[26/28] incubator-taverna-common-activities git commit: Temporarily empty repository

[st...@apache.org]

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
deleted file mode 100755
index 3541b8f..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
+++ /dev/null
@@ -1,563 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- *  written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- *  University of Luebeck, Institute for Neuro- and Bioinformatics
- *  University of Luebeck, Institute for Dermatolgy
- *
- *  This package 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 3 of the License, or
- *  (at your option) any later version.
- *
- *  This package 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 package; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.local;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.Reader;
-import java.io.UnsupportedEncodingException;
-import java.io.Writer;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-
-import net.sf.taverna.t2.reference.AbstractExternalReference;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.Identified;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.impl.external.file.FileReference;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrl;
-
-/**
- * The job is executed locally, i.e. not via the grid.
- * @author Hajo Krabbenhoeft
- */
-public class LocalUseCaseInvocation extends UseCaseInvocation {
-
-	private static Logger logger = Logger.getLogger(LocalUseCaseInvocation.class);
-
-	private final File tempDir;
-	
-	public static String LOCAL_USE_CASE_INVOCATION_TYPE = "789663B8-DA91-428A-9F7D-B3F3DA185FD4";
-	
-	private Process running;
-
-	private final String shellPrefix;
-
-	private final String linkCommand;
-
-	private Reader stdInReader = null;
-	
-	private static Map<String, Set<String>> runIdToTempDir = Collections.synchronizedMap(new HashMap<String, Set<String>> ());
-	
-	private static String LOCAL_INVOCATION_FILE = "localInvocations";
-
-	public LocalUseCaseInvocation(UseCaseDescription desc, boolean retrieveData, String mainTempDirectory, String shellPrefix, String linkCommand) throws IOException {
-
-		usecase = desc;
-		setRetrieveData(retrieveData);
-		this.shellPrefix = shellPrefix;
-		this.linkCommand = linkCommand;
-		
-		if (mainTempDirectory != null) {
-		
-			File mainTempDir = new File(mainTempDirectory);
-
-			tempDir = File.createTempFile("usecase", "dir", mainTempDir);
-		} else {
-			tempDir = File.createTempFile("usecase", "dir");
-		}
-		tempDir.delete();
-		tempDir.mkdir();
-		logger.info("mainTempDirectory is " + mainTempDirectory);
-		logger.info("Using tempDir " + tempDir.getAbsolutePath());
-
-	}
-
-	void recDel(File c) {
-		File[] files = c.listFiles();
-		if (files != null) {
-			for (File cc : files)
-				recDel(cc);
-		}
-		c.delete();
-	}
-	
-	private String setOneBinaryInput(ReferenceService referenceService,
-			T2Reference t2Reference, ScriptInput input, String targetSuffix)
-			throws InvocationException {
-
-		if (input.isFile() || input.isTempFile()) {
-			// Try to get it as a file
-			String target = tempDir.getAbsolutePath() + "/" + targetSuffix;
-			FileReference fileRef = getAsFileReference(referenceService,
-					t2Reference);
-			if (fileRef != null) {
-
-				if (!input.isForceCopy()) {
-					if (linkCommand != null) {
-						String source = fileRef.getFile().getAbsolutePath();
-						String actualLinkCommand = getActualOsCommand(
-								linkCommand, source, targetSuffix, target);
-						logger.info("Link command is " + actualLinkCommand);
-						String[] splitCmds = actualLinkCommand.split(" ");
-						ProcessBuilder builder = new ProcessBuilder(splitCmds);
-						builder.directory(tempDir);
-						try {
-							int code = builder.start().waitFor();
-							if (code == 0) {
-								return target;
-							} else {
-								logger.error("Link command gave errorcode: "
-										+ code);
-							}
-
-						} catch (InterruptedException e) {
-							// go through
-						} catch (IOException e) {
-							// go through
-						}
-
-					}
-				}
-			}
-
-			InputStream is = null;
-			OutputStream os = null;
-			is = getAsStream(referenceService, t2Reference);
-
-			try {
-				os = new FileOutputStream(target);
-			} catch (FileNotFoundException e) {
-				throw new InvocationException(e);
-			}
-
-			try {
-				IOUtils.copyLarge(is, os);
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-			try {
-				is.close();
-				os.close();
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-			return target;
-		} else {
-			String value = (String) referenceService.renderIdentifier(
-					t2Reference, String.class, this.getContext());
-			return value;
-		}
-	}
-	
-	@Override
-	public String setOneInput(ReferenceService referenceService,
-			T2Reference t2Reference, ScriptInput input)
-			throws InvocationException {
-
-		if (input.getCharsetName() == null) {
-			input.setCharsetName(Charset.defaultCharset().name());
-		}
-		String target = null;
-		String targetSuffix = null;
-		if (input.isFile()) {
-			targetSuffix = input.getTag();
-		} else if (input.isTempFile()) {
-			targetSuffix = "tempfile." + (nTempFiles++) + ".tmp";
-		}
-
-		if (input.isBinary()) {
-			return setOneBinaryInput(referenceService, t2Reference, input,
-					targetSuffix);
-		}
-
-		logger.info("Target is " + target);
-		if (input.isFile() || input.isTempFile()) {
-			target = tempDir.getAbsolutePath() + "/" + targetSuffix;
-			// Try to get it as a file
-			Reader r;
-			Writer w;
-			FileReference fileRef = getAsFileReference(referenceService,
-					t2Reference);
-			if (fileRef != null) {
-
-				if (!input.isForceCopy()) {
-					if (linkCommand != null) {
-						String source = fileRef.getFile().getAbsolutePath();
-						String actualLinkCommand = getActualOsCommand(
-								linkCommand, source, targetSuffix, target);
-						logger.info("Link command is " + actualLinkCommand);
-						String[] splitCmds = actualLinkCommand.split(" ");
-						ProcessBuilder builder = new ProcessBuilder(splitCmds);
-						builder.directory(tempDir);
-						try {
-							int code = builder.start().waitFor();
-							if (code == 0) {
-								return target;
-							} else {
-								logger.error("Link command gave errorcode: "
-										+ code);
-							}
-
-						} catch (InterruptedException e) {
-							// go through
-						} catch (IOException e) {
-							// go through
-						}
-
-					}
-				}
-
-				if (fileRef.getDataNature().equals(ReferencedDataNature.TEXT)) {
-					r = new InputStreamReader(fileRef.openStream(this
-							.getContext()), Charset.forName(fileRef
-							.getCharset()));
-				} else {
-					try {
-						r = new FileReader(fileRef.getFile());
-					} catch (FileNotFoundException e) {
-						throw new InvocationException(e);
-					}
-				}
-			} else {
-				r = new InputStreamReader(getAsStream(referenceService,
-						t2Reference));
-			}
-			try {
-				w = new OutputStreamWriter(new FileOutputStream(target), input
-						.getCharsetName());
-			} catch (UnsupportedEncodingException e) {
-				throw new InvocationException(e);
-			} catch (FileNotFoundException e) {
-				throw new InvocationException(e);
-			}
-			try {
-				IOUtils.copyLarge(r, w);
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-			try {
-				r.close();
-				w.close();
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-			return target;
-		} else {
-			String value = (String) referenceService.renderIdentifier(
-					t2Reference, String.class, this.getContext());
-			return value;
-		}
-	}
-	
-	private void forgetRun() {
-		Set<String> directories = runIdToTempDir.get(getRunId());
-		try {
-			directories.remove(tempDir.getCanonicalPath());
-		} catch (IOException e) {
-			logger.error(e);
-		}
-	}
-
-	private static void deleteDirectory(String location) {
-		try {
-			FileUtils.deleteDirectory(new File(location));
-		} catch (IOException e) {
-			logger.error("Problem deleting " + location, e);
-		}
-	}
-	
-	public static void cleanup(String runId) {
-		Set<String> tempDirectories = runIdToTempDir.get(runId);
-		if (tempDirectories != null) {
-			for (String tempDir : tempDirectories) {
-				deleteDirectory(tempDir);
-			}
-			runIdToTempDir.remove(runId);
-		}
-	}
-	
-	@Override
-	protected void submit_generate_job_inner() throws InvocationException {
-		tags.put("uniqueID", "" + getSubmissionID());
-		String command = usecase.getCommand();
-		for (String cur : tags.keySet()) {
-		    command = command.replaceAll("\\Q%%" + cur + "%%\\E", Matcher.quoteReplacement(tags.get(cur)));
-		}
-
-		List<String> cmds = new ArrayList<String>();
-		if ((shellPrefix != null) && !shellPrefix.isEmpty()) {
-			String[] prefixCmds = shellPrefix.split(" ");
-			for (int i = 0; i < prefixCmds.length; i++) {
-				cmds.add(prefixCmds[i]);
