ToolDescription
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/59a0dc12 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/59a0dc12 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/59a0dc12 Branch: refs/heads/docker Commit: 59a0dc12ca2e3c5fe11e0889b4b50c3aa4b57c43 Parents: b13a0fe Author: Stian Soiland-Reyes <[email protected]> Authored: Wed May 4 01:08:03 2016 +0100 Committer: Stian Soiland-Reyes <[email protected]> Committed: Wed May 4 01:08:03 2016 +0100 ---------------------------------------------------------------------- .../externaltool/ExternalToolActivity.java | 6 +- .../ExternalToolActivityConfigurationBean.java | 8 +- .../externaltool/InvocationCreator.java | 4 +- .../externaltool/desc/ToolDescription.java | 897 +++++++++++++++++++ .../externaltool/desc/UseCaseDescription.java | 897 ------------------- .../externaltool/desc/UseCaseEnumeration.java | 16 +- .../externaltool/invocation/ToolInvocation.java | 4 +- .../local/LocalInvocationCreator.java | 4 +- .../externaltool/local/LocalToolInvocation.java | 4 +- .../externaltool/ssh/SshInvocationCreator.java | 4 +- .../externaltool/ssh/SshToolInvocation.java | 4 +- 11 files changed, 924 insertions(+), 924 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java index b2fae4e..99a3c7c 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java @@ -27,7 +27,7 @@ import java.util.Map; import org.apache.taverna.activities.externaltool.desc.ScriptInput; import org.apache.taverna.activities.externaltool.desc.ScriptInputUser; import org.apache.taverna.activities.externaltool.desc.ScriptOutput; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.InvocationException; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationGroup; @@ -67,7 +67,7 @@ public class ExternalToolActivity extends AbstractAsynchronousActivity<ExternalT private static Logger logger = Logger.getLogger(ExternalToolActivity.class); private ExternalToolActivityConfigurationBean configurationBean; - private UseCaseDescription mydesc; + private ToolDescription mydesc; private List<InvocationCreator> invocationCreators; @@ -280,7 +280,7 @@ public class ExternalToolActivity extends AbstractAsynchronousActivity<ExternalT this.invocationCreators = invocationCreators; } - private ToolInvocation getInvocation(InvocationMechanism mechanism, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { + private ToolInvocation getInvocation(InvocationMechanism mechanism, ToolDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { ToolInvocation result = null; InvocationCreator creator = null; for (InvocationCreator c : invocationCreators) { http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java index 74c9070..7c4f479 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java @@ -21,7 +21,7 @@ package org.apache.taverna.activities.externaltool; import java.util.List; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.manager.InvocationGroup; import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.apache.taverna.activities.externaltool.manager.MechanismCreator; @@ -43,7 +43,7 @@ public final class ExternalToolActivityConfigurationBean { protected String repositoryUrl; protected String externaltoolid; - protected UseCaseDescription useCaseDescription = null; + protected ToolDescription useCaseDescription = null; private boolean edited = false; private List<MechanismCreator> mechanismCreators; @@ -106,7 +106,7 @@ public final class ExternalToolActivityConfigurationBean { /** * @return the useCaseDescription */ - public UseCaseDescription getUseCaseDescription() { + public ToolDescription getUseCaseDescription() { return useCaseDescription; } @@ -114,7 +114,7 @@ public final class ExternalToolActivityConfigurationBean { * @param useCaseDescription the useCaseDescription to set */ @ConfigurationProperty(name = "toolDescription", label = "Tool Description") - public void setUseCaseDescription(UseCaseDescription useCaseDescription) { + public void setUseCaseDescription(ToolDescription useCaseDescription) { this.useCaseDescription = useCaseDescription; } http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java index b5394c4..9893728 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java @@ -21,7 +21,7 @@ package org.apache.taverna.activities.externaltool; import java.util.Map; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.apache.taverna.reference.ReferenceService; @@ -35,6 +35,6 @@ public interface InvocationCreator { public boolean canHandle(String mechanismType); - public ToolInvocation convert(InvocationMechanism mechanism, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService); + public ToolInvocation convert(InvocationMechanism mechanism, ToolDescription description, Map<String, T2Reference> data, ReferenceService referenceService); } http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ToolDescription.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ToolDescription.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ToolDescription.java new file mode 100644 index 0000000..5e2dde0 --- /dev/null +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ToolDescription.java @@ -0,0 +1,897 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ + +package org.apache.taverna.activities.externaltool.desc; + +import java.io.IOException; +import java.io.InputStream; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; + +import javax.swing.ImageIcon; + +import org.apache.taverna.activities.externaltool.ExternalToolActivity; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; +import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy; +import org.apache.taverna.workflowmodel.serialization.DeserializationException; +import org.apache.taverna.workflowmodel.utils.Tools; + +import org.apache.log4j.Logger; +import org.jdom.Document; +import org.jdom.Element; +import org.jdom.JDOMException; +import org.jdom.input.SAXBuilder; + +import org.apache.commons.lang.StringUtils; + +/** + * Class representation of XML-description of UseCases + */ +@ConfigurationBean(uri = ExternalToolActivity.URI + "#ToolDescription") +public class ToolDescription { + + private static Logger logger = Logger.getLogger(ToolDescription.class); + + /** + * Identifier