contentPane.add(jpAllNavigation, BorderLayout.NORTH);
-    
-    taResponse = new JTextArea(20, 20);
-    taResponse.setEditable(true);
-    
-    spResponse = new JScrollPane(taResponse);
-    spResponse.setBorder(BorderFactory.createCompoundBorder(
-        BorderFactory.createEmptyBorder(0, 5, 5, 5),
-        BorderFactory.createEtchedBorder()));
-    contentPane.add(spResponse, BorderLayout.CENTER);
-    
-    this.pack();
-    this.setLocationRelativeTo(null); // center on screen
-  }
-  
-  
-  /**
-   * Click handler for the only button there is - the "GO!" button 
-   */
-  public void actionPerformed(ActionEvent e)
-  {
-    if (e.getSource().equals(bGo))
-    {
-      try { 
-        switch ((RESTActivity.HTTP_METHOD)cbHttpMethod.getSelectedItem()) {
-          case GET:    doGET(); break;
-          case POST:   doPOST(); break;
-          case PUT:    doPUT(); break;
-          case DELETE: doDELETE(); break;
-        }
-      }
-      catch (Exception ex) {
-        taResponse.setText(ex + "\n\n" + ex.getStackTrace());
-      }
-    }
-  }
-  
-  
-  private void doGET() {
-    HttpGet httpGet = new HttpGet(tfAddressBar.getText());
-    httpGet.addHeader("Accept", "application/xml");
-    performHTTPRequest(httpGet);
-  }
-  
-  
-  private void doPOST() throws UnsupportedEncodingException {
-//    // POST TO MYEXPERIMENT - basic auth
-//    HttpPost httpPost = new HttpPost("http://sandbox.myexperiment.org/comment.xml");
-//    httpPost.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
-//    httpPost.addHeader("Accept", "application/xml");
-//    httpPost.addHeader("Content-Type", "application/xml");
-//    httpPost.setEntity(new StringEntity("<comment><subject resource=\"http://sandbox.myexperiment.org/files/226\"/><comment>1234567</comment></comment>"));
-//    performHTTPRequest(httpPost);
-    
-    // POST TO BIOCATALOGUE - no auth
-    HttpPost httpPost = new HttpPost(tfAddressBar.getText());
-    httpPost.addHeader("Accept", "application/xml");
-    httpPost.addHeader("Content-Type", "application/xml");
-    httpPost.setEntity(new StringEntity("<searchByData><searchType>input</searchType><limit>20</limit><data>test</data></searchByData>"));
-    performHTTPRequest(httpPost);
-  }
-  
-  
-  private void doPUT() throws UnsupportedEncodingException {
-    HttpPut httpPut = new HttpPut("http://sandbox.myexperiment.org/comment.xml?id=251");
-    httpPut.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
-    httpPut.addHeader("Accept", "application/xml");
-    httpPut.addHeader("Content-Type", "application/xml");
-    httpPut.setEntity(new StringEntity("<comment><subject resource=\"http://sandbox.myexperiment.org/files/226\"/><comment>12345678</comment></comment>"));
-    performHTTPRequest(httpPut);
-  }
-  
-  
-  private void doDELETE() {
-    HttpDelete httpDelete = new HttpDelete("http://sandbox.myexperiment.org/comment.xml?id=251");
-    httpDelete.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
-    httpDelete.addHeader("Accept", "application/xml");
-    performHTTPRequest(httpDelete);
-  }
-  
-  
-  private void performHTTPRequest(HttpRequestBase httpRequest) {
-    try {
-      StringBuilder responseStr = new StringBuilder();
-      // ---------------------------------------------
-      
-      HttpClient httpClient = new DefaultHttpClient();
-      HttpContext localContext = new BasicHttpContext();
-      
-      HttpResponse response = httpClient.execute(httpRequest, localContext);
-      // ---
-      // TRACK WHERE THE FINAL REDIRECT ENDS UP - target host + URI
-      HttpHost target = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_TARGET_HOST);
-      HttpUriRequest req = (HttpUriRequest) localContext.getAttribute(ExecutionContext.HTTP_REQUEST);
-
-      responseStr.append("Final request URI: " + req.getMethod() + " " + target + req.getURI() + "\n");
-//      System.out.println("Target host: " + target);
-//      System.out.println("Final request URI: " + req.getURI());
-//      System.out.println("Final request method: " + req.getMethod());
-      // ---
-      responseStr.append(response.getStatusLine() + "\n");
-      
-      HttpEntity entity = response.getEntity();
-      responseStr.append(entity.getContentType() + "\n\n");
-      
-      if (entity != null) {
-        InputStream in = entity.getContent();
-        BufferedReader reader = new BufferedReader(new InputStreamReader(in));
-        
-        String str;
-        while ((str = reader.readLine()) != null) {
-          responseStr.append(str + "\n");
-        }
-        
-        taResponse.setText(responseStr.toString());
-        taResponse.setCaretPosition(0);
-      }
-      
-      httpClient.getConnectionManager().shutdown();
-    }
-    catch (Exception ex) {
-      taResponse.setText(ex.getMessage() + "\n\n" + ex.getStackTrace());
-    }
-  }
-  
-  
-  public static void main(String[] args)
-  {
-    ApacheHttpClientUsageTest frame = new ApacheHttpClientUsageTest();
-    frame.setVisible(true);
-    frame.tfAddressBar.setCaretPosition(frame.tfAddressBar.getText().length());
-  }
-  
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ExampleActivityTest.java.bak
----------------------------------------------------------------------
diff --git a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ExampleActivityTest.java.bak b/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ExampleActivityTest.java.bak
deleted file mode 100644
index 56b6904..0000000
--- a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/ExampleActivityTest.java.bak