-			}
-			cmds.add(command);
-		} else {
-			String[] splitCmds = command.split(" ");
-			for (int i = 0; i < splitCmds.length; i++) {
-				cmds.add(splitCmds[i]);
-			}
-		}
-	
-		ProcessBuilder builder = new ProcessBuilder(cmds);
-		builder.directory(tempDir);
-
-		for (int i = 0; i < cmds.size(); i++) {
-			logger.info("cmds[" + i + "] = " + cmds.get(i));
-		}
-		logger.info("Command is " + command + " in directory " + tempDir);
-		try {
-			running = builder.start();
-			if (stdInReader != null) {
-				BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(running.getOutputStream()));
-				IOUtils.copyLarge(stdInReader, writer);
-				writer.close();
-			}
-		} catch (IOException e) {
-			throw new InvocationException(e);
-		}
-	}
-
-	private void copy_stream(InputStream read, OutputStream write) throws IOException {
-		int a = read.available();
-		if (a > 0) {
-			byte[] buf = new byte[a];
-			read.read(buf);
-			write.write(buf);
-		}
-	}
-
-	@Override
-	public HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException {
-		ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
-		ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
-		while (true) {
-			try {
-				copy_stream(running.getInputStream(), stdout_buf);
-				copy_stream(running.getErrorStream(), stderr_buf);
-			} catch (IOException e1) {
-				throw new InvocationException(e1);
-			}
-			try {
-				int exitcode = running.exitValue();
-				if (!usecase.getValidReturnCodes().contains(exitcode)) {
-					try {
-						throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString("US-ASCII"));
-					} catch (UnsupportedEncodingException e) {
-						throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString());
-					}
-				}
-				else
-					break;
-			} catch (IllegalThreadStateException e) {
-
-				try {
-					Thread.sleep(100);
-				} catch (InterruptedException e1) {
-					throw new InvocationException(e);
-				}
-
-			}
-		}
-
-		HashMap<String, Object> results = new HashMap<String, Object>();
-			results.put("STDOUT", stdout_buf.toByteArray());
-			results.put("STDERR", stderr_buf.toByteArray());
-
-		for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs().entrySet()) {
-			ScriptOutput scriptOutput = cur.getValue();
-			File result = new File(tempDir.getAbsoluteFile() + "/" + cur.getValue().getPath());
-			if (result.exists()) {
-				AbstractExternalReference ref;
-				if (isRetrieveData()) {
-					FileInputStream is;
-					try {
-						is = new FileInputStream(result);
-					} catch (FileNotFoundException e) {
-						throw new InvocationException(e);
-					}
-					if (scriptOutput.isBinary()) {
-						ref = inlineByteArrayReferenceBuilder.createReference(is, null);
-					} else {
-						ref = inlineStringReferenceBuilder.createReference(is, null);
-					}
-					try {
-						is.close();
-					} catch (IOException e) {
-						throw new InvocationException(e);
-					}
-				}
-				else {
-					ref = new FileReference(result);
-					if (scriptOutput.isBinary()) {
-						((FileReference) ref)
-								.setDataNature(ReferencedDataNature.BINARY);
-					} else {
-						((FileReference) ref)
-								.setDataNature(ReferencedDataNature.TEXT);
-						((FileReference) ref).setCharset("UTF-8");
-					}
-				}
-				results.put(cur.getKey(), ref);
-			} else {
-				ErrorDocument ed = referenceService.getErrorDocumentService().registerError("No result for " + cur.getKey(), 0, getContext());
-				results.put(cur.getKey(), ed);
-			}
-		}
-		
-		if (isRetrieveData()) {
-			forgetRun();
-			try {
-				deleteDirectory(tempDir.getCanonicalPath());
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-		}
-
-		return results;
-	}
-
-	private FileReference getAsFileReference(ReferenceService referenceService, T2Reference t2Reference) {
-		Identified identified = referenceService.resolveIdentifier(t2Reference, null, null);
-		if (identified instanceof ReferenceSet) {
-			for (ExternalReferenceSPI ref : ((ReferenceSet) identified).getExternalReferences()) {
-				if (ref instanceof FileReference) {
-					return (FileReference) ref;
-				}
-			}
-		}
-		return null;
-	}
-
-	@Override
-	public void setStdIn(ReferenceService referenceService,
-			T2Reference t2Reference) {
-		stdInReader = new BufferedReader(new InputStreamReader(getAsStream(referenceService, t2Reference)));
-	}
-
-	@Override
-	public void rememberRun(String runId) {
-		this.setRunId(runId);
-		Set<String> directories = runIdToTempDir.get(runId);
-		if (directories == null) {
-			directories = Collections.synchronizedSet(new HashSet<String> ());
-			runIdToTempDir.put(runId, directories);
-		}
-		try {
-			directories.add(tempDir.getCanonicalPath());
-		} catch (IOException e) {
-			logger.error("Unable to record temporary directory: " + tempDir, e);
-		}
-	}
-
-	public static void load(File directory) {
-		File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
-		if (!invocationsFile.exists()) {
-			return;
-		}
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new FileReader(invocationsFile));
-			String line = reader.readLine();
-			while (line != null) {
-				String[] parts = line.split(" ");
-				if (parts.length != 2) {
-					break;
-				}
-				String runId = parts[0];
-				String tempDirString = parts[1];
-				Set<String> tempDirs = runIdToTempDir.get(runId);
-				if (tempDirs == null) {
-					tempDirs = new HashSet<String>();
-					runIdToTempDir.put(runId, tempDirs);
-				}
-				tempDirs.add(tempDirString);
-				line = reader.readLine();
-			}
-		} catch (FileNotFoundException e) {
-			logger.error(e);
-		} catch (IOException e) {
-			logger.error(e);
-		} finally {
-			if (reader != null) {
-				try {
-					reader.close();
-				} catch (IOException e) {
-					logger.error(e);
-				}
-			}
-		}
-	}
-
-	public static void persist(File directory) {
-		File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
-		BufferedWriter writer = null;
-		try {
-			writer = new BufferedWriter(new FileWriter(invocationsFile));
-			for (String runId : runIdToTempDir.keySet()) {
-				for (String tempDir : runIdToTempDir.get(runId)) {
-					writer.write(runId);
-					writer.write(" ");
-					writer.write(tempDir);
-					writer.newLine();
-				}
-			}
-		} catch (IOException e) {
-			logger.error(e);
-		} finally {
-			if (writer != null) {
-				try {
-					writer.close();
-				} catch (IOException e) {
-					logger.error(e);
-				}
-			}
-		}
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
deleted file mode 100644
index 60d3bec..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- *  written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- *  University of Luebeck, Institute for Neuro- and Bioinformatics
- *  University of Luebeck, Institute for Dermatolgy
- *
- *  This package 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 3 of the License, or
- *  (at your option) any later version.
- *
- *  This package 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 package; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.UIKeyboardInteractive;
-import com.jcraft.jsch.UserInfo;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-
-final class SshAutoLoginTrustEveryone implements UserInfo, UIKeyboardInteractive {
-	
-	private static Logger logger = Logger.getLogger(SshAutoLoginTrustEveryone.class);
-
-	private final AskUserForPw askUserForPw;
-
-	public SshAutoLoginTrustEveryone(AskUserForPw askUserForPw) {
-		super();
-		this.askUserForPw = askUserForPw;
-	}
-
-	public void showMessage(String arg0) {
-		logger.info(arg0);
-	}
-
-	public boolean promptYesNo(String arg0) {
-		if (arg0.startsWith("The authenticity of host"))
-			return true;
-		return false;
-	}
-
-	public boolean promptPassword(String arg0) {
-		return true;
-	}
-
-	public boolean promptPassphrase(String arg0) {
-		return true;
-	}
-
-	public String getPassword() {
-		return askUserForPw.getPassword();
-	}
-
-	public String getPassphrase() {
-		return askUserForPw.getPassphrase();
-	}
-
-	public String[] promptKeyboardInteractive(String destination, String name, String instruction, String[] prompt, boolean[] echo) {
-		if (prompt.length >= 1 && prompt[0].toLowerCase().startsWith("password"))
-			return new String[] { askUserForPw.getPassword() };
-		return null;
-	}
-}
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
deleted file mode 100644
index 92b065e..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
+++ /dev/null
@@ -1,159 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- *  written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- *  University of Luebeck, Institute for Neuro- and Bioinformatics
- *  University of Luebeck, Institute for Dermatolgy
- *
- *  This package 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 3 of the License, or
- *  (at your option) any later version.