for the retrieval of this UseCase in the sharedRepository + * database, respectively its XML export. + */ + private String usecaseid = ""; + /** + * Workflow Elements now can get a group identifier. There may be subgroups + * divided by : + */ + private String group = ""; + /** + * Textual description of the use case itself. This description is very + * short to fit on the single line that is prepared for such descriptions in + * the Taverna workflow element list. + */ + private String description = ""; + /** + * What is actually executed on the shell. + */ + private String command = ""; + + /** + * Accessor function of command + * + * @return shell-executable series of commands + */ + public String getCommand() { + if (null == command) { + // FIXME: Is this possible? + return ""; + } else { + return command; + } + } + + /** + * Routine that may be executed as a first check if the program is indeed + * installed. + */ + private String test_local = null; + + /** + * URL of an icon that would help users to recognise the use case + */ + private String icon_url = null; + + private int preparingTimeoutInSeconds = 20 * 60; // 20 minutes + private int executionTimeoutInSeconds = 30 * 60; // 30 minutes + + private List<String> tags = new ArrayList<String>(); + private List<RuntimeEnvironmentConstraint> REs = new ArrayList<RuntimeEnvironmentConstraint>(); + private ArrayList<String> queue_preferred = new ArrayList<String>(); + private ArrayList<String> queue_deny = new ArrayList<String>(); + + private List<ScriptInputStatic> static_inputs = new ArrayList<ScriptInputStatic>(); + private Map<String, ScriptInput> inputs = new HashMap<String, ScriptInput>(); + private Map<String, ScriptOutput> outputs = new HashMap<String, ScriptOutput>(); + + private boolean includeStdIn = false; + private boolean includeStdOut = true; + private boolean includeStdErr = true; + + private List<Integer> validReturnCodes = new ArrayList<Integer>(); + + /** + * Default constructor to make xstream happy + */ + public ToolDescription() { + + } + + /** + * Constructor, for special purpose usecases. + * + * @param usecaseid + */ + public ToolDescription(String usecaseid) { + this.setUsecaseid(usecaseid); + } + + /** + * Constructor, expects an input stream containing the xml. for example, use + * getClass().getClassLoader().getResourceAsStream("..") to load a usecase + * from your program jar + */ + public ToolDescription(InputStream programAsStream) throws DeserializationException { + SAXBuilder builder = new SAXBuilder(); + Document doc; + try { + doc = builder.build(programAsStream); + programAsStream.close(); + } catch (JDOMException e) { + throw new DeserializationException("Error deserializing usecase", e); + } catch (IOException e) { + throw new DeserializationException("Error deserializing usecase", e); + } + readFromXmlElement(doc.getRootElement()); + } + + /** + * Constructor, expects an XML-root to dissect. + */ + public ToolDescription(Element programNode) throws DeserializationException { + readFromXmlElement(programNode); + } + +/** + * Produce an XML description of the ToolDescription + */ + public Element writeToXMLElement() { + Element programNode = new Element("program"); + programNode.setAttribute("name", getUsecaseid()); + programNode.setAttribute("description", getDescription()); + // Always use element version of command +// programNode.setAttribute("command", getCommand()); + Element commandNode = new Element("command"); + commandNode.addContent(getCommand()); + programNode.addContent(commandNode); + programNode.setAttribute("timeout", Integer.toString(getExecutionTimeoutInSeconds())); + programNode.setAttribute("preparing_timeout", Integer.toString(getPreparingTimeoutInSeconds())); + programNode.setAttribute("includeStdIn", Boolean.toString(isIncludeStdIn())); + programNode.setAttribute("includeStdOut", Boolean.toString(isIncludeStdOut())); + programNode.setAttribute("includeStdErr", Boolean.toString(isIncludeStdErr())); + for (ScriptInputStatic si : getStatic_inputs()) { + Element staticNode = new Element("static"); + if (si.isBinary()) { + staticNode.setAttribute("binary", "true"); + } + if (si.isForceCopy()) { + staticNode.setAttribute("forceCopy", "true"); + } + if (si.isFile()) { + Element fileNode = new Element("file"); + fileNode.setAttribute("path", si.getTag()); + staticNode.addContent(fileNode); + } else if (si.isTempFile()) { + Element tempfileNode = new Element("tempfile"); + tempfileNode.setAttribute("tag", si.getTag()); + staticNode.addContent(tempfileNode); + } else { + Element replaceNode = new Element("replace"); + replaceNode.setAttribute("tag", si.getTag()); + staticNode.addContent(replaceNode); + } + if (si.getUrl() != null) { + Element contentNode = new Element("content"); + contentNode.setAttribute("url", si.getUrl()); + staticNode.addContent(contentNode); + } else { + Element contentNode = new Element("content"); + contentNode.addContent((String) si.getContent()); + staticNode.addContent(contentNode); + } + programNode.addContent(staticNode); + } + for (Entry<String, ScriptInput> entry : getInputs().entrySet()) { + String name = entry.getKey(); + ScriptInputUser si = (ScriptInputUser) entry.getValue(); + Element inputNode = new Element("input"); + inputNode.setAttribute("name", name); + if (si.isBinary()) { + inputNode.setAttribute("binary", "true"); + } + if (si.isForceCopy()) { + inputNode.setAttribute("forceCopy", "true"); + } + if (si.isConcatenate()) { + inputNode.setAttribute("concatenate", "true"); + } + if (si.isList()) { + inputNode.setAttribute("list", "true"); + } + if (si.isFile()) { + Element fileNode = new Element("file"); + fileNode.setAttribute("path", si.getTag()); + inputNode.addContent(fileNode); + } else if (si.isTempFile()) { + Element tempfileNode = new Element("tempfile"); + tempfileNode.setAttribute("tag", si.getTag()); + inputNode.addContent(tempfileNode); + } else { + Element replaceNode = new Element("replace"); + replaceNode.setAttribute("tag", si.getTag()); + inputNode.addContent(replaceNode); + } + for (String mime : si.getMime()) { + Element mimeNode = new