+++ /dev/null
@@ -1,153 +0,0 @@
-package net.sf.taverna.t2.activities.rest;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class ExampleActivityTest {
-
-	private RESTActivityConfigurationBean configBean;
-
-	private RESTActivity activity = new RESTActivity();
-
-	@Before
-	public void makeConfigBean() throws Exception {
-		configBean = new RESTActivityConfigurationBean();
-		configBean.setExampleString("something");
-		configBean
-				.setExampleUri(URI.create("http://localhost:8080/myEndPoint"));
-	}
-
-	@Test(expected = ActivityConfigurationException.class)
-	public void invalidConfiguration() throws ActivityConfigurationException {
-		RESTActivityConfigurationBean invalidBean = new RESTActivityConfigurationBean();
-		invalidBean.setExampleString("invalidExample");
-		// Should throw ActivityConfigurationException
-		activity.configure(invalidBean);
-	}
-
-	@Test
-	public void executeAsynch() throws Exception {
-		activity.configure(configBean);
-
-		Map<String, Object> inputs = new HashMap<String, Object>();
-		inputs.put("firstInput", "hello");
-
-		Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>();
-		expectedOutputTypes.put("simpleOutput", String.class);
-		expectedOutputTypes.put("moreOutputs", ExternalReferenceSPI.class);
-
-		Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
-				activity, inputs, expectedOutputTypes);
-
-		assertEquals("Unexpected outputs", 2, outputs.size());
-		assertEquals("da39a3ee5e6b4b0d3255bfef95601890afd80709", outputs.get("simpleOutput"));
-		ErrorDocument errorDoc = (ErrorDocument) outputs.get("moreOutputs");
-		assertEquals("java.lang.Exception: There are no more values",
-		             errorDoc.getExceptionMessage());
-
-	}
-	
-	
-	
-	@Test
-  public void checksumOfExtraData() throws Exception {
-    configBean.setExampleString("specialCase");
-	  activity.configure(configBean);
-
-    Map<String, Object> inputs = new HashMap<String, Object>();
-    inputs.put("firstInput", "hello");
-    inputs.put("extraData", Arrays.asList("Test1".getBytes("utf8"),
-        "Test2".getBytes("utf8")));
-
-
-    Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>();
-    expectedOutputTypes.put("simpleOutput", String.class);
-    expectedOutputTypes.put("moreOutputs", ExternalReferenceSPI.class);
-    expectedOutputTypes.put("report", String.class);
-
-
-    Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
-        activity, inputs, expectedOutputTypes);
-
-    assertEquals("Unexpected outputs", 3, outputs.size());
-    assertEquals("35bceb434ff8e69fb89b829e461c921a28b423b3", outputs.get("simpleOutput"));
-    ErrorDocument errorDoc = (ErrorDocument) outputs.get("moreOutputs");
-    assertEquals("java.lang.Exception: There are no more values",
-                 errorDoc.getExceptionMessage());
-
-  }
-	
-	
-
-	@Test
-	public void reConfiguredActivity() throws Exception {
-		assertEquals("Unexpected inputs", 0, activity.getInputPorts().size());
-		assertEquals("Unexpected outputs", 0, activity.getOutputPorts().size());
-
-		activity.configure(configBean);
-		assertEquals("Unexpected inputs", 1, activity.getInputPorts().size());
-		assertEquals("Unexpected outputs", 2, activity.getOutputPorts().size());
-
-		activity.configure(configBean);
-		// Should not change on reconfigure
-		assertEquals("Unexpected inputs", 1, activity.getInputPorts().size());
-		assertEquals("Unexpected outputs", 2, activity.getOutputPorts().size());
-	}
-
-	@Test
-	public void reConfiguredSpecialPorts() throws Exception {
-		activity.configure(configBean);
-
-		RESTActivityConfigurationBean specialBean = new RESTActivityConfigurationBean();
-		specialBean.setExampleString("specialCase");
-		specialBean.setExampleUri(URI
-				.create("http://localhost:8080/myEndPoint"));
-		activity.configure(specialBean);		
-		// Should now have added the optional ports
-		assertEquals("Unexpected inputs", 2, activity.getInputPorts().size());
-		assertEquals("Unexpected outputs", 3, activity.getOutputPorts().size());
-	}
-
-	@Test
-	public void configureActivity() throws Exception {
-		Set<String> expectedInputs = new HashSet<String>();
-		expectedInputs.add("firstInput");
-
-		Set<String> expectedOutputs = new HashSet<String>();
-		expectedOutputs.add("simpleOutput");
-		expectedOutputs.add("moreOutputs");
-
-		activity.configure(configBean);
-
-		Set<ActivityInputPort> inputPorts = activity.getInputPorts();
-		assertEquals(expectedInputs.size(), inputPorts.size());
-		for (ActivityInputPort inputPort : inputPorts) {
-			assertTrue("Wrong input : " + inputPort.getName(), expectedInputs
-					.remove(inputPort.getName()));
-		}
-
-		Set<OutputPort> outputPorts = activity.getOutputPorts();
-		assertEquals(expectedOutputs.size(), outputPorts.size());
-		for (OutputPort outputPort : outputPorts) {
-			assertTrue("Wrong output : " + outputPort.getName(),
-					expectedOutputs.remove(outputPort.getName()));
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/URISignatureHandlerTest.java
----------------------------------------------------------------------
diff --git a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/URISignatureHandlerTest.java b/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/URISignatureHandlerTest.java
deleted file mode 100644
index 8aad5ec..0000000
--- a/taverna-rest-activity/src/test/java/net/sf/taverna/t2/activities/rest/URISignatureHandlerTest.java
+++ /dev/null
@@ -1,594 +0,0 @@
-package net.sf.taverna.t2.activities.rest;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.junit.*;