- *
- *  This package 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 package; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
-
-public class SshNode {
-	
-    public static String DEFAULT_HOST = "127.0.0.1";
-    public static int DEFAULT_PORT = 22;
-    public static String DEFAULT_DIRECTORY = "/tmp/";
-
-    private String host = DEFAULT_HOST;
-    private int port = DEFAULT_PORT;
-    private String directory = DEFAULT_DIRECTORY;
-	
-	private SshUrl url;
-	
-	private String linkCommand = null;
-	private String copyCommand = null;
-	private boolean retrieveData = false;
-
-	/**
-	 * 
-	 */
-	SshNode() {
-		super();
-		linkCommand = InvocationMechanism.UNIX_LINK;
-		copyCommand = InvocationMechanism.UNIX_COPY;
-		
-	}
-	/**
-	 * @param directory the directory to set
-	 */
-	public void setDirectory(String directory) {
-		if ((directory != null) && !directory.isEmpty()) {
-			if (!directory.endsWith("/")) {
-				directory = directory + "/";
-			}
-			this.directory = directory;
-		}
-	}
-
-	/**
-	 * @return the directory
-	 */
-	public String getDirectory() {
-		return directory;
-	}
-
-	/**
-	 * @param host the host to set
-	 */
-	public void setHost(String host) {
-		this.host = host;
-	}
-
-	/**
-	 * @return the host
-	 */
-	public String getHost() {
-		return host;
-	}
-
-	/**
-	 * @param port the port to set
-	 */
-	public void setPort(int port) {
-		this.port = port;
-	}
-
-	/**
-	 * @return the port
-	 */
-	public int getPort() {
-		return port;
-	}
-	
-	SshUrl getUrl() {
-		if (url == null) {
-			url = new SshUrl(this);
-		}
-		return url;
-	}
-	
-	public int hashCode() {
-		return getUrl().hashCode();	
-	}
-
-	public boolean equals(Object obj) {
-		if ((obj == null) || !(obj instanceof SshNode)) {
-			return false;
-		}
-		return (this.hashCode() == obj.hashCode());
-	}
-	/**
-	 * @return the linkCommand
-	 */
-	public String getLinkCommand() {
-		return linkCommand;
-	}
-	/**
-	 * @param linkCommand the linkCommand to set
-	 */
-	public void setLinkCommand(String linkCommand) {
-		if ((linkCommand != null) && linkCommand.isEmpty()) {
-			this.linkCommand = null;
-		} else {
-			this.linkCommand = linkCommand;
-		}	}
-	/**
-	 * @return the copyCommand
-	 */
-	public String getCopyCommand() {
-		return copyCommand;
-	}
-	/**
-	 * @param copyCommand the copyCommand to set
-	 */
-	public void setCopyCommand(String copyCommand) {
-		if ((copyCommand != null) && copyCommand.isEmpty()) {
-			this.copyCommand = null;
-		} else {
-			this.copyCommand = copyCommand;
-		}
-	}
-	
-	/**
-	 * @return the retrieveData
-	 */
-	public boolean isRetrieveData() {
-		return retrieveData;
-	}
-	/**
-	 * @param retrieveData the retrieveData to set
-	 */
-	public void setRetrieveData(boolean retrieveData) {
-		this.retrieveData = retrieveData;
-	}
-	
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
deleted file mode 100644
index 2d8f4bb..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
+++ /dev/null
@@ -1,56 +0,0 @@
-/**
- * 
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-/**
- * @author alanrw
- *
- */
-public class SshNodeFactory {
-	
-	private Map<String, SshNode> nodeMap = Collections.synchronizedMap(new HashMap<String, SshNode> ());
-	
-	private static SshNodeFactory INSTANCE = new SshNodeFactory();
-	
-	private SshNode defaultNode;
-	
-	private SshNodeFactory() {
-		defaultNode = getSshNode(SshNode.DEFAULT_HOST, SshNode.DEFAULT_PORT, SshNode.DEFAULT_DIRECTORY);
-	}
-
-	public SshNode getDefaultNode() {
-		return defaultNode;
-	}
-
-	public static SshNodeFactory getInstance() {
-		return INSTANCE;
-	}
-	
-	public SshNode getSshNode(String host, int port, String directory) {
-		String url = makeUrl(host, port, directory);
-		if (nodeMap.containsKey(url)) {
-			return nodeMap.get(url);
-		}
-		else {
-			SshNode newNode = new SshNode();
-			newNode.setHost(host);
-			newNode.setPort(port);
-			newNode.setDirectory(directory);
-			nodeMap.put(url, newNode);
-			return newNode;
-		}
-	}
-	
-	public boolean containsSshNode(String host, int port, String directory) {
-		return nodeMap.containsKey(makeUrl(host, port, directory));
-	}
-	
-	public static String makeUrl(String host, int port, String directory) {
-		return ("ssh://" + host + ":" + port + directory);
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
deleted file mode 100755
index c6a5851..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
+++ /dev/null
@@ -1,148 +0,0 @@
-/**
- * 
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-
-import de.uni_luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-
-/**
- * @author alanrw
- *
- */
-public class SshPool {
-	
-	private static Logger logger = Logger.getLogger(SshPool.class);
-
-	
-	private static JSch jsch = new JSch();
-	
-    private static int CONNECT_TIMEOUT = 10000; // milliseconds
-
-	private static Map<SshNode, Session> sessionMap = Collections.synchronizedMap(new HashMap<SshNode, Session> ());
-	private static Map<Session, ChannelSftp> sftpGetMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
-	private static Map<Session, ChannelSftp> sftpPutMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
-	
-	public static Session getSshSession(final SshUrl sshUrl, final AskUserForPw askUserForPw) throws JSchException {
-		return getSshSession(sshUrl.getSshNode(), askUserForPw);
-	}
-	
-	public static synchronized Session getSshSession(final SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
-
-		Session s = sessionMap.get(sshNode);
-		if ((s != null) && s.isConnected()) {
-			logger.info("Reusing session");
-			return s;
-		}
-		if (s != null) {
-			logger.info("Session was not connected");
-		}
-		if (s == null) {
-			logger.info("No session found for " + sshNode.toString());
-		}
-
-		if (askUserForPw.getKeyfile().length() > 0) {
-			jsch.addIdentity(askUserForPw.getKeyfile());
-		}
-		logger.info("Using host is " + sshNode.getHost() + " and port " + sshNode.getPort());
-		Session sshSession = jsch.getSession(askUserForPw.getUsername(), sshNode.getHost(), sshNode.getPort());
-		sshSession.setUserInfo(new SshAutoLoginTrustEveryone(askUserForPw));
-		sshSession.connect(CONNECT_TIMEOUT);
-		
-		askUserForPw.authenticationSucceeded();
-		sessionMap.put(sshNode, sshSession);
-		if (sshSession == null) {
-			logger.error("Returning a null session");
-		}
-		return sshSession;
-	}
-	
-	public static ChannelSftp getSftpGetChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
-		return getSftpGetChannel(getSshSession(sshNode, askUserForPw));
-	}
-
-	private static synchronized ChannelSftp getSftpGetChannel(Session session) throws JSchException {
-		ChannelSftp result = sftpGetMap.get(session);
-		if (!session.isConnected()) {
-			logger.warn("Session is not connected");
-		}
-		if (result == null) {
-			logger.info("Creating new sftp channel");
-			result = (ChannelSftp) session.openChannel("sftp");
-			sftpGetMap.put(session, result);
-		}
-		else {
-			logger.info("Reusing sftp channel");			
-		}
-		if (!result.isConnected()) {
-			logger.info("Connecting");
-			result.connect();
-		} else {
-			logger.info("Already connected");
-		}
-		return result;
-	}
-	
-	public static ChannelSftp getSftpPutChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
-		return getSftpPutChannel(getSshSession(sshNode, askUserForPw));
-	}
-
-	private static synchronized ChannelSftp getSftpPutChannel(Session session) throws JSchException {
-	    ChannelSftp result = null;
-	    synchronized(sftpPutMap) {
-		result = sftpPutMap.get(session);
-		if (!session.isConnected()) {
-			logger.info("Session is not connected");
-		}
-		if (result == null) {
-			logger.info("Creating new sftp channel");
-			result = (ChannelSftp) session.openChannel("sftp");
-			sftpPutMap.put(session, result);
-		}
-		else {
-			logger.info("Reusing sftp channel");			
-		}
-	    }
-	    if (!result.isConnected()) {
-		logger.info("Connecting");
-		result.connect(CONNECT_TIMEOUT);
-	    } else {
-		logger.info("Already connected");
-	    }
-	    return result;
-	}
-	
-	public static synchronized ChannelExec openExecChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
-		return (ChannelExec) getSshSession(sshNode, askUserForPw).openChannel("exec");
-	}
-
-	private static synchronized ChannelExec openExecChannel(Session session) throws JSchException {
-		return (ChannelExec) session.openChannel("exec");
-	}
-
-}
-
-
-
-
-
-
-
-
-
-
-
-
-

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
deleted file mode 100644
index 0431153..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
+++ /dev/null
@@ -1,208 +0,0 @@
-/**
- *
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.io.InputStream;
-
-import net.sf.taverna.t2.activities.externaltool.RetrieveLoginFromTaverna;
-import net.sf.taverna.t2.reference.AbstractExternalReference;
-import net.sf.taverna.t2.reference.DereferenceException;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceContext;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.SftpException;
-
-/**
- * @author alanrw
- *
- */
-public class SshReference extends AbstractExternalReference implements
-	ExternalReferenceSPI {