Element("mime"); + mimeNode.setAttribute("type", mime); + inputNode.addContent(mimeNode); + } + programNode.addContent(inputNode); + } + for (Entry<String, ScriptOutput> entry : getOutputs().entrySet()) { + String name = entry.getKey(); + ScriptOutput so = entry.getValue(); + Element outputNode = new Element("output"); + outputNode.setAttribute("name", name); + if (so.isBinary()) { + outputNode.setAttribute("binary", "true"); + } + Element fromfileNode = new Element("fromfile"); + fromfileNode.setAttribute("path", so.getPath()); + outputNode.addContent(fromfileNode); + for (String mime : so.getMime()) { + Element mimeNode = new Element("mime"); + mimeNode.setAttribute("type", mime); + outputNode.addContent(mimeNode); + } + programNode.addContent(outputNode); + } + for (RuntimeEnvironmentConstraint rec : getREs()) { + Element rteNode = new Element("rte"); + rteNode.setAttribute("name", rec.getID()); + rteNode.setAttribute("relation", rec.getRelation()); + programNode.addContent(rteNode); + } + if ((group != null) && !group.isEmpty()) { + Element groupNode = new Element("group"); + groupNode.setAttribute("name", group); + programNode.addContent(groupNode); + } + if ((test_local != null) && !test_local.isEmpty()) { + Element testNode = new Element("test"); + testNode.setAttribute("local", test_local); + programNode.addContent(testNode); + } + if ((icon_url != null) && !icon_url.isEmpty()) { + Element iconNode = new Element("icon"); + iconNode.setAttribute("url", icon_url); + programNode.addContent(iconNode); + } + if (!getQueue_preferred().isEmpty() || !getQueue_deny().isEmpty()) { + Element queueNode = new Element("queue"); + for (String url : getQueue_preferred()) { + Element preferredNode = new Element("prefer"); + preferredNode.setAttribute("url", url); + queueNode.addContent(preferredNode); + } + for (String url : getQueue_deny()) { + Element denyNode = new Element("deny"); + denyNode.setAttribute("url", url); + queueNode.addContent(denyNode); + } + programNode.addContent(queueNode); + } + Element validReturnCodesNode = new Element("validReturnCodes"); + validReturnCodesNode.setAttribute("codes", getReturnCodesAsText()); + programNode.addContent(validReturnCodesNode); + + return programNode; + } + /** + * Specifies the ToolDescription from the root of an XML description + * which is accessible online. + * + * @param programNode + * @throws DeserializationException + */ + private void readFromXmlElement(Element programNode) throws DeserializationException { + if (programNode.getName().compareToIgnoreCase("program") != 0) + throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'"); + + setUsecaseid(programNode.getAttributeValue("name")); + setDescription(programNode.getAttributeValue("description")); + setCommand(programNode.getAttributeValue("command")); + String timeoutStr = programNode.getAttributeValue("timeout"); + if (timeoutStr != null) + setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr)); + timeoutStr = programNode.getAttributeValue("preparing_timeout"); + if (timeoutStr != null) + setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr)); + + String includeStdInStr = programNode.getAttributeValue("includeStdIn"); + if (includeStdInStr != null && !includeStdInStr.isEmpty()) { + setIncludeStdIn(includeStdInStr.equals("true")); + } + + String includeStdOutStr = programNode.getAttributeValue("includeStdOut"); + if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) { + setIncludeStdOut(includeStdOutStr.equals("true")); + } + + String includeStdErrStr = programNode.getAttributeValue("includeStdErr"); + if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) { + setIncludeStdErr(includeStdErrStr.equals("true")); + } + + for (Object cur_ob : programNode.getChildren()) { + Element cur = (Element) cur_ob; + + String name = cur.getAttributeValue("name"); + + String type = cur.getName(); + boolean binary = false; + if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) { + binary = true; + } + boolean list = false; + if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) { + list = true; + } + boolean concatenate = false; + if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) { + concatenate = true; + } + boolean forceCopy = false; + if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) { + forceCopy = true; + } + + Element inner = null; + String innerType = null, tag = null, path = null; + if (cur.getChildren().size() > 0) { + inner = (Element) cur.getChildren().get(0); + innerType = inner.getName(); + tag = inner.getAttributeValue("tag"); + path = inner.getAttributeValue("path"); + } + // build mime type declaration list + ArrayList<String> mime = new ArrayList<String>(); + for (Object child : cur.getChildren()) { + Element curChild = (Element) child; + if (curChild.getName().equalsIgnoreCase("mime")) { + mime.add(curChild.getAttributeValue("type")); + } + } + if (type.equalsIgnoreCase("static")) { + ScriptInputStatic si = new ScriptInputStatic(); + Element content = cur.getChild("content"); + if (content == null) + throw new DeserializationException("FIXME: script tag without embedded content tag"); + si.setUrl(content.getAttributeValue("url")); + if (si.getUrl() == null) + si.setContent(content.getText()); + fillInputDescription(si, binary, forceCopy, innerType, tag, path); + getStatic_inputs().add(si); + } else if (type.equalsIgnoreCase("input")) { + ScriptInputUser indesc = new ScriptInputUser(); + indesc.setList(list); + indesc.setMime(mime); + indesc.setConcatenate(concatenate); + fillInputDescription(indesc, binary, forceCopy, innerType, tag, path); + getInputs().put(Tools.sanitiseName(name), indesc); + } else if (type.equalsIgnoreCase("output")) { + ScriptOutput outdesc = new ScriptOutput(); + outdesc.setMime(mime); + + boolean ok = true; + if (null == innerType) { + // don't know what to do + throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?"); + } else if (innerType.equalsIgnoreCase("fromfile")) { + outdesc.setPath(path); + outdesc.setBinary(binary); + } else { + throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'"); + } + if (ok) { + getOutputs().put(Tools.sanitiseName(name), outdesc); + } + } else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) { + getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation"))); + } else