-
-import static org.junit.Assert.*;
-
-public class URISignatureHandlerTest {
-	// ==========================================================================
-	// TEST URIs
-	// ==========================================================================
-
-	final String validURI_NoPlaceholders = "http://sysmo-db.org/sops/";
-	final String validURI_PlaceholdersInMainPartOfURIOnly = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}";
-	final String validURI_PlaceholdersInQueryStringOnly = "http://sandbox.myexperiment.org/user.xml?id={user_id}&verbose=true";
-	final String validURI_3MixedPlaceholders = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={unit}";
-
-	final String badURI_nullURI = null;
-	final String badURI_emptyURI = "";
-	final String badURI_SingleOpeningSymbolNoClosingSymbol = "http://sysmo-db.org/sops/{sop_id/experimental_conditions";
-	final String badURI_SingleClosingSymbolNoOpeningSymbol = "http://sysmo-db.org/sops/sop_id}/experimental_conditions";
-	final String badURI_DoubleOpeningSymbolsNoClosingSymbol = "http://sysmo-db.org/sops/{{sop_id/experimental_conditions";
-	final String badURI_DoubleOpeningSymbols = "http://sysmo-db.org/sops/{{sop_id}/experimental_conditions";
-	final String badURI_DoubleOpeningSymbolsSpaced = "http://sysmo-db.org/sops/{sop_{id}/experimental_conditions";
-	final String badURI_DoubleClosingSymbols = "http://sysmo-db.org/sops/{sop_id}}/experimental_conditions";
-	final String badURI_DoubleClosingSymbolsSpaced = "http://sysmo-db.org/sops/{sop}_id}/experimental_conditions";
-	final String badURI_NestedPlaceholders = "http://sandbox.myexperiment.org/user.xml?id={user_{id}}&verbose=true";
-	final String badURI_NestedPlaceholdersSpaced = "http://sandbox.myexperiment.org/user.xml?id={us{er}_id}&verbose=true";
-	final String badURI_DuplicatePlaceholders = "http://sandbox.myexperiment.org/user.xml?id={user_id}&verbose={user_id}";
-	final String badURI_DuplicatePlaceholdersWithOthers = "http://sysmo-db.org/sops/{unit}/experimental_conditions/{cond_id}?condition_unit={unit}";
-	
-     final String validURI_MultipleQueryString =
-            "http://dr-site.esrin.esa.int/{catalogue}/genesi/ASA_IMS_1P/rdf/?count={count?}&startPage={startPage?}&startIndex={startIndex?}&q={searchTerms?}"; 	
-
-	// ==========================================================================
-	// TEST URI SIGNATURE BOOLEAN VALIDATION
-	// ==========================================================================
-
-	// success cases
-
-	@Test
-	public void isValid_validURI_NoPlaceholders() {
-		assertTrue(URISignatureHandler.isValid(validURI_NoPlaceholders));
-	}
-
-	@Test
-	public void isValid_validURI_PlaceholdersInMainPartOfURIOnly() {
-		assertTrue(URISignatureHandler
-				.isValid(validURI_PlaceholdersInMainPartOfURIOnly));
-	}
-
-	@Test
-	public void isValid_validURI_PlaceholdersInQueryStringOnly() {
-		assertTrue(URISignatureHandler
-				.isValid(validURI_PlaceholdersInQueryStringOnly));
-	}
-
-	@Test
-	public void isValid_validURI_MixedPlaceholders() {
-		assertTrue(URISignatureHandler.isValid(validURI_3MixedPlaceholders));
-	}
-
- 	@Test
- 	public void isValid_validURI_MultipleQueryString() {
- 		assertTrue(URISignatureHandler.isValid(validURI_MultipleQueryString));
- 	}
- 	
-	// failure cases
-
-	@Test
-	public void isValid_badURI_nullURI() {
-		assertFalse(URISignatureHandler.isValid(badURI_nullURI));
-	}
-
-	@Test
-	public void isValid_badURI_emptyURI() {
-		assertFalse(URISignatureHandler.isValid(badURI_emptyURI));
-	}
-
-	@Test
-	public void isValid_badURI_SingleOpeningSymbolNoClosingSymbol() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_SingleOpeningSymbolNoClosingSymbol));
-	}
-
-	@Test
-	public void isValid_badURI_SingleClosingSymbolNoOpeningSymbol() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_SingleClosingSymbolNoOpeningSymbol));
-	}
-
-	@Test
-	public void isValid_badURI_DoubleOpeningSymbolsNoClosingSymbol() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_DoubleOpeningSymbolsNoClosingSymbol));
-	}
-
-	@Test
-	public void isValid_badURI_DoubleOpeningSymbols() {
-		assertFalse(URISignatureHandler.isValid(badURI_DoubleOpeningSymbols));
-	}
-
-	@Test
-	public void isValid_badURI_DoubleOpeningSymbolsSpaced() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_DoubleOpeningSymbolsSpaced));
-	}
-
-	@Test
-	public void isValid_badURI_DoubleClosingSymbols() {
-		assertFalse(URISignatureHandler.isValid(badURI_DoubleClosingSymbols));
-	}
-
-	@Test
-	public void isValid_badURI_DoubleClosingSymbolsSpaced() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_DoubleClosingSymbolsSpaced));
-	}
-
-	@Test
-	public void isValid_badURI_NestedPlaceholders() {
-		assertFalse(URISignatureHandler.isValid(badURI_NestedPlaceholders));
-	}
-
-	@Test
-	public void isValid_badURI_NestedPlaceholdersSpaced() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_NestedPlaceholdersSpaced));
-	}
-
-	@Test
-	public void isValid_badURI_DuplicatePlaceholders() {
-		assertFalse(URISignatureHandler.isValid(badURI_DuplicatePlaceholders));
-	}
-
-	@Test
-	public void isValid_badURI_DuplicatePlaceholdersWithOthers() {
-		assertFalse(URISignatureHandler
-				.isValid(badURI_DuplicatePlaceholdersWithOthers));
-	}
-
-	// ==========================================================================
-	// TEST URI SIGNATURE DETAILED VALIDATION
-	// ==========================================================================
-
-	// success cases
-
-	@Test