-
-	private static Logger logger = Logger.getLogger(SshReference.class);
-
-
-	private String host = "127.0.0.1";
-	private int port = 22;
-	private String directory = "/tmp/";
-	private String subDirectory;
-	private String fileName;
-
-	private CredentialManager credentialManager;
-
-	private int dataNatureInteger = ReferencedDataNature.UNKNOWN.ordinal();
-	private String charset = "UTF-8";
-	
-	public SshReference() {
-		super();
-	}
-
-	public SshReference(SshUrl url) {
-		super();
-		this.host = url.getSshNode().getHost();
-		this.port = url.getSshNode().getPort();
-		this.directory = url.getSshNode().getDirectory();
-		this.subDirectory = url.getSubDirectory();
-		this.fileName = url.getFileName();
-		this.setDataNature(url.getDataNature());
-		this.setCharset(url.getCharset());
-	}
-
-	/* (non-Javadoc)
-	 * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#getApproximateSizeInBytes()
-	 */
-	@Override
-	public Long getApproximateSizeInBytes() {
-		return 10000L;
-	}
-
-	/* (non-Javadoc)
-	 * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#openStream(net.sf.taverna.t2.reference.ReferenceContext)
-	 */
-	@Override
-	public InputStream openStream(ReferenceContext context)
-			throws DereferenceException {
-		try {
-			SshNode node = SshNodeFactory.getInstance().getSshNode(this.getHost(), this.getPort(), this.getDirectory());
-			String fullPath = getDirectory() +  getSubDirectory() + "/" + getFileName();
-			ChannelSftp channel = SshPool.getSftpGetChannel(node, new RetrieveLoginFromTaverna(new SshUrl(node).toString(), credentialManager));
-			logger.info("Opening stream on " + fullPath);
-			return (channel.get(fullPath));
-		} catch (JSchException e) {
-			//TODO
-			logger.error(e);
-		} catch (SftpException e) {
-			// TODO Auto-generated catch block
-			logger.error(e);
-		}
-		return null;
-	}
-
-	/**
-	 * @return the host
-	 */
-	public String getHost() {
-		return host;
-	}
-
-	/**
-	 * @param host the host to set
-	 */
-	public void setHost(String host) {
-		this.host = host;
-	}
-
-	/**
-	 * @return the port
-	 */
-	public int getPort() {
-		return port;
-	}
-
-	/**
-	 * @param port the port to set
-	 */
-	public void setPort(int port) {
-		this.port = port;
-	}
-
-	/**
-	 * @return the directory
-	 */
-	public String getDirectory() {
-		return directory;
-	}
-
-	/**
-	 * @param directory the directory to set
-	 */
-	public void setDirectory(String directory) {
-		this.directory = directory;
-	}
-
-	/**
-	 * @return the subDirectory
-	 */
-	public String getSubDirectory() {
-		return subDirectory;
-	}
-
-	/**
-	 * @param subDirectory the subDirectory to set
-	 */
-	public void setSubDirectory(String subDirectory) {
-		this.subDirectory = subDirectory;
-	}
-
-	/**
-	 * @return the fileName
-	 */
-	public String getFileName() {
-		return fileName;
-	}
-
-	/**
-	 * @param fileName the fileName to set
-	 */
-	public void setFileName(String fileName) {
-		this.fileName = fileName;
-	}
-
-	public String getFullPath() {
-		return getDirectory() + "/" + getSubDirectory() + "/" + getFileName();
-	}
-	
-	public ReferencedDataNature getDataNature() {
-		return ReferencedDataNature.values()[dataNatureInteger];
-	}
-
-	public void setDataNature(ReferencedDataNature dataNature) {
-		this.dataNatureInteger = dataNature.ordinal();
-	}
-
-	public String getCharset() {
-		return charset;
-	}
-
-	public void setCredentialManager(CredentialManager credentialManager) {
-		this.credentialManager = credentialManager;
-	}
-
-	public void setCharset(String charset) {
-		this.charset = charset;
-	}
-
-	/**
-	 * @return the dataNatureInteger
-	 */
-	public int getDataNatureInteger() {
-		return dataNatureInteger;
-	}
-
-	/**
-	 * @param dataNatureInteger the dataNatureInteger to set
-	 */
-	public void setDataNatureInteger(int dataNatureInteger) {
-		this.dataNatureInteger = dataNatureInteger;
-	}
-	
-	public SshReference clone() {
-		SshReference result = new SshReference();
-		result.setHost(this.getHost());
-		result.setPort(this.getPort());
-		result.setDirectory(this.getDirectory());
-		result.setSubDirectory(this.getSubDirectory());
-		result.setFileName(this.getFileName());
-		result.setDataNature(this.getDataNature());
-		result.setCharset(this.getCharset());
-		return result;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
deleted file mode 100644
index eb5f269..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
+++ /dev/null
@@ -1,153 +0,0 @@
-/**
- * 
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-
-/**
- * @author alanrw
- *
- */
-public class SshUrl {
-	
-	private SshNode sshNode;
-	private String subDirectory;
-	private String fileName;
-
-	private ReferencedDataNature dataNature = ReferencedDataNature.UNKNOWN;
-	private String charset = "UTF-8";
-	
-
-	public SshUrl(SshNode sshNode) {
-		this.setSshNode(sshNode);
-	}
-	
-
-	/**
-	 * @return the host
-	 */
-	public String getHost() {
-		return getSshNode().getHost();
-	}
-	/**
-	 * @param host the host to set
-	 */
-	public void setHost(String host) {
-		getSshNode().setHost(host);
-	}
-	/**
-	 * @return the port
-	 */
-	public int getPort() {
-		return getSshNode().getPort();
-	}
-	/**
-	 * @param port the port to set
-	 */
-	public void setPort(int port) {
-		getSshNode().setPort(port);
-	}
-	/**
-	 * @return the directory
-	 */
-	public String getDirectory() {
-		return getSshNode().getDirectory();
-	}
-	/**
-	 * @param directory the directory to set
-	 */
-	public void setDirectory(String directory) {
-		getSshNode().setDirectory(directory);
-	}
-	/**
-	 * @return the subDirectory
-	 */
-	public String getSubDirectory() {
-		return subDirectory;
-	}
-	/**
-	 * @param subDirectory the subDirectory to set
-	 */
-	public void setSubDirectory(String subDirectory) {
-		this.subDirectory = subDirectory;
-	}
-	/**
-	 * @return the fileName
-	 */
-	public String getFileName() {
-		return fileName;
-	}
-	/**
-	 * @param fileName the fileName to set
-	 */
-	public void setFileName(String fileName) {
-		this.fileName = fileName;
-	}
-	
-	public String toString() {
-		String result = SshNodeFactory.makeUrl(getHost(), getPort(), getDirectory());
-		if (getSubDirectory() != null) {
-			result += getSubDirectory();
-		}
-		if (getFileName() != null) {
-			result += "/" + getFileName();
-		}
-		return result;
-	}
-	
-	public int hashCode() {
-		return toString().hashCode();
-		
-	}
-	
-	public boolean equals(Object obj) {
-		if ((obj == null) || !(obj instanceof SshUrl)) {
-			return false;
-		}
-		return (this.hashCode() == obj.hashCode());
-	}
-	
-	public SshUrl getBaseUrl() {
-		SshUrl result = new SshUrl(this.getSshNode());
-		return result;
-	}
-
-
-	/**
-	 * @return the sshNode
-	 */
-	public SshNode getSshNode() {
-		return sshNode;
-	}
-
-
-	/**
-	 * @param sshNode the sshNode to set
-	 */
-	public void setSshNode(SshNode sshNode) {
-		this.sshNode = sshNode;
-	}
-	
-	public ReferencedDataNature getDataNature() {
-		return dataNature;
-	}
-
-
-	public void setDataNature(ReferencedDataNature dataNature) {
-		this.dataNature = dataNature;
-	}
-
-
-	public String getCharset() {
-		return charset;
-	}
-
-
-	public void setCharset(String charset) {
-		this.charset = charset;
-	}
-
-
-	
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
deleted file mode 100644
index 6a9b2dc..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/**
- *
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceContext;
-import net.sf.taverna.t2.reference.ValueToReferenceConversionException;
-import net.sf.taverna.t2.reference.ValueToReferenceConverterSPI;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-
-/**
- * @author alanrw
- *
- */
-public class SshUrlToSshReference implements ValueToReferenceConverterSPI {
-
-	private CredentialManager credentialManager;
-
-	/* (non-Javadoc)
-	 * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#canConvert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
-	 */
-	@Override
-	public boolean canConvert(Object o, ReferenceContext context) {
-		return (o instanceof SshUrl);
-	}
-
-	/* (non-Javadoc)
-	 * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#convert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
-	 */
-	@Override
-	public ExternalReferenceSPI convert(Object o, ReferenceContext context)
-			throws ValueToReferenceConversionException {
-		SshReference result = new SshReference((SshUrl) o);
-		result.setCredentialManager(credentialManager);
-		return result;
-	}
-
-	public void setCredentialManager(CredentialManager credentialManager) {
-		this.credentialManager = credentialManager;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
deleted file mode 100755
index 29e475d..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
+++ /dev/null
@@ -1,563 +0,0 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- *  written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- *  University of Luebeck, Institute for Neuro- and Bioinformatics
- *  University of Luebeck, Institute for Dermatolgy
- *
- *  This package 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 3 of the License, or
- *  (at your option) any later version.