if (type.equalsIgnoreCase("group")) { + group = name; + } else if (type.equalsIgnoreCase("test")) { + test_local = cur.getAttributeValue("local"); + } else if (type.equalsIgnoreCase("icon")) { + icon_url = cur.getAttributeValue("url"); + } else if (type.equalsIgnoreCase("queue")) { + for (Object child_ob : cur.getChildren()) { + Element child = (Element) child_ob; + if (child.getName().equalsIgnoreCase("prefer")) + getQueue_preferred().add(child.getAttributeValue("url")); + else if (child.getName().equalsIgnoreCase("deny")) + getQueue_deny().add(child.getAttributeValue("url")); + else + throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry"); + } + } else if (type.equalsIgnoreCase("command")) { + // i like to have the ability to inject complete shell script + // fragments into the use case, + // so this should be replace and should allow multiple lines + if ((getCommand() != null) && !getCommand().isEmpty()) { + throw new DeserializationException("You have specified both command attribute and command tag."); + } + setCommand(cur.getText()); + } else if (type.equalsIgnoreCase("validReturnCodes")) { + String codeString = cur.getAttributeValue("codes"); + if (codeString != null) { + setReturnCodesAsText(codeString); + } + } + else { + throw new DeserializationException("Unexpected and uninterpreted attribute " + type); + } + } + } + + private void fillInputDescription(ScriptInput fillMe, boolean binary, boolean forceCopy, String innerType, String tag, String path) throws DeserializationException { + fillMe.setBinary(binary); + fillMe.setForceCopy(forceCopy); + if (null == innerType) { + // don't know what to do + throw new DeserializationException("FIXME: Found null == innerType for input, is this the bug?"); + } else if (innerType.equalsIgnoreCase("replace")) { + fillMe.setTag(tag); + fillMe.setTempFile(false); + fillMe.setFile(false); + getTags().add(tag); + } else if (innerType.equalsIgnoreCase("tempfile")) { + fillMe.setTag(tag); + fillMe.setTempFile(true); + fillMe.setFile(false); + getTags().add(tag); + } else if (innerType.equalsIgnoreCase("file")) { + fillMe.setTag(path); + fillMe.setTempFile(false); + fillMe.setFile(true); + } else { + throw new DeserializationException("Problem reading input port: unknown innerType '" + innerType + "'"); + } + } + + /** + * returns icon that is referenced in use case description + */ + public ImageIcon getImageIcon() { + if (null == icon_url) return null; + try { + URL u = new URL(icon_url); + return new ImageIcon(u, getUsecaseid()); + } catch (Exception e) { + logger.error(e); + return null; + } + } + + /** + * String representation of the use case. It also contains interesting + * information on the availability of resources in the grid to actually + * execute that workflow element. + * + * @return String + */ + @Override + public String toString() { + List<String> hlp = new ArrayList<String>(); + hlp.add("usecaseid: " + getUsecaseid()); + hlp.add("description: " + getDescription()); + hlp.add("group: " + group); + hlp.add("test: " + test_local); + hlp.add("tags: " + getTags()); + for (Map.Entry<String, ScriptInput> cur : getInputs().entrySet()) { + hlp.add(">" + cur.getKey() + ">: " + cur.getValue().toString()); + } + for (Map.Entry<String, ScriptOutput> cur : getOutputs().entrySet()) { + hlp.add("<" + cur.getKey() + "<: " + cur.getValue().toString()); + } + hlp.add("RE: " + getREs().toString()); + hlp.add("preferred queues: " + getQueue_preferred()); + hlp.add("denied queues: " + getQueue_deny()); + String tos = super.toString() + "["; + for (int i = 0; i < hlp.size(); i++) { + if (i != 0) + tos += ", "; + tos += hlp.get(i); + } + return tos + " ]"; + } + + /** + * hajo's test just pass an url or file url to an xml file + * + * @throws IOException + * @throws MalformedURLException + * @throws DeserializationException + */ + public static void main(String[] argv) throws MalformedURLException, IOException, DeserializationException { + ToolDescription d = new ToolDescription(new URL(argv[0]).openStream()); + logger.info(d.getCommand()); + } + + /** + * @param command the command to set + */ + @ConfigurationProperty(name = "command", label = "Command", description="What is actually executed on the shell") + public void setCommand(String command) { + this.command = command; + } + + /** + * @param description the description to set + */ + @ConfigurationProperty(name = "description", label = "Description", description="Textual description of the tool", required=false, uri="http://purl.org/dc/elements/1.1/description";) + public void setDescription(String description) { + this.description = description; + } + + /** + * @return the description + */ + public String getDescription() { + return description; + } + + /** + * @param executionTimeoutInSeconds the executionTimeoutInSeconds to set + */ + @ConfigurationProperty(name = "executionTimeoutInSeconds", label = "Execution Timeout In Seconds") + public void setExecutionTimeoutInSeconds(int executionTimeoutInSeconds) { + this.executionTimeoutInSeconds = executionTimeoutInSeconds; + } + + /** + * @return the executionTimeoutInSeconds + */ + public int getExecutionTimeoutInSeconds() { + return executionTimeoutInSeconds; + } + + /** + * @param inputs the inputs to set + */ + public void setInputs(Map<String, ScriptInput> inputs) { + this.inputs = inputs; + } + + @ConfigurationProperty(name = "inputs", label = "Inputs", required=false) + public void setInputs(Set<InputMap> inputs) { + if (inputs != null) { + this.inputs = new HashMap<String, ScriptInput>(); + for (InputMap inputMap : inputs) { + this.inputs.put(inputMap.getPort(), inputMap.getInput()); + } + } else { + this.inputs = null; + } + } + + /** + * @return the inputs + */ + public Map<String, ScriptInput> getInputs() { + if (inputs == null) { + inputs = new HashMap<String, ScriptInput>(); + } + return inputs; + } + + /** + * @param outputs the outputs to set + */ + public void setOutputs(Map<String, ScriptOutput> outputs) { + this.outputs = outputs; + } + + @ConfigurationProperty(name = "outputs", label = "Outputs", required=false) + public void setOutputs(Set<OutputMap> outputs) { + if (outputs != null) { + this.outputs = new HashMap<String, ScriptOutput>(); + for (OutputMap outputMap : outputs) { + this.outputs.put(outputMap.getPort(), outputMap.getOutput()); + } + } else { + this.outputs = null; + } + } + + /** + * @return the outputs + */ + public Map<String, ScriptOutput> getOutputs() { + if (outputs == null) { + outputs = new HashMap<String, ScriptOutput>(); + } + return outputs; + } + + /** + * @param preparingTimeoutInSeconds the preparingTimeoutInSeconds to set + */ + @ConfigurationProperty(name = "preparingTimeoutInSeconds", label = "Preparing Timeout In Seconds") + public void setPreparingTimeoutInSeconds(int preparingTimeoutInSeconds) { + this.preparingTimeoutInSeconds = preparingTimeoutInSeconds; + } + + /** + * @return the preparingTimeoutInSeconds + */ + public int getPreparingTimeoutInSeconds() { + return preparingTimeoutInSeconds; + } + + /** + * @param queue_deny the queue_deny to set + */ + public void setQueue_deny(ArrayList<String> queue_deny) { + this.queue_deny = queue_deny; + } + + /** + * @return the queue_deny + */ + public ArrayList<String> getQueue_deny() { + if (queue_deny == null) { + queue_deny = new ArrayList<String>(); + } + return queue_deny; + } + + /** + * @param queue_preferred the queue_preferred to set + */ + public void setQueue_preferred(ArrayList<String> queue_preferred) { + this.queue_preferred = queue_preferred; + } + + /** + * @return the queue_preferred + */ + public ArrayList<String> getQueue_preferred() { + if (queue_preferred == null) { + queue_preferred = new ArrayList<String>(); + } + return queue_preferred; + } + + /** + * @param rEs the rEs to set + */ + public void setREs(List<RuntimeEnvironmentConstraint> rEs) { + REs = rEs; + } + + /** + * @return the rEs + */ + public List<RuntimeEnvironmentConstraint> getREs() { + if (REs == null) { + REs = new ArrayList<RuntimeEnvironmentConstraint>(); + } + return REs; + } + + /** + * @param static_inputs the static_inputs to set + */ + @ConfigurationProperty(name = "staticInputs", label = "Static Inputs", ordering=OrderPolicy.NON_ORDERED, required=false) + public void setStatic_inputs(List<ScriptInputStatic> static_inputs) { + this.static_inputs = static_inputs; + } + + /** + * @return the static_inputs + */ + public List<ScriptInputStatic> getStatic_inputs() { + if (static_inputs == null) { + static_inputs = new ArrayList<ScriptInputStatic>(); + } + return static_inputs; + } + + /** + * @param tags the tags to set + */ + public void setTags(List<String> tags) { + this.tags = tags; + } + + /** + * @return the tags + */ + public List<String> getTags() { + if (tags == null) { + tags = new ArrayList<String>(); + } + return tags; + } + + /** + * @param usecaseid the usecaseid to set + */ + @ConfigurationProperty(name = "usecaseid", label = "Title", uri="http://purl.org/dc/elements/1.1/title";, required=false) + public void setUsecaseid(String usecaseid) { + this.usecaseid = usecaseid; + } + + /** + * @return the usecaseid + */ + public String getUsecaseid() { + return usecaseid; + } + + public boolean isIncludeStdIn() { + return includeStdIn; + } + + @ConfigurationProperty(name = "includeStdIn", label = "Include STDIN") + public void setIncludeStdIn(boolean includeStdIn) { + this.includeStdIn = includeStdIn; + } + + public boolean isIncludeStdOut() { + return includeStdOut; + } + + @ConfigurationProperty(name = "includeStdOut", label = "Include STDOUT") + public void setIncludeStdOut(boolean includeStdOut) { + this.includeStdOut = includeStdOut; + } + + public boolean isIncludeStdErr() { + return includeStdErr; + } + + @ConfigurationProperty(name = "includeStdErr", label = "Include STDERR") + public void setIncludeStdErr(boolean includeStdErr) { + this.includeStdErr = includeStdErr; + } + + /** + * @return the validReturnCodes + */ + public List<Integer> getValidReturnCodes() { + if (validReturnCodes == null) { + validReturnCodes = new ArrayList<Integer>(); + } + if (validReturnCodes.isEmpty()) { + validReturnCodes.add(0); + } + return validReturnCodes; + } + + /** + * @param validReturnCodes the validReturnCodes to set + */ + public void setValidReturnCodes(List<Integer> validReturnCodes) { + this.validReturnCodes = validReturnCodes; + } + + public String getReturnCodesAsText() { + return StringUtils.join(getValidReturnCodes(), ","); + } + + public void setReturnCodesAsText(String text) { + if (getValidReturnCodes() == null) { + validReturnCodes = new ArrayList<Integer>(); + } + validReturnCodes.clear(); + String[] codes = text.split(","); + for (String code : codes) { + try { + Integer codeInt = new Integer(code); + if (!validReturnCodes.contains(codeInt)) { + validReturnCodes.add(codeInt); + } + } + catch (NumberFormatException e) { + logger.error(e); + } + } + if (validReturnCodes.isEmpty()) { + validReturnCodes.add(0); + } + Collections.sort(validReturnCodes); + } + + /** + * @return the group + */ + public String getGroup() { + return group; + } + + /** + * @param group the group to set + */ + public void setGroup(String group) { + this.group = group; + } + + /** + * @return the icon_url + */ + public String getIcon_url() { + return icon_url; + } + + @ConfigurationBean(uri = ExternalToolActivity.URI + "#OutputMap") + public static class OutputMap { + private String port; + + private ScriptOutput output; + + public String getPort() { + return port; + } + + @ConfigurationProperty(name = "port", label = "Port") + public void setPort(String port) { + this.port = port; + } + + public ScriptOutput getOutput() { + return output; + } + + @ConfigurationProperty(name = "output", label = "Output") + public void setOutput(ScriptOutput output) { + this.output = output; + } + } + + @ConfigurationBean(uri = ExternalToolActivity.URI + "#InputMap") + public static class InputMap { + private String port; + + private ScriptInputUser input; + + public String getPort() { + return port; + } + + @ConfigurationProperty(name = "port", label = "Port") + public void setPort(String port) { + this.port = port; + } + + public ScriptInputUser getInput() { + return input; + } + + @ConfigurationProperty(name = "input", label = "Input") + public void setInput(ScriptInputUser