-	public void validate_validURI_NoPlaceholders() {
-		// nothing should happen when this is executed if validation succeeds
-		URISignatureHandler.validate(validURI_NoPlaceholders);
-	}
-
-	@Test
-	public void validate_validURI_PlaceholdersInMainPartOfURIOnly() {
-		// nothing should happen when this is executed if validation succeeds
-		URISignatureHandler.validate(validURI_PlaceholdersInMainPartOfURIOnly);
-	}
-
-	@Test
-	public void validate_validURI_PlaceholdersInQueryStringOnly() {
-		// nothing should happen when this is executed if validation succeeds
-		URISignatureHandler.validate(validURI_PlaceholdersInQueryStringOnly);
-	}
-
-	@Test
-	public void validate_validURI_MixedPlaceholders() {
-		// nothing should happen when this is executed if validation succeeds
-		URISignatureHandler.validate(validURI_3MixedPlaceholders);
-	}
-
- 	@Test
- 	public void validate_validURI_validURI_Multiple() {
- 		URISignatureHandler.validate(validURI_MultipleQueryString);
- 	}
-	
-	// failure cases
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_nullURI() {
-		URISignatureHandler.validate(badURI_nullURI);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_emptyURI() {
-		URISignatureHandler.validate(badURI_emptyURI);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_SingleOpeningSymbolNoClosingSymbol() {
-		URISignatureHandler.validate(badURI_SingleOpeningSymbolNoClosingSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_SingleClosingSymbolNoOpeningSymbol() {
-		URISignatureHandler.validate(badURI_SingleClosingSymbolNoOpeningSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DoubleOpeningSymbolsNoClosingSymbol() {
-		URISignatureHandler
-				.validate(badURI_DoubleOpeningSymbolsNoClosingSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DoubleOpeningSymbols() {
-		URISignatureHandler.validate(badURI_DoubleOpeningSymbols);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DoubleOpeningSymbolsSpaced() {
-		URISignatureHandler.validate(badURI_DoubleOpeningSymbolsSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DoubleClosingSymbols() {
-		URISignatureHandler.validate(badURI_DoubleClosingSymbols);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DoubleClosingSymbolsSpaced() {
-		URISignatureHandler.validate(badURI_DoubleClosingSymbolsSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_NestedPlaceholders() {
-		URISignatureHandler.validate(badURI_NestedPlaceholders);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_NestedPlaceholdersSpaced() {
-		URISignatureHandler.validate(badURI_NestedPlaceholdersSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DuplicatePlaceholders() {
-		URISignatureHandler.validate(badURI_DuplicatePlaceholders);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void validate_badURI_DuplicatePlaceholdersWithOthers() {
-		URISignatureHandler.validate(badURI_DuplicatePlaceholdersWithOthers);
-	}
-
-	// ==========================================================================
-	// TEST PLACEHOLDER EXTRACTION FROM URI SIGNATURE
-	// ==========================================================================
-
-	// success cases
-
-	@Test
-	public void extractPlaceholders_validURI_NoPlaceholders() {
-		List<String> placeholders = URISignatureHandler
-				.extractPlaceholders(validURI_NoPlaceholders);
-		assertNotNull(placeholders);
-		assertEquals(0, placeholders.size());
-	}
-
-	@Test
-	public void extractPlaceholders_validURI_PlaceholdersInMainPartOfURIOnly() {
-		List<String> placeholders = URISignatureHandler
-				.extractPlaceholders(validURI_PlaceholdersInMainPartOfURIOnly);
-		assertNotNull(placeholders);
-		assertEquals(2, placeholders.size());
-		assertEquals("Wrong first placeholder", "sop_id", placeholders.get(0));
-		assertEquals("Wrong second placeholder", "cond_id", placeholders.get(1));
-	}
-
-	@Test
-	public void extractPlaceholders_validURI_PlaceholdersInQueryStringOnly() {
-		List<String> placeholders = URISignatureHandler
-				.extractPlaceholders(validURI_PlaceholdersInQueryStringOnly);
-		assertNotNull(placeholders);
-		assertEquals(1, placeholders.size());
-		assertEquals("Wrong first placeholder", "user_id", placeholders.get(0));
-	}
-
-	@Test
-	public void extractPlaceholders_validURI_MixedPlaceholders() {
-		List<String> placeholders = URISignatureHandler
-				.extractPlaceholders(validURI_3MixedPlaceholders);
-		assertNotNull(placeholders);
-		assertEquals("Wrong number of placeholders extracted", 3, placeholders
-				.size());
-		assertEquals("Wrong first placeholder", "sop_id", placeholders.get(0));
-		assertEquals("Wrong second placeholder", "cond_id", placeholders.get(1));
-		assertEquals("Wrong third placeholder", "unit", placeholders.get(2));
-	}
-
-	@Test
- 	public void extractPlaceholders_validURI_MultipleQueryString() {
- 		List<String> placeholders = URISignatureHandler
- 				.extractPlaceholders(validURI_MultipleQueryString);
- 		assertNotNull(placeholders);
- 		assertEquals(5, placeholders.size());
- 		assertEquals("Wrong first placeholder", "catalogue", placeholders.get(0));
- 		assertEquals("Wrong second placeholder", "count?", placeholders.get(1));
- 		assertEquals("Wrong third placeholder", "startPage?", placeholders.get(2));
- 		assertEquals("Wrong fourth placeholder", "startIndex?", placeholders.get(3));
- 		assertEquals("Wrong fifth placeholder", "searchTerms?", placeholders.get(4));
- 	}
-	
-	// failure cases
-
-	/*
-	 * These tests are all meant to generate an exception - therefore, no need
-	 * to evaluate generated values, as there will be none returned.