- *
- *  This package 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 package; if not, write to the Free Software
- *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-import java.util.Set;
-import java.util.Vector;
-import java.util.regex.Matcher;
-
-import net.sf.taverna.t2.activities.externaltool.RetrieveLoginFromTaverna;
-import net.sf.taverna.t2.reference.AbstractExternalReference;
-import net.sf.taverna.t2.reference.ErrorDocument;
-import net.sf.taverna.t2.reference.ErrorDocumentServiceException;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.Identified;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceSet;
-import net.sf.taverna.t2.reference.ReferencedDataNature;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.SftpException;
-import com.jcraft.jsch.ChannelSftp.LsEntry;
-
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-
-/**
- * The job is executed by connecting to a worker pc using ssh, i.e. not via the
- * grid.
- * 
- * @author Hajo Krabbenhoeft
- */
-public class SshUseCaseInvocation extends UseCaseInvocation {
-
-	private static Logger logger = Logger.getLogger(SshUseCaseInvocation.class);
-
-	private SshUrl location = null;
-
-	private InputStream stdInputStream = null;
-
-	public static final String SSH_USE_CASE_INVOCATION_TYPE = "D0A4CDEB-DD10-4A8E-A49C-8871003083D8";
-	private String tmpname;
-	private final SshNode workerNode;
-	private final AskUserForPw askUserForPw;
-
-	private ChannelExec running;
-
-	private List<String> precedingCommands = new ArrayList<String>();
-
-	private final ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
-	private final ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
-
-	private static Map<String, Object> nodeLock = Collections
-			.synchronizedMap(new HashMap<String, Object>());
-
-	private static Map<String, Set<SshUrl>> runIdToTempDir = Collections
-			.synchronizedMap(new HashMap<String, Set<SshUrl>>());
-
-	private static String SSH_INVOCATION_FILE = "sshInvocations";
-
-	private final CredentialManager credentialManager;
-
-	public static String test(final SshNode workerNode,
-			final AskUserForPw askUserForPw) {
-		try {
-			Session sshSession = SshPool
-					.getSshSession(workerNode, askUserForPw);
-
-			ChannelSftp sftpTest = (ChannelSftp) sshSession.openChannel("sftp");
-			sftpTest.connect();
-			sftpTest.cd(workerNode.getDirectory());
-			sftpTest.disconnect();
-			sshSession.disconnect();
-		} catch (JSchException e) {
-			return e.toString();
-		} catch (SftpException e) {
-			return e.toString();
-		}
-		return null;
-	}
-
-	public SshUseCaseInvocation(UseCaseDescription desc, SshNode workerNodeA,
-			AskUserForPw askUserForPwA, CredentialManager credentialManager)
-			throws JSchException, SftpException {
-		this.workerNode = workerNodeA;
-		this.credentialManager = credentialManager;
-
-		setRetrieveData(workerNodeA.isRetrieveData());
-		this.askUserForPw = askUserForPwA;
-		usecase = desc;
-
-		ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode, askUserForPw);
-		synchronized (getNodeLock(workerNode)) {
-
-			logger.info("Changing remote directory to "
-					+ workerNode.getDirectory());
-			sftp.cd(workerNode.getDirectory());
-			Random rnd = new Random();
-			while (true) {
-				tmpname = "usecase" + rnd.nextLong();
-				try {
-					sftp.lstat(workerNode.getDirectory() + tmpname);
-					continue;
-				} catch (Exception e) {
-					// file seems to not exist :)
-				}
-				sftp.mkdir(workerNode.getDirectory() + tmpname);
-				sftp.cd(workerNode.getDirectory() + tmpname);
-				break;
-			}
-		}
-	}
-
-	private static void recursiveDelete(ChannelSftp sftp, String path)
-			throws SftpException, JSchException {
-		Vector<?> entries = sftp.ls(path);
-		for (Object object : entries) {
-			LsEntry entry = (LsEntry) object;
-			if (entry.getFilename().equals(".")
-					|| entry.getFilename().equals("..")) {
-				continue;
-			}
-			if (entry.getAttrs().isDir()) {
-				recursiveDelete(sftp, path + entry.getFilename() + "/");
-			} else {
-				sftp.rm(path + entry.getFilename());
-			}
-		}
-		sftp.rmdir(path);
-	}
-
-	private static void deleteDirectory(SshUrl directory,
-			CredentialManager credentialManager) throws InvocationException {
-		URI uri;
-		try {
-			uri = new URI(directory.toString());
-
-			ChannelSftp sftp;
-			SshNode workerNode;
-			String fullPath = uri.getPath();
-			String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
-			String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
-			try {
-				workerNode = SshNodeFactory.getInstance().getSshNode(
-						uri.getHost(), uri.getPort(), path);
-
-				sftp = SshPool.getSftpPutChannel(workerNode,
-						new RetrieveLoginFromTaverna(workerNode.getUrl()
-								.toString(), credentialManager));
-			} catch (JSchException e) {
-				throw new InvocationException(e);
-			}
-			synchronized (getNodeLock(workerNode)) {
-				try {
-					sftp.cd(path);
-					recursiveDelete(sftp, path + "/" + tempDir + "/");
-				} catch (SftpException e) {
-					throw new InvocationException(e);
-				} catch (JSchException e) {
-					throw new InvocationException(e);
-				}
-			}
-		} catch (URISyntaxException e1) {
-			throw new InvocationException(e1);
-		}
-	}
-
-	public static void cleanup(String runId, CredentialManager credentialManager)
-			throws InvocationException {
-		Set<SshUrl> tempDirectories = runIdToTempDir.get(runId);
-		if (tempDirectories != null) {
-			for (SshUrl tempUrl : tempDirectories) {
-				deleteDirectory(tempUrl, credentialManager);
-			}
-			runIdToTempDir.remove(runId);
-		}
-	}
-
-	@Override
-	protected void submit_generate_job_inner() throws InvocationException {
-		tags.put("uniqueID", "" + getSubmissionID());
-		String command = usecase.getCommand();
-		for (String cur : tags.keySet()) {
-			command = command.replaceAll("\\Q%%" + cur + "%%\\E",
-					Matcher.quoteReplacement(tags.get(cur)));
-		}
-		String fullCommand = "cd " + workerNode.getDirectory() + tmpname;
-		for (String preceding : precedingCommands) {
-			fullCommand += " && " + preceding;
-		}
-		fullCommand += " && " + command;
-
-		logger.info("Full command is " + fullCommand);
-
-		try {
-			running = SshPool.openExecChannel(workerNode, askUserForPw);
-			running.setCommand(fullCommand);
-			running.setOutputStream(stdout_buf);
-			running.setErrStream(stderr_buf);
-			if (stdInputStream != null) {
-				running.setInputStream(stdInputStream);
-			}
-			running.connect();
-		} catch (JSchException e) {
-			throw new InvocationException(e);
-		}
-
-	}
-
-	@Override
-	public HashMap<String, Object> submit_wait_fetch_results(
-			ReferenceService referenceService) throws InvocationException {
-		while (!running.isClosed()) {
-			try {
-				Thread.sleep(1000);
-			} catch (InterruptedException e) {
-				throw new InvocationException("Invocation interrupted:"
-						+ e.getMessage());
-			}
-		}
-
-		int exitcode = running.getExitStatus();
-		if (!usecase.getValidReturnCodes().contains(exitcode)) {
-			try {
-				throw new InvocationException("Invalid exit code " + exitcode
-						+ ":" + stderr_buf.toString("US-ASCII"));
-			} catch (UnsupportedEncodingException e) {
-				throw new InvocationException("Invalid exit code " + exitcode
-						+ ":" + stderr_buf.toString());
-			}
-		}
-
-		HashMap<String, Object> results = new HashMap<String, Object>();
-
-		results.put("STDOUT", stdout_buf.toByteArray());
-		results.put("STDERR", stderr_buf.toByteArray());
-		try {
-			stdout_buf.close();
-			stderr_buf.close();
-		} catch (IOException e2) {
-			throw new InvocationException(e2);
-		}
-
-		try {
-			ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
-					askUserForPw);
-			synchronized (getNodeLock(workerNode)) {
-				for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs()
-						.entrySet()) {
-					ScriptOutput scriptOutput = cur.getValue();
-					String fullPath = workerNode.getDirectory() + tmpname + "/"
-							+ scriptOutput.getPath();
-					try {
-						if (sftp.stat(fullPath) != null) {
-							SshUrl url = new SshUrl(workerNode);
-							url.setSubDirectory(tmpname);
-							url.setFileName(scriptOutput.getPath());
-							if (scriptOutput.isBinary()) {
-								url.setDataNature(ReferencedDataNature.BINARY);
-							} else {
-								url.setDataNature(ReferencedDataNature.TEXT);
-								url.setCharset("UTF-8");
-							}
-							if (isRetrieveData()) {
-								SshReference urlRef = new SshReference(url);
-								InputStream is = urlRef.openStream(null);
-								AbstractExternalReference ref;
-								if (scriptOutput.isBinary()) {
-									ref = inlineByteArrayReferenceBuilder
-											.createReference(is, null);
-								} else {
-									ref = inlineStringReferenceBuilder