input) { + this.input = input; + } + } + +} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java deleted file mode 100644 index 934330f..0000000 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java +++ /dev/null @@ -1,897 +0,0 @@ -/* - * Licensed to the Apache Software Foundation (ASF) under one - * or more contributor license agreements. See the NOTICE file - * distributed with this work for additional information - * regarding copyright ownership. The ASF licenses this file - * to you under the Apache License, Version 2.0 (the - * "License"); you may not use this file except in compliance - * with the License. You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ - -package org.apache.taverna.activities.externaltool.desc; - -import java.io.IOException; -import java.io.InputStream; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Map.Entry; -import java.util.Set; - -import javax.swing.ImageIcon; - -import org.apache.taverna.activities.externaltool.ExternalToolActivity; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy; -import org.apache.taverna.workflowmodel.serialization.DeserializationException; -import org.apache.taverna.workflowmodel.utils.Tools; - -import org.apache.log4j.Logger; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.input.SAXBuilder; - -import org.apache.commons.lang.StringUtils; - -/** - * Class representation of XML-description of UseCases - */ -@ConfigurationBean(uri = ExternalToolActivity.URI + "#ToolDescription") -public class UseCaseDescription { - - private static Logger logger = Logger.getLogger(UseCaseDescription.class); - - /** - * Identifier for the retrieval of this UseCase in the sharedRepository - * database, respectively its XML export. - */ - private String usecaseid = ""; - /** - * Workflow Elements now can get a group identifier. There may be subgroups - * divided by : - */ - private String group = ""; - /** - * Textual description of the use case itself. This description is very - * short to fit on the single line that is prepared for such descriptions in - * the Taverna workflow element list. - */ - private String description = ""; - /** - * What is actually executed on the shell. - */ - private String command = ""; - - /** - * Accessor function of command - * - * @return shell-executable series of commands - */ - public String getCommand() { - if (null == command) { - // FIXME: Is this possible? - return ""; - } else { - return command; - } - } - - /** - * Routine that may be executed as a first check if the program is indeed - * installed. - */ - private String test_local = null; - - /** - * URL of an icon that would help users to recognise the use case - */ - private String icon_url = null; - - private int preparingTimeoutInSeconds = 20 * 60; // 20 minutes - private int executionTimeoutInSeconds = 30 * 60; // 30 minutes - - private List<String> tags = new ArrayList<String>(); - private List<RuntimeEnvironmentConstraint> REs = new ArrayList<RuntimeEnvironmentConstraint>(); - private ArrayList<String> queue_preferred = new ArrayList<String>(); - private ArrayList<String> queue_deny = new ArrayList<String>(); - - private List<ScriptInputStatic> static_inputs = new ArrayList<ScriptInputStatic>(); - private Map<String, ScriptInput> inputs = new HashMap<String, ScriptInput>(); - private Map<String, ScriptOutput> outputs = new HashMap<String, ScriptOutput>(); - - private boolean includeStdIn = false; - private boolean includeStdOut = true; - private boolean includeStdErr = true; - - private List<Integer> validReturnCodes = new ArrayList<Integer>(); - - /** - * Default constructor to make xstream happy - */ - public UseCaseDescription() { - - } - - /** - * Constructor, for special purpose usecases. - * - * @param usecaseid - */ - public UseCaseDescription(String usecaseid) { - this.setUsecaseid(usecaseid); - } - - /** - * Constructor, expects an input stream containing the xml. for example, use - * getClass().getClassLoader().getResourceAsStream("..") to load a usecase - * from your program jar - */ - public UseCaseDescription(InputStream programAsStream) throws DeserializationException { - SAXBuilder builder = new SAXBuilder(); - Document doc; - try { - doc = builder.build(programAsStream); - programAsStream.close(); - } catch (JDOMException e) { - throw new DeserializationException("Error deserializing usecase", e); - } catch (IOException e) { - throw new DeserializationException("Error deserializing usecase", e); - } - readFromXmlElement(doc.getRootElement()); - } - - /** - * Constructor, expects an XML-root to dissect. - */ - public UseCaseDescription(Element programNode) throws DeserializationException { - readFromXmlElement(programNode); - } - -/** - * Produce an XML description of the UseCaseDescription - */ - public Element writeToXMLElement() { - Element programNode = new Element("program"); - programNode.setAttribute("name", getUsecaseid()); - programNode.setAttribute("description", getDescription()); - // Always use element version of command -// programNode.setAttribute("command", getCommand()); - Element commandNode = new Element("command"); - commandNode.addContent(getCommand()); - programNode.addContent(commandNode); - programNode.setAttribute("timeout", Integer.toString(getExecutionTimeoutInSeconds())); - programNode.setAttribute("preparing_timeout", Integer.toString(getPreparingTimeoutInSeconds())); - programNode.setAttribute("includeStdIn", Boolean.toString(isIncludeStdIn())); - programNode.setAttribute("includeStdOut", Boolean.toString(isIncludeStdOut())); - programNode.setAttribute("includeStdErr", Boolean.toString(isIncludeStdErr())); - for (ScriptInputStatic si : getStatic_inputs()) { - Element staticNode = new Element("static"); - if (si.isBinary()) { - staticNode.setAttribute("binary", "true"); - } - if (si.isForceCopy()) { - staticNode.setAttribute("forceCopy", "true"); - } - if (si.isFile()) { - Element fileNode = new Element("file"); - fileNode.setAttribute("path", si.getTag()); - staticNode.addContent(fileNode); - } else if (si.isTempFile()) { - Element tempfileNode = new Element("tempfile"); - tempfileNode.setAttribute("tag", si.getTag()); - staticNode.addContent(tempfileNode); - } else { - Element replaceNode = new Element("replace"); - replaceNode.setAttribute("tag", si.getTag()); - staticNode.addContent(replaceNode); - } - if (si.getUrl() != null) { - Element contentNode = new Element("content"); - contentNode.setAttribute("url", si.getUrl()); - staticNode.addContent(contentNode); - } else { - Element contentNode = new Element("content"); - contentNode.addContent((String) si.getContent()); - staticNode.addContent(contentNode); - } - programNode.addContent(staticNode); - } - for (Entry<String, ScriptInput> entry : getInputs().entrySet()) { - String name = entry.getKey(); - ScriptInputUser si = (ScriptInputUser) entry.getValue(); - Element inputNode = new Element("input"); - inputNode.setAttribute("name", name); - if (si.isBinary()) { - inputNode.setAttribute("binary", "true"); - } - if (si.isForceCopy()) { - inputNode.setAttribute("forceCopy", "true"); - } - if (si.isConcatenate()) { - inputNode.setAttribute("concatenate", "true"); - } - if (si.isList()) { - inputNode.setAttribute("list", "true"); - } - if (si.isFile()) { - Element fileNode = new Element("file"); - fileNode.setAttribute("path", si.getTag()); - inputNode.addContent(fileNode); - } else if (si.isTempFile()) { - Element tempfileNode = new Element("tempfile"); - tempfileNode.setAttribute("tag", si.getTag()); - inputNode.addContent(tempfileNode); - } else { - Element replaceNode = new Element("replace"); - replaceNode.setAttribute("tag", si.getTag()); - inputNode.addContent(replaceNode); - } - for (String mime : si.getMime()) { - Element mimeNode = new Element("mime"); - mimeNode.setAttribute("type", mime); - inputNode.addContent(mimeNode); - } - programNode.addContent(inputNode); - } - for (Entry<String, ScriptOutput> entry : getOutputs().entrySet()) { - String name = entry.getKey(); - ScriptOutput so = entry.getValue(); - Element outputNode = new Element("output"); - outputNode.setAttribute("name", name); - if (so.isBinary()) { - outputNode.setAttribute("binary", "true"); - } - Element fromfileNode = new Element("fromfile"); - fromfileNode.setAttribute("path", so.getPath()); - outputNode.addContent(fromfileNode); - for (String mime : so.getMime()) { - Element mimeNode = new Element("mime"); - mimeNode.setAttribute("type", mime); - outputNode.addContent(mimeNode); - } - programNode.addContent(outputNode); - } - for (RuntimeEnvironmentConstraint rec : getREs()) { - Element rteNode = new Element("rte"); - rteNode.setAttribute("name", rec.getID()); - rteNode.setAttribute("relation", rec.getRelation()); - programNode.addContent(rteNode); - } - if ((group != null) && !group.isEmpty()) { - Element groupNode = new Element("group"); - groupNode.setAttribute("name", group); - programNode.addContent(groupNode); - } - if ((test_local != null) && !test_local.isEmpty()) { - Element testNode = new Element("test"); - testNode.setAttribute("local", test_local); - programNode.addContent(testNode); - } - if ((icon_url != null) && !icon_url.isEmpty()) { - Element iconNode = new Element("icon"); - iconNode.setAttribute("url", icon_url); - programNode.addContent(iconNode); - } - if (!getQueue_preferred().isEmpty() || !getQueue_deny().isEmpty()) { - Element queueNode = new Element("queue"); - for (String url : getQueue_preferred()) { - Element preferredNode = new Element("prefer"); - preferredNode.setAttribute("url", url); - queueNode.addContent(preferredNode); - } - for (String url : getQueue_deny()) { - Element denyNode = new Element("deny"); - denyNode.setAttribute("url", url); - queueNode.addContent(denyNode); - } - programNode.addContent(queueNode); - } - Element validReturnCodesNode = new Element("validReturnCodes"); - validReturnCodesNode.setAttribute("codes", getReturnCodesAsText()); - programNode.addContent(validReturnCodesNode); - - return programNode; - } - /** - * Specifies the UseCaseDescription from the root of an XML description - * which is accessible online. - * - * @param programNode - * @throws DeserializationException - */ - private void readFromXmlElement(Element programNode) throws DeserializationException { - if (programNode.getName().compareToIgnoreCase("program") != 0) - throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'"); - - setUsecaseid(programNode.getAttributeValue("name")); - setDescription(programNode.getAttributeValue("description")); - setCommand(programNode.getAttributeValue("command")); - String timeoutStr = programNode.getAttributeValue("timeout"); - if (timeoutStr != null) - setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr)); - timeoutStr = programNode.getAttributeValue("preparing_timeout"); - if (timeoutStr != null) - setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr)); - - String includeStdInStr = programNode.getAttributeValue("includeStdIn"); - if (includeStdInStr != null && !includeStdInStr.isEmpty()) { - setIncludeStdIn(includeStdInStr.equals("true")); - } - - String includeStdOutStr = programNode.getAttributeValue("includeStdOut"); - if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) { - setIncludeStdOut(includeStdOutStr.equals("true")); - } - - String includeStdErrStr = programNode.getAttributeValue("includeStdErr"); - if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) { - setIncludeStdErr(includeStdErrStr.equals("true")); - } - - for (Object cur_ob : programNode.getChildren()) { - Element cur = (Element) cur_ob; - - String name = cur.getAttributeValue("name"); - - String type = cur.getName(); - boolean binary = false; - if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) { - binary = true; - } - boolean list = false; - if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) { - list = true; - } - boolean concatenate = false; - if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) { - concatenate = true; - } - boolean forceCopy = false; - if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) { - forceCopy = true; - } - - Element inner = null; - String innerType = null, tag = null, path = null; - if (cur.getChildren().size() > 0) { - inner = (Element) cur.getChildren().get(0); - innerType = inner.getName(); - tag = inner.getAttributeValue("tag"); - path = inner.getAttributeValue("path"); - } - // build mime type