-	 */
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_nullURI() {
-		URISignatureHandler.extractPlaceholders(badURI_nullURI);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_emptyURI() {
-		URISignatureHandler.extractPlaceholders(badURI_emptyURI);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_SingleOpeningSymbolNoClosingSymbol() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_SingleOpeningSymbolNoClosingSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_SingleClosingSymbolNoOpeningSymbol() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_SingleClosingSymbolNoOpeningSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DoubleOpeningSymbolsNoClosingSymbol() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_DoubleOpeningSymbolsNoClosingSymbol);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DoubleOpeningSymbols() {
-		URISignatureHandler.extractPlaceholders(badURI_DoubleOpeningSymbols);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DoubleOpeningSymbolsSpaced() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_DoubleOpeningSymbolsSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DoubleClosingSymbols() {
-		URISignatureHandler.extractPlaceholders(badURI_DoubleClosingSymbols);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DoubleClosingSymbolsSpaced() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_DoubleClosingSymbolsSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_NestedPlaceholders() {
-		URISignatureHandler.extractPlaceholders(badURI_NestedPlaceholders);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_NestedPlaceholdersSpaced() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_NestedPlaceholdersSpaced);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DuplicatePlaceholders() {
-		URISignatureHandler.extractPlaceholders(badURI_DuplicatePlaceholders);
-	}
-
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void extractPlaceholders_badURI_DuplicatePlaceholdersWithOthers() {
-		URISignatureHandler
-				.extractPlaceholders(badURI_DuplicatePlaceholdersWithOthers);
-	}
-
-	// ==========================================================================
-	// TEST COMPLETE URI GENERATION FROM URI SIGNATURE + PARAMETERS
-	// ==========================================================================
-
-	// success cases
-
-	@SuppressWarnings("serial")
-	@Test
-	public void generateCompleteURI_successfulURIGeneration() {
-		String uriSignature = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={unit}";
-		Map<String, String> parameters = new HashMap<String, String>() {
-			{
-				put("sop_id", "111");
-				put("unit", "33");
-				put("cond_id", "2222");
-			}
-		};
-
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				uriSignature, parameters, true);
-		assertEquals(
-				"http://sysmo-db.org/sops/111/experimental_conditions/2222?condition_unit=33",
-				completeURI);
-	}
-
-	@SuppressWarnings("serial")
-	@Test
-	public void generateCompleteURI_successfulURIGeneration_URLParameterEscaping() {
-		String uriSignature = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={unit}";
-		Map<String, String> parameters = new HashMap<String, String>() {
-			{
-				put("sop_id", "1 11");
-				put("unit", "3;3");
-				put("cond_id", "2/2$2&2:");
-			}
-		};
-
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				uriSignature, parameters, true);
-		System.err.println(completeURI);
-		assertEquals(
-				"http://sysmo-db.org/sops/1%2011/experimental_conditions/2%2F2%242%262%3A?condition_unit=3%3B3",
-				completeURI);
-	}
-
-	@SuppressWarnings("serial")
-	@Test
-	public void generateCompleteURI_successfulURIGeneration_noURLParameterEscaping() {
-		String uriSignature = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={unit}";
-		Map<String, String> parameters = new HashMap<String, String>() {
-			{
-				put("sop_id", "1 11");
-				put("unit", "3;3");
-				put("cond_id", "2/2$2&2:");
-			}
-		};
-
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				uriSignature, parameters, false);
-		assertEquals(
-				"http://sysmo-db.org/sops/1 11/experimental_conditions/2/2$2&2:?condition_unit=3;3",
-				completeURI);
-	}
-	
- 	@SuppressWarnings("serial")
- 	@Test
- 	public void generateCompleteURI_successfulURIGeneration_optionalParams() {
- 		String uriSignature = "http://dr-site.esrin.esa.int/{catalogue}/genesi/ASA_IMS_1P/rdf/?count={count?}&startPage={startPage?}&startIndex={startIndex?}&q={searchTerms?}";
- 		Map<String, String> allParameters = new HashMap<String, String>() {
- 			{
- 				put("catalogue", "catalogue");
- 				put("count?", "10");
- 				put("startPage?", "1");
- 				put("startIndex?", "1");
- 				put("searchTerms?", "term1");
- 			}
- 		};
- 
- 		Map<String, String> parametersMissingOptional = new HashMap<String, String>() {
- 			{
- 				put("catalogue", "catalogue");
- 				put("count?", "10");
- 				put("searchTerms?", "term1");
- 			}
- 		};
- 
- 		Map<String, String> parametersMissingFirstOptional = new HashMap<String, String>() {
- 			{
- 				put("catalogue", "catalogue");
- 				put("startPage?", "1");
- 				put("startIndex?", "1");
- 				put("searchTerms?", "term1");
- 			}
- 		};
- 
- 		String completeURI1 = URISignatureHandler.generateCompleteURI(
- 				uriSignature, allParameters, false);
- 		assertEquals(
-				"http://dr-site.esrin.esa.int/catalogue/genesi/ASA_IMS_1P/rdf/?count=10&startPage=1&startIndex=1&q=term1",
- 				completeURI1);
- 
- 		String completeURI2 = URISignatureHandler.generateCompleteURI(
- 				uriSignature, parametersMissingOptional, false);
- 		assertEquals(