-											.createReference(is, null);
-								}
-								try {
-									is.close();
-								} catch (IOException e) {
-									throw new InvocationException(e);
-								}
-								results.put(cur.getKey(), ref);
-							} else {
-								results.put(cur.getKey(), url);
-							}
-						} else {
-							ErrorDocument ed = referenceService
-									.getErrorDocumentService().registerError(
-											"No result for " + cur.getKey(), 0,
-											getContext());
-							results.put(cur.getKey(), ed);
-						}
-					} catch (SftpException e) {
-						ErrorDocument ed = referenceService
-								.getErrorDocumentService().registerError(
-										"No result for " + cur.getKey(), 0,
-										getContext());
-						results.put(cur.getKey(), ed);
-
-					}
-				}
-			}
-		} catch (JSchException e1) {
-			throw new InvocationException(e1);
-		} catch (ErrorDocumentServiceException e) {
-			throw new InvocationException(e);
-		}
-
-		if (running != null) {
-			running.disconnect();
-		}
-		if (stdInputStream != null) {
-			try {
-				stdInputStream.close();
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-		}
-
-		if (isRetrieveData()) {
-			forgetRun();
-			deleteDirectory(location, credentialManager);
-
-		}
-		return results;
-	}
-
-	@Override
-	public String setOneInput(ReferenceService referenceService,
-			T2Reference t2Reference, ScriptInput input)
-			throws InvocationException {
-		String target = null;
-		String remoteName = null;
-		if (input.isFile()) {
-			remoteName = input.getTag();
-		} else if (input.isTempFile()) {
-			remoteName = "tempfile." + (nTempFiles++) + ".tmp";
-
-		}
-		if (input.isFile() || input.isTempFile()) {
-			SshReference sshRef = getAsSshReference(referenceService,
-					t2Reference, workerNode);
-			target = workerNode.getDirectory() + tmpname + "/" + remoteName;
-			logger.info("Target is " + target);
-			if (sshRef != null) {
-				if (!input.isForceCopy()) {
-					String linkCommand = workerNode.getLinkCommand();
-					if (linkCommand != null) {
-						String actualLinkCommand = getActualOsCommand(
-								linkCommand, sshRef.getFullPath(), remoteName,
-								target);
-						precedingCommands.add(actualLinkCommand);
-						return target;
-
-					}
-				}
-				String copyCommand = workerNode.getCopyCommand();
-				if (copyCommand != null) {
-					String actualCopyCommand = getActualOsCommand(copyCommand,
-							sshRef.getFullPath(), remoteName, target);
-					precedingCommands.add(actualCopyCommand);
-					return target;
-				}
-			}
-			try {
-				ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
-						askUserForPw);
-				synchronized (getNodeLock(workerNode)) {
-					InputStream r = getAsStream(referenceService, t2Reference);
-					sftp.put(r, target);
-					r.close();
-				}
-			} catch (SftpException e) {
-				throw new InvocationException(e);
-			} catch (JSchException e) {
-				throw new InvocationException(e);
-			} catch (IOException e) {
-				throw new InvocationException(e);
-			}
-			return target;
-		} else {
-			String value = (String) referenceService.renderIdentifier(
-					t2Reference, String.class, this.getContext());
-			return value;
-
-		}
-	}
-
-	public SshReference getAsSshReference(ReferenceService referenceService,
-			T2Reference t2Reference, SshNode workerNode) {
-		Identified identified = referenceService.resolveIdentifier(t2Reference,
-				null, null);
-		if (identified instanceof ReferenceSet) {
-			for (ExternalReferenceSPI ref : ((ReferenceSet) identified)
-					.getExternalReferences()) {
-				if (ref instanceof SshReference) {
-					SshReference sshRef = (SshReference) ref;
-					if (sshRef.getHost().equals(workerNode.getHost())) {
-						return sshRef;
-					}
-				}
-			}
-		}
-		return null;
-	}
-
-	private static Object getNodeLock(final SshNode node) {
-		return getNodeLock(node.getHost());
-	}
-
-	private static synchronized Object getNodeLock(String hostName) {
-		if (!nodeLock.containsKey(hostName)) {
-			nodeLock.put(hostName, new Object());
-		}
-		return nodeLock.get(hostName);
-	}
-
-	@Override
-	public void setStdIn(ReferenceService referenceService,
-			T2Reference t2Reference) {
-		stdInputStream = new BufferedInputStream(getAsStream(referenceService,
-				t2Reference));
-	}
-
-	@Override
-	public void rememberRun(String runId) {
-		this.setRunId(runId);
-		Set<SshUrl> directories = runIdToTempDir.get(runId);
-		if (directories == null) {
-			directories = Collections.synchronizedSet(new HashSet<SshUrl>());
-			runIdToTempDir.put(runId, directories);
-		}
-		location = new SshUrl(workerNode);
-		location.setSubDirectory(tmpname);
-		directories.add(location);
-	}
-
-	private void forgetRun() {
-		Set<SshUrl> directories = runIdToTempDir.get(getRunId());
-		directories.remove(location);
-	}
-
-	public static void load(File directory) {
-		File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
-		if (!invocationsFile.exists()) {
-			return;
-		}
-		BufferedReader reader = null;
-		try {
-			reader = new BufferedReader(new FileReader(invocationsFile));
-			String line = reader.readLine();
-			while (line != null) {
-				String[] parts = line.split(" ");
-				if (parts.length != 2) {
-					break;
-				}
-				String runId = parts[0];
-				String urlString = parts[1];
-				Set<SshUrl> urls = runIdToTempDir.get(runId);
-				if (urls == null) {
-					urls = new HashSet<SshUrl>();
-					runIdToTempDir.put(runId, urls);
-				}
-				URI uri = new URI(urlString);
-				String fullPath = uri.getPath();
-				String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
-				String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
-				SshNode node = SshNodeFactory.getInstance().getSshNode(
-						uri.getHost(), uri.getPort(), path);
-				SshUrl newUrl = new SshUrl(node);
-				newUrl.setSubDirectory(tempDir);
-				urls.add(newUrl);
-				line = reader.readLine();
-			}
-		} catch (FileNotFoundException e) {
-			logger.error(e);
-		} catch (URISyntaxException e) {
-			logger.error(e);
-		} catch (IOException e) {
-			logger.error(e);
-		} finally {
-			if (reader != null) {
-				try {
-					reader.close();
-				} catch (IOException e) {
-					logger.error(e);
-				}
-			}
-		}
-	}
-
-	public static void persist(File directory) {
-		File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
-		BufferedWriter writer = null;
-		try {
-			writer = new BufferedWriter(new FileWriter(invocationsFile));
-			for (String runId : runIdToTempDir.keySet()) {
-				for (SshUrl url : runIdToTempDir.get(runId)) {
-					writer.write(runId);
-					writer.write(" ");
-					writer.write(url.toString());
-					writer.newLine();
-				}
-			}
-		} catch (IOException e) {
-			logger.error(e);
-		} finally {
-			if (writer != null) {
-				try {
-					writer.close();
-				} catch (IOException e) {
-					logger.error(e);
-				}
-			}
-		}
-	}
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivity.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivity.java b/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivity.java
deleted file mode 100755
index 1e6ef77..0000000
--- a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivity.java
+++ /dev/null
@@ -1,301 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2009 Hajo Nils Krabbenhoeft, INB, University of Luebeck
- *
- *  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.externaltool;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroup;
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
-import net.sf.taverna.t2.annotation.Annotated;
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.reference.WorkflowRunIdEntity;
-import net.sf.taverna.t2.workflowmodel.EditException;
-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.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-
-/**
- * This is the main class of the use case activity plugin. Here we store the
- * configuration and the description of a use case activity, configure the input
- * and output port and provide use case activity invocation
- *
- * @author Hajo Nils Krabbenhoeft
- */
-public class ExternalToolActivity extends AbstractAsynchronousActivity<ExternalToolActivityConfigurationBean> {
-
-	public static final String URI = "http://ns.taverna.org.uk/2010/activity/tool";
-
-	private static final String STDERR = "STDERR";
-
-	private static final String STDOUT = "STDOUT";
-
-	private static final String STDIN = "STDIN";
-
-	private static Logger logger = Logger.getLogger(ExternalToolActivity.class);
-
-	private ExternalToolActivityConfigurationBean configurationBean;
-	private UseCaseDescription mydesc;
-
-	private List<InvocationCreator> invocationCreators;
-
-	/**
-	 * Add the given MIME types to the given input/output port.
