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; - } - -}