- 				"http://dr-site.esrin.esa.int/catalogue/genesi/ASA_IMS_1P/rdf/?count=10&q=term1",
- 				completeURI2);
- 
- 		String completeURI3 = URISignatureHandler.generateCompleteURI(
- 				uriSignature, parametersMissingFirstOptional, false);
- 		assertEquals(
- 				"http://dr-site.esrin.esa.int/catalogue/genesi/ASA_IMS_1P/rdf/?startPage=1&startIndex=1&q=term1",
- 				completeURI3);
- 	}
- 
-	@Test
-	public void generateCompleteURI_signatureWithNoPlaceholders_nullParameterMap() {
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				validURI_NoPlaceholders, null, true);
-		assertEquals(validURI_NoPlaceholders, completeURI);
-	}
-
-	@Test
-	public void generateCompleteURI_signatureWithNoPlaceholders_emptyParameterMap() {
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				validURI_NoPlaceholders, Collections
-						.<String, String> emptyMap(), true);
-		assertEquals(validURI_NoPlaceholders, completeURI);
-	}
-
-	// failure cases
-
-	@Test(expected = URISignatureHandler.URIGenerationFromSignatureException.class)
-	public void generateCompleteURI_signatureWithPlaceholders_nullParameterMap() {
-		URISignatureHandler.generateCompleteURI(validURI_3MixedPlaceholders,
-				null, true);
-	}
-
-	@Test(expected = URISignatureHandler.URIGenerationFromSignatureException.class)
-	public void generateCompleteURI_signatureWithPlaceholders_emptyParameterMap() {
-		URISignatureHandler.generateCompleteURI(validURI_3MixedPlaceholders,
-				Collections.<String, String> emptyMap(), true);
-	}
-
-	@SuppressWarnings("serial")
-	@Test
-	public void generateCompleteURI_signatureWithPlaceholders_missingParameterURIGeneration_FailureNotExpected() {
-		String uriSignature = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={unit}";
-		Map<String, String> parameters = new HashMap<String, String>() {
-			{
-				put("sop_id", "111");
-				put("cond_id", "2222");
-			}
-		};
-
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				uriSignature, parameters, true);
-
-		assertEquals(
-				"http://sysmo-db.org/sops/111/experimental_conditions/2222",
-				completeURI);
-	}
-
-	// the following failure case is just to confirm the validation of the URI
-	// signature by the validation mechanism, which is the same for
-	// generateCompleteURI()
-	// and extractPlaceholders()
-
-	@SuppressWarnings("serial")
-	@Test(expected = URISignatureHandler.URISignatureParsingException.class)
-	public void generateCompleteURI_duplicatePlaceholderURIGeneration_FailureExpected() {
-		String uriSignature = "http://sysmo-db.org/sops/{sop_id}/experimental_conditions/{cond_id}?condition_unit={sop_id}";
-		Map<String, String> parameters = new HashMap<String, String>() {
-			{
-				put("sop_id", "111");
-				put("unit", "33");
-				put("cond_id", "2222");
-			}
-		};
-
-		String completeURI = URISignatureHandler.generateCompleteURI(
-				uriSignature, parameters, true);
-
-		assertEquals(
-				"http://sysmo-db.org/sops/111/experimental_conditions/2222?condition_unit=33",
-				completeURI);
-	}
-
-	@SuppressWarnings("serial")
- 	@Test(expected = URISignatureHandler.URIGenerationFromSignatureException.class)
- 	public void generateCompleteURI_failureURIGeneration_optionalParams() {
- 		String uriSignature = "http://dr-site.esrin.esa.int/{catalogue}/genesi/ASA_IMS_1P/rdf/?count={count?}&startPage={startPage?}&startIndex={startIndex?}&q={searchTerms?}";
- 
- 		Map<String, String> parametersMissingCompulsory = new HashMap<String, String>() {
- 			{
- 				put("count?", "10");
- 				put("startPage?", "1");
- 				put("startIndex?", "1");
- 				put("searchTerms?", "term1");
- 			}
- 		};
- 
- 		String completeURI = URISignatureHandler.generateCompleteURI(
- 				uriSignature, parametersMissingCompulsory, false);
- 
- 		assertEquals(
- 				"http://dr-site.esrin.esa.int/catalogue/genesi/ASA_IMS_1P/rdf/?count={count?}&startPage={startPage?}&startIndex={startIndex?}&q={searchTerms?}",
- 				completeURI);
- 	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ApacheHttpClientUsageTest.java.bak
----------------------------------------------------------------------
diff --git a/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ApacheHttpClientUsageTest.java.bak b/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ApacheHttpClientUsageTest.java.bak
new file mode 100644
index 0000000..c966a57
--- /dev/null
+++ b/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ApacheHttpClientUsageTest.java.bak
@@ -0,0 +1,215 @@
+package org.apache.taverna.activities.rest;
+
+import java.awt.BorderLayout;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.UnsupportedEncodingException;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
+
+import org.apache.commons.codec.binary.Base64;
+import org.apache.http.HttpEntity;
+import org.apache.http.HttpHost;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpDelete;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.client.methods.HttpPut;
+import org.apache.http.client.methods.HttpRequestBase;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.entity.StringEntity;
+import org.apache.http.impl.client.DefaultHttpClient;
+import org.apache.http.protocol.BasicHttpContext;
+import org.apache.http.protocol.ExecutionContext;
+import org.apache.http.protocol.HttpContext;
+
+/**
+ * 
+ * @author Sergejs Aleksejevs
+ */
+public class ApacheHttpClientUsageTest extends JFrame implements ActionListener
+{
+  private JComboBox cbHttpMethod;
+  private JTextField tfAddressBar;
+  private JButton bGo;
+  private JTextArea taResponse;
+  private JScrollPane spResponse;
+  
+  
+  /**
+   * Constructor is solely involved in the UI initialisation.