-	 *
-	 * @param annotated
-	 *            The port to which to add the MIME types.
-	 * @param mimeTypes
-	 *            A list of Strings specifying the MIME types to add.
-	 */
-	private void addMimeTypes(Annotated<?> annotated, List<String> mimeTypes) {
-		for (String mimeType : mimeTypes) {
-			MimeType mimeTypeAnnotation = new MimeType();
-			mimeTypeAnnotation.setText(mimeType);
-			try {
-				getEdits().getAddAnnotationChainEdit(annotated, mimeTypeAnnotation).doEdit();
-			} catch (EditException e) {
-				Logger.getLogger(ExternalToolActivity.class).error(e);
-			}
-		}
-	}
-
-	/**
-	 * Create a new input port with the given name, depth, element class and
-	 * MIME types.
-	 *
-	 * @param portName
-	 *            Name of the new port
-	 * @param portDepth
-	 *            Depth of the new port
-	 * @param translatedElementClass
-	 *            Which class of elements would this port like?
-	 * @param mimeTypes
-	 *            Accepted mime types for this port
-	 */
-	private void addInputWithMime(String portName, int portDepth, Class<?> translatedElementClass, List<String> mimeTypes) {
-		List<Class<? extends ExternalReferenceSPI>> handledReferenceSchemes = Collections.emptyList();
-		ActivityInputPort inputPort = getEdits().createActivityInputPort(portName, portDepth, true, handledReferenceSchemes,
-				translatedElementClass);
-		inputPorts.add(inputPort);
-		if (mimeTypes != null) {
-			addMimeTypes(inputPort, mimeTypes);
-		}
-	}
-
-	/**
-	 * Create a new output port with the given MIME types
-	 *
-	 * @param portName
-	 *            Name of the new port
-	 * @param portDepth
-	 *            Depth of the new port
-	 * @param mimeTypes
-	 *            Accepted mime types for this port
-	 */
-	private void addOutputWithMime(String portName, int portDepth, List<String> mimeTypes) {
-		ActivityOutputPort outputPort = getEdits().createActivityOutputPort(portName, portDepth, portDepth);
-		outputPorts.add(outputPort);
-		addMimeTypes(outputPort, mimeTypes);
-	}
-
-	@Override
-	public void configure(ExternalToolActivityConfigurationBean bean) throws ActivityConfigurationException {
-		this.configurationBean = bean;
-
-		try {
-			mydesc = bean.getUseCaseDescription();
-
-			inputPorts.clear();
-			outputPorts.clear();
-
-			if (mydesc != null) {
-
-			// loop through all script inputs and add them as taverna activity
-			// input ports
-			for (Map.Entry<String, ScriptInput> cur : mydesc.getInputs().entrySet()) {
-				ScriptInputUser scriptInputUser = (ScriptInputUser) cur.getValue();
-				// if the input port is a list, depth is 1 otherwise it is a
-				// single element, therefore depth 0
-				// if the input port is binary, we would like byte arrays,
-				// otherwise we require strings
-				addInputWithMime(cur.getKey(), scriptInputUser.isList() ? 1 : 0, cur.getValue().isBinary() ? byte[].class : String.class, scriptInputUser.getMime());
-
-			}
-			// loop through all script outputs and add them to taverna
-			for (Map.Entry<String, ScriptOutput> cur : mydesc.getOutputs().entrySet()) {
-				addOutputWithMime(cur.getKey(), 0, cur.getValue().getMime());
-			}
-			}
-
-			if (mydesc.isIncludeStdIn()) {
-				addInputWithMime(STDIN, 0, byte[].class, null);
-			}
-			if (mydesc.isIncludeStdOut()) {
-				addOutput(STDOUT, 0);
-			}
-			if (mydesc.isIncludeStdErr()) {
-				addOutput(STDERR, 0);
-			}
-		} catch (Exception e) {
-			throw new ActivityConfigurationException("Couldn't create ExternalTool Activity", e);
-		}
-	}
-
-	@Override
-	public ExternalToolActivityConfigurationBean getConfiguration() {
-		if (configurationBean != null) {
-			InvocationGroup invocationGroup = configurationBean.getInvocationGroup();
-			if (invocationGroup == null) {
-				if (configurationBean.getMechanism() != null) {
-					configurationBean.convertMechanismToDetails();
-				}
-			} else {
-				if (invocationGroup.getMechanism() != null) {
-					invocationGroup.convertMechanismToDetails();
-				}
-			}
-		}
-		return configurationBean;
-	}
-
-	public ExternalToolActivityConfigurationBean getConfigurationNoConversion() {
-		return configurationBean;
-	}
-
-	public InvocationMechanism recreateMechanism() {
-		if (configurationBean.getInvocationGroup() != null) {
-			if (configurationBean.getInvocationGroup().getMechanism() == null) {
-				configurationBean.getInvocationGroup().convertDetailsToMechanism();
-			}
-			return configurationBean.getInvocationGroup().getMechanism();
-		} else {
-			if (configurationBean.getMechanism() == null) {
-				configurationBean.convertDetailsToMechanism();
-			}
-			return configurationBean.getMechanism();
-		}
-	}
-
-	@Override
-	public void executeAsynch(final Map<String, T2Reference> data, final AsynchronousActivityCallback callback) {
-
-		callback.requestRun(new Runnable() {
-
-			public void run() {
-				ReferenceService referenceService = callback.getContext().getReferenceService();
-				UseCaseInvocation invoke = null;
-
-				/**
-				 * Note that retrying needs to be either done via Taverna's retry mechanism or as part of the specific invocation
-				 */
-				try {
-
-					invoke = getInvocation(recreateMechanism(),
-							configurationBean.getUseCaseDescription(), data, referenceService);
-					if (invoke == null) {
-						logger.error("Invoke is null");
-						callback.fail("No invocation mechanism found");
-					}
-					String runId = callback.getContext()
-							.getEntities(WorkflowRunIdEntity.class).get(0)
-							.getWorkflowRunId();
-					logger.info("Run id is " + runId);
-					invoke.rememberRun(runId);
-
-					invoke.setContext(callback.getContext());
-
-					// look at every use dynamic case input
-					for (String cur : invoke.getInputs()) {
-						if (!cur.equals(STDIN)) {
-							invoke.setInput(cur, referenceService,
-									data.get(cur));
-						}
-					}
-
-					if (mydesc.isIncludeStdIn() && (data.get(STDIN) != null)) {
-						invoke.setStdIn(referenceService, data.get(STDIN));
-					}
-
-					// submit the use case to its invocation mechanism
-					invoke.submit_generate_job(referenceService);
-
-					// retrieve the result.