+   */
+  public ApacheHttpClientUsageTest()
+  {
+    Container contentPane = this.getContentPane();
+    contentPane.setLayout(new BorderLayout(5,5));
+    
+    bGo = new JButton("GO!");
+    bGo.addActionListener(this);
+    bGo.setDefaultCapable(true);
+    this.getRootPane().setDefaultButton(bGo);
+    
+    tfAddressBar = new JTextField(50);
+    tfAddressBar.setPreferredSize(new Dimension(0,bGo.getPreferredSize().height));
+    tfAddressBar.setText("http://test.biocatalogue.org/");
+    
+    JPanel jpAddressBar = new JPanel();
+    jpAddressBar.add(tfAddressBar);
+    jpAddressBar.add(bGo);
+    
+    cbHttpMethod = new JComboBox(RESTActivity.HTTP_METHOD.values());
+    cbHttpMethod.setBorder(BorderFactory.createCompoundBorder(
+        BorderFactory.createEmptyBorder(5, 5, 5, 5),
+        cbHttpMethod.getBorder()));
+    
+    JPanel jpAllNavigation = new JPanel(new BorderLayout());
+    jpAllNavigation.add(jpAddressBar, BorderLayout.NORTH);
+    jpAllNavigation.add(cbHttpMethod, BorderLayout.CENTER);
+    
+    contentPane.add(jpAllNavigation, BorderLayout.NORTH);
+    
+    taResponse = new JTextArea(20, 20);
+    taResponse.setEditable(true);
+    
+    spResponse = new JScrollPane(taResponse);
+    spResponse.setBorder(BorderFactory.createCompoundBorder(
+        BorderFactory.createEmptyBorder(0, 5, 5, 5),
+        BorderFactory.createEtchedBorder()));
+    contentPane.add(spResponse, BorderLayout.CENTER);
+    
+    this.pack();
+    this.setLocationRelativeTo(null); // center on screen
+  }
+  
+  
+  /**
+   * Click handler for the only button there is - the "GO!" button 
+   */
+  public void actionPerformed(ActionEvent e)
+  {
+    if (e.getSource().equals(bGo))
+    {
+      try { 
+        switch ((RESTActivity.HTTP_METHOD)cbHttpMethod.getSelectedItem()) {
+          case GET:    doGET(); break;
+          case POST:   doPOST(); break;
+          case PUT:    doPUT(); break;
+          case DELETE: doDELETE(); break;
+        }
+      }
+      catch (Exception ex) {
+        taResponse.setText(ex + "\n\n" + ex.getStackTrace());
+      }
+    }
+  }
+  
+  
+  private void doGET() {
+    HttpGet httpGet = new HttpGet(tfAddressBar.getText());
+    httpGet.addHeader("Accept", "application/xml");
+    performHTTPRequest(httpGet);
+  }
+  
+  
+  private void doPOST() throws UnsupportedEncodingException {
+//    // POST TO MYEXPERIMENT - basic auth
+//    HttpPost httpPost = new HttpPost("http://sandbox.myexperiment.org/comment.xml");
+//    httpPost.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
+//    httpPost.addHeader("Accept", "application/xml");
+//    httpPost.addHeader("Content-Type", "application/xml");
+//    httpPost.setEntity(new StringEntity("<comment><subject resource=\"http://sandbox.myexperiment.org/files/226\"/><comment>1234567</comment></comment>"));
+//    performHTTPRequest(httpPost);
+    
+    // POST TO BIOCATALOGUE - no auth
+    HttpPost httpPost = new HttpPost(tfAddressBar.getText());
+    httpPost.addHeader("Accept", "application/xml");
+    httpPost.addHeader("Content-Type", "application/xml");
+    httpPost.setEntity(new StringEntity("<searchByData><searchType>input</searchType><limit>20</limit><data>test</data></searchByData>"));
+    performHTTPRequest(httpPost);
+  }
+  
+  
+  private void doPUT() throws UnsupportedEncodingException {
+    HttpPut httpPut = new HttpPut("http://sandbox.myexperiment.org/comment.xml?id=251");
+    httpPut.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
+    httpPut.addHeader("Accept", "application/xml");
+    httpPut.addHeader("Content-Type", "application/xml");
+    httpPut.setEntity(new StringEntity("<comment><subject resource=\"http://sandbox.myexperiment.org/files/226\"/><comment>12345678</comment></comment>"));
+    performHTTPRequest(httpPut);
+  }
+  
+  
+  private void doDELETE() {
+    HttpDelete httpDelete = new HttpDelete("http://sandbox.myexperiment.org/comment.xml?id=251");
+    httpDelete.addHeader("Authorization", "Basic " + new String(Base64.encodeBase64(("LOGIN" + ":" + "PASSWORD").getBytes())));
+    httpDelete.addHeader("Accept", "application/xml");
+    performHTTPRequest(httpDelete);
+  }
+  
+  
+  private void performHTTPRequest(HttpRequestBase httpRequest) {
+    try {
+      StringBuilder responseStr = new StringBuilder();
+      // ---------------------------------------------
+      
+      HttpClient httpClient = new DefaultHttpClient();
+      HttpContext localContext = new BasicHttpContext();
+      
+      HttpResponse response = httpClient.execute(httpRequest, localContext);
+      // ---
+      // TRACK WHERE THE FINAL REDIRECT ENDS UP - target host + URI
+      HttpHost target = (HttpHost) localContext.getAttribute(ExecutionContext.HTTP_TARGET_HOST);
+      HttpUriRequest req = (HttpUriRequest) localContext.getAttribute(ExecutionContext.HTTP_REQUEST);
+
+      responseStr.append("Final request URI: " + req.getMethod() + " " + target + req.getURI() + "\n");
+//      System.out.println("Target host: " + target);
+//      System.out.println("Final request URI: " + req.getURI());
+//      System.out.println("Final request method: " + req.getMethod());
+      // ---
+      responseStr.append(response.getStatusLine() + "\n");
+      
+      HttpEntity entity = response.getEntity();
+      responseStr.append(entity.getContentType() + "\n\n");
+      
+      if (entity != null) {
+        InputStream in = entity.getContent();
+        BufferedReader reader = new BufferedReader(new InputStreamReader(in));
+        
+        String str;
+        while ((str = reader.readLine()) != null) {
+          responseStr.append(str + "\n");
+        }
+        
+        taResponse.setText(responseStr.toString());
+        taResponse.setCaretPosition(0);
+      }
+      
+      httpClient.getConnectionManager().shutdown();
+    }
+    catch (Exception ex) {
+      taResponse.setText(ex.getMessage() + "\n\n" + ex.getStackTrace());
+    }
+  }
+  
+  
+  public static void main(String[] args)
+  {
+    ApacheHttpClientUsageTest frame = new ApacheHttpClientUsageTest();
+    frame.setVisible(true);
+    frame.tfAddressBar.setCaretPosition(frame.tfAddressBar.getText().length());
+  }
+  
+}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/433612be/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ExampleActivityTest.java.bak
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diff --git a/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ExampleActivityTest.java.bak b/taverna-rest-activity/src/test/java/org/apache/taverna/activities/rest/ExampleActivityTest.java.bak
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+package org.apache.taverna.activities.rest;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.taverna.activities.testutils.ActivityInvoker;
+import org.apache.taverna.reference.ErrorDocument;
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.workflowmodel.OutputPort;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class ExampleActivityTest {
+
+	private RESTActivityConfigurationBean configBean;
+
+	private RESTActivity activity = new RESTActivity();
+
+	@Before
+	public void makeConfigBean() throws Exception {
+		configBean = new RESTActivityConfigurationBean();
+		configBean.setExampleString("something");
+		configBean
+				.setExampleUri(URI.create("http://localhost:8080/myEndPoint"));
+	}
+
+	@Test(expected = ActivityConfigurationException.class)
+	public void invalidConfiguration() throws ActivityConfigurationException {
+		RESTActivityConfigurationBean invalidBean = new RESTActivityConfigurationBean();
+		invalidBean.setExampleString("invalidExample");
+		// Should throw ActivityConfigurationException
+		activity.configure(invalidBean);
+	}
+
+	@Test
+	public void executeAsynch() throws Exception {
+		activity.configure(configBean);
+
+		Map<String, Object> inputs = new HashMap<String, Object>();
+		inputs.put("firstInput", "hello");
+
+		Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>();
+		expectedOutputTypes.put("simpleOutput", String.class);
+		expectedOutputTypes.put("moreOutputs", ExternalReferenceSPI.class);
+
+		Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
+				activity, inputs, expectedOutputTypes);
+
+		assertEquals("Unexpected outputs", 2, outputs.size());
+		assertEquals("da39a3ee5e6b4b0d3255bfef95601890afd80709", outputs.get("simpleOutput"));
+		ErrorDocument errorDoc = (ErrorDocument) outputs.get("moreOutputs");
+		assertEquals("java.lang.Exception: There are no more values",
+		             errorDoc.getExceptionMessage());
+
+	}
+	
+	
+	
+	@Test
+  public void checksumOfExtraData() throws Exception {
+    configBean.setExampleString("specialCase");
+	  activity.configure(configBean);
+
+    Map<String, Object> inputs = new HashMap<String, Object>();
+    inputs.put("firstInput", "hello");
+    inputs.put("extraData", Arrays.asList("Test1".getBytes("utf8"),
+        "Test2".getBytes("utf8")));
+
+
+    Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>();
+    expectedOutputTypes.put("simpleOutput", String.class);
+    expectedOutputTypes.put("moreOutputs", ExternalReferenceSPI.class);
+    expectedOutputTypes.put("report", String.class);
+
+
+    Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
+        activity, inputs, expectedOutputTypes);
+
+    assertEquals("Unexpected outputs", 3, outputs.size());
+    assertEquals("35bceb434ff8e69fb89b829e461c921a28b423b3", outputs.get("simpleOutput"));
+    ErrorDocument errorDoc = (ErrorDocument) outputs.get("moreOutputs");
+    assertEquals("java.lang.Exception: There are no more values",
+                 errorDoc.getExceptionMessage());
+
+  }
+	
+	
+
+	@Test
+	public void reConfiguredActivity() throws Exception {
+		assertEquals("Unexpected inputs", 0, activity.getInputPorts().size());
+		assertEquals("Unexpected outputs", 0, activity.getOutputPorts().size());
+
+		activity.configure(configBean);
+		assertEquals("Unexpected inputs", 1, activity.getInputPorts().size());
+		assertEquals("Unexpected outputs", 2, activity.getOutputPorts().size());
+
+		activity.configure(configBean);
+		// Should not change on reconfigure
+		assertEquals("Unexpected inputs", 1, activity.getInputPorts().size());
+		assertEquals("Unexpected outputs", 2, activity.getOutputPorts().size());
+	}
+
+	@Test
+	public void reConfiguredSpecialPorts() throws Exception {
+		activity.configure(configBean);
+
+		RESTActivityConfigurationBean specialBean = new RESTActivityConfigurationBean();
+		specialBean.setExampleString("specialCase");
+		specialBean.setExampleUri(URI
+				.create("http://localhost:8080/myEndPoint"));
+		activity.configure(specialBean);		
+		// Should now have added the optional ports
+		assertEquals("Unexpected inputs", 2, activity.getInputPorts().size());
+		assertEquals("Unexpected outputs", 3, activity.getOutputPorts().size());
+	}
+
+	@Test
+	public void configureActivity() throws Exception {
+		Set<String> expectedInputs = new HashSet<String>();
+		expectedInputs.add("firstInput");
+
+		Set<String> expectedOutputs = new HashSet<String>();
+		expectedOutputs.add("simpleOutput");
+		expectedOutputs.add("moreOutputs");
+
+		activity.configure(configBean);
+
+		Set<ActivityInputPort> inputPorts = activity.getInputPorts();
+		assertEquals(expectedInputs.size(), inputPorts.size());
+		for (ActivityInputPort inputPort : inputPorts) {
+			assertTrue("Wrong input : " + inputPort.getName(), expectedInputs
+					.remove(inputPort.getName()));
+		}
+
+		Set<OutputPort> outputPorts = activity.getOutputPorts();
+		assertEquals(expectedOutputs.size(), outputPorts.size());
+		for (OutputPort outputPort : outputPorts) {
+			assertTrue("Wrong output : " + outputPort.getName(),
+					expectedOutputs.remove(outputPort.getName()));
+		}
+	}
+}