-					Map<String, Object> downloads = invoke
-							.submit_wait_fetch_results(referenceService);
-					Map<String, T2Reference> result = new HashMap<String, T2Reference>();
-					for (Map.Entry<String, Object> cur : downloads.entrySet()) {
-						Object value = cur.getValue();
-
-						// register the result value with taverna
-						T2Reference reference = referenceService.register(
-								value, 0, true, callback.getContext());
-
-						// store the reference into the activity result
-						// set
-						result.put(cur.getKey(), reference);
-					}
-					callback.receiveResult(result, new int[0]);
-				} catch (InvocationException e) {
-					callback.fail(e.getMessage(), e);
-				}
-			}
-
-		});
-
-	}
-
-	public void setInvocationCreators(List<InvocationCreator> invocationCreators) {
-		this.invocationCreators = invocationCreators;
-	}
-
-	private UseCaseInvocation getInvocation(InvocationMechanism mechanism, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) {
-		UseCaseInvocation result = null;
-		InvocationCreator creator = null;
-		for (InvocationCreator c : invocationCreators) {
-			if (c.canHandle(mechanism.getType())) {
-				creator = c;
-				break;
-			}
-		}
-		if (creator != null) {
-			result = creator.convert(mechanism, description, data, referenceService);
-		}
-		return result;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityConfigurationBean.java b/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityConfigurationBean.java
deleted file mode 100755
index ce3387b..0000000
--- a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityConfigurationBean.java
+++ /dev/null
@@ -1,194 +0,0 @@
-package net.sf.taverna.t2.activities.externaltool;
-
-import java.util.List;
-
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationGroup;
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
-import net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#Config")
-public final class ExternalToolActivityConfigurationBean {
-
-	private InvocationGroup group;
-
-	private String mechanismType;
-
-	private String mechanismName;
-
-	private String mechanismXML;
-
-	private transient InvocationMechanism mechanism;
-
-	protected String repositoryUrl;
-	protected String externaltoolid;
-	protected UseCaseDescription useCaseDescription = null;
-	private boolean edited = false;
-
-	private List<MechanismCreator> mechanismCreators;
-
-    public boolean isEdited() {
-		return edited;
-	}
-
-	public ExternalToolActivityConfigurationBean() {
-	}
-
-	public InvocationGroup getInvocationGroup() {
-	    return group;
-	}
-
-	@ConfigurationProperty(name = "invocationGroup", label = "InvocationGroup", required=false)
-	public void setInvocationGroup(
-			InvocationGroup group) {
-		this.group = group;
-		clearMechanismInformation();
-	}
-
-	private void clearMechanismInformation() {
-		this.mechanismType = null;
-		this.mechanismName = null;
-		this.mechanismXML = null;
-		this.mechanism = null;
-	}
-
-	/**
-	 * @return the repositoryUrl
-	 */
-	public String getRepositoryUrl() {
-		return repositoryUrl;
-	}
-
-	/**
-	 * @param repositoryUrl the repositoryUrl to set
-	 */
-	@ConfigurationProperty(name = "repositoryUrl", label = "Repository URL", required=false)
-	public void setRepositoryUrl(String repositoryUrl) {
-		this.repositoryUrl = repositoryUrl;
-	}
-
-	/**
-	 * @return the externaltoolid
-	 */
-	public String getExternaltoolid() {
-		return externaltoolid;
-	}
-
-	/**
-	 * @param externaltoolid the externaltoolid to set
-	 */
-	@ConfigurationProperty(name = "toolId", label = "Tool ID")
-	public void setExternaltoolid(String externaltoolid) {
-		this.externaltoolid = externaltoolid;
-	}
-
-	/**
-	 * @return the useCaseDescription
-	 */
-	public UseCaseDescription getUseCaseDescription() {
-		return useCaseDescription;
-	}
-
-	/**
-	 * @param useCaseDescription the useCaseDescription to set
-	 */
-	@ConfigurationProperty(name = "toolDescription", label = "Tool Description")
-	public void setUseCaseDescription(UseCaseDescription useCaseDescription) {
-		this.useCaseDescription = useCaseDescription;
-	}
-
-	@ConfigurationProperty(name = "edited", label = "Edited", required=false)
-	public void setEdited(boolean b) {
-		this.edited  = b;
-	}
-
-	/**
-	 * Note this also sets the details
-	 *
-	 * @param mechanism the mechanism to set
-	 */
-	public void setMechanism(InvocationMechanism mechanism) {
-		this.mechanism = mechanism;
-		convertMechanismToDetails();
-		this.group = null;
-	}
-
-	public void convertMechanismToDetails() {
-		if (mechanism != null) {
-			this.setMechanismXML(mechanism.getXML());
-			this.setMechanismName(mechanism.getName());
-			this.setMechanismType(mechanism.getType());
-		}
-	}
-
-	/**
-	 * @param mechanismType the mechanismType to set
-	 */
-	@ConfigurationProperty(name = "mechanismType", label = "Mechanism Type", required=false)
-	public void setMechanismType(String mechanismType) {
-		this.mechanismType = mechanismType;
-	}
-
-	/**
-	 * @param mechanismName the mechanismName to set
-	 */
-	@ConfigurationProperty(name = "mechanismName", label = "Mechanism Name", required=false)
-	public void setMechanismName(String mechanismName) {
-		this.mechanismName = mechanismName;
-	}
-
-	/**
-	 * @param mechanismXML the mechanismXML to set
-	 */
-	@ConfigurationProperty(name = "mechanismXML", label = "Mechanism XML", required=false)
-	public void setMechanismXML(String mechanismXML) {
-		this.mechanismXML = mechanismXML;
-	}
-
-	public void convertDetailsToMechanism() {
-		if (mechanismXML != null) {
-			for (MechanismCreator mc : mechanismCreators) {
-				if (mc.canHandle(getMechanismType())) {
-					mechanism = mc.convert(getMechanismXML(), getMechanismName());
-					break;
-				}
-			}
-		}
-	}
-
-	/**
-	 * @return the mechanism
-	 */
-	public InvocationMechanism getMechanism() {
-
-		return mechanism;
-	}
-
-	/**
-	 * @return the mechanismType
-	 */
-	public String getMechanismType() {
-		return mechanismType;
-	}
-
-	/**
-	 * @return the mechanismName
-	 */
-	public String getMechanismName() {
-		return mechanismName;
-	}
-
-	/**
-	 * @return the mechanismXML
-	 */
-	public String getMechanismXML() {
-		return mechanismXML;
-	}
-
-	public void setMechanismCreators(List<MechanismCreator> mechanismCreators) {
-		this.mechanismCreators = mechanismCreators;
-	}
-
-}

http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2e8f451e/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityFactory.java b/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityFactory.java
deleted file mode 100644
index dc27b11..0000000
--- a/taverna-external-tool-activity/src/main/java/net/sf/taverna/t2/activities/externaltool/ExternalToolActivityFactory.java
+++ /dev/null
@@ -1,100 +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.externaltool;
-
-import java.io.IOException;
-import java.net.URI;
-import java.util.List;
-import java.util.Set;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator;
-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;
-
-/**
- * An {@link ActivityFactory} for creating <code>ExternalToolActivity</code>.
- *
- * @author David Withers
- */
-public class ExternalToolActivityFactory implements ActivityFactory {
-
-	private List<InvocationCreator> invocationCreators;
-
-	private List<MechanismCreator> mechanismCreators;
-
-        private Edits edits;
-
-	@Override
-	public ExternalToolActivity createActivity() {
-		ExternalToolActivity activity = new ExternalToolActivity();
-		activity.setInvocationCreators(invocationCreators);
-                activity.setEdits(edits);
-		return activity;
-	}
-
-	@Override
-	public URI getActivityType() {
-		return URI.create(ExternalToolActivity.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 setInvocationCreators(List<InvocationCreator> invocationCreators) {
-		this.invocationCreators = invocationCreators;
-	}
-
-	public void setMechanismCreators(List<MechanismCreator> mechanismCreators) {
-		this.mechanismCreators = mechanismCreators;
-	}
-
-	@Override
-	public Set<ActivityInputPort> getInputPorts(JsonNode configuration)
-			throws ActivityConfigurationException {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-	@Override
-	public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration)
-			throws ActivityConfigurationException {
-		// TODO Auto-generated method stub
-		return null;
-	}
-
-        public void setEdits(Edits edits) {
-		this.edits = edits;
-	}
-
-}