declaration list - ArrayList<String> mime = new ArrayList<String>(); - for (Object child : cur.getChildren()) { - Element curChild = (Element) child; - if (curChild.getName().equalsIgnoreCase("mime")) { - mime.add(curChild.getAttributeValue("type")); - } - } - if (type.equalsIgnoreCase("static")) { - ScriptInputStatic si = new ScriptInputStatic(); - Element content = cur.getChild("content"); - if (content == null) - throw new DeserializationException("FIXME: script tag without embedded content tag"); - si.setUrl(content.getAttributeValue("url")); - if (si.getUrl() == null) - si.setContent(content.getText()); - fillInputDescription(si, binary, forceCopy, innerType, tag, path); - getStatic_inputs().add(si); - } else if (type.equalsIgnoreCase("input")) { - ScriptInputUser indesc = new ScriptInputUser(); - indesc.setList(list); - indesc.setMime(mime); - indesc.setConcatenate(concatenate); - fillInputDescription(indesc, binary, forceCopy, innerType, tag, path); - getInputs().put(Tools.sanitiseName(name), indesc); - } else if (type.equalsIgnoreCase("output")) { - ScriptOutput outdesc = new ScriptOutput(); - outdesc.setMime(mime); - - boolean ok = true; - if (null == innerType) { - // don't know what to do - throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?"); - } else if (innerType.equalsIgnoreCase("fromfile")) { - outdesc.setPath(path); - outdesc.setBinary(binary); - } else { - throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'"); - } - if (ok) { - getOutputs().put(Tools.sanitiseName(name), outdesc); - } - } else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) { - getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation"))); - } else if (type.equalsIgnoreCase("group")) { - group = name; - } else if (type.equalsIgnoreCase("test")) { - test_local = cur.getAttributeValue("local"); - } else if (type.equalsIgnoreCase("icon")) { - icon_url = cur.getAttributeValue("url"); - } else if (type.equalsIgnoreCase("queue")) { - for (Object child_ob : cur.getChildren()) { - Element child = (Element) child_ob; - if (child.getName().equalsIgnoreCase("prefer")) - getQueue_preferred().add(child.getAttributeValue("url")); - else if (child.getName().equalsIgnoreCase("deny")) - getQueue_deny().add(child.getAttributeValue("url")); - else - throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry"); - } - } else if (type.equalsIgnoreCase("command")) { - // i like to have the ability to inject complete shell script - // fragments into the use case, - // so this should be replace and should allow multiple lines - if ((getCommand() != null) && !getCommand().isEmpty()) { - throw new DeserializationException("You have specified both command attribute and command tag."); - } - setCommand(cur.getText()); - } else if (type.equalsIgnoreCase("validReturnCodes")) { - String codeString = cur.getAttributeValue("codes"); - if (codeString != null) { - setReturnCodesAsText(codeString); - } - } - else { - throw new DeserializationException("Unexpected and uninterpreted attribute " + type); - } - } - } - - private void fillInputDescription(ScriptInput fillMe, boolean binary, boolean forceCopy, String innerType, String tag, String path) throws DeserializationException { - fillMe.setBinary(binary); - fillMe.setForceCopy(forceCopy); - if (null == innerType) { - // don't know what to do - throw new DeserializationException("FIXME: Found null == innerType for input, is this the bug?"); - } else if (innerType.equalsIgnoreCase("replace")) { - fillMe.setTag(tag); - fillMe.setTempFile(false); - fillMe.setFile(false); - getTags().add(tag); - } else if (innerType.equalsIgnoreCase("tempfile")) { - fillMe.setTag(tag); - fillMe.setTempFile(true); - fillMe.setFile(false); - getTags().add(tag); - } else if (innerType.equalsIgnoreCase("file")) { - fillMe.setTag(path); - fillMe.setTempFile(false); - fillMe.setFile(true); - } else { - throw new DeserializationException("Problem reading input port: unknown innerType '" + innerType + "'"); - } - } - - /** - * returns icon that is referenced in use case description - */ - public ImageIcon getImageIcon() { - if (null == icon_url) return null; - try { - URL u = new URL(icon_url); - return new ImageIcon(u, getUsecaseid()); - } catch (Exception e) { - logger.error(e); - return null; - } - } - - /** - * String representation of the use case. It also contains interesting - * information on the availability of resources in the grid to actually - * execute that workflow element. - * - * @return String - */ - @Override - public String toString() { - List<String> hlp = new ArrayList<String>(); - hlp.add("usecaseid: " + getUsecaseid()); - hlp.add("description: " + getDescription()); - hlp.add("group: " + group); - hlp.add("test: " + test_local); - hlp.add("tags: " + getTags()); - for (Map.Entry<String, ScriptInput> cur : getInputs().entrySet()) { - hlp.add(">" + cur.getKey() + ">: " + cur.getValue().toString()); - } - for (Map.Entry<String, ScriptOutput> cur : getOutputs().entrySet()) { - hlp.add("<" + cur.getKey() + "<: " + cur.getValue().toString()); - } - hlp.add("RE: " + getREs().toString()); - hlp.add("preferred queues: " + getQueue_preferred()); - hlp.add("denied queues: " + getQueue_deny()); - String tos = super.toString() + "["; - for (int i = 0; i < hlp.size(); i++) { - if (i != 0) - tos += ", "; - tos += hlp.get(i); - } - return tos + " ]"; - } - - /** - * hajo's test just pass an url or file url to an xml file - * - * @throws IOException - * @throws MalformedURLException - * @throws DeserializationException - */ - public static void main(String[] argv) throws MalformedURLException, IOException, DeserializationException { - UseCaseDescription d = new UseCaseDescription(new URL(argv[0]).openStream()); - logger.info(d.getCommand()); - } - - /** - * @param command the command to set - */ - @ConfigurationProperty(name = "command", label = "Command", description="What is actually executed on the shell") - public void setCommand(String command) { - this.command = command; - } - - /** - * @param description the description to set - */ - @ConfigurationProperty(name = "description", label = "Description", description="Textual description of the tool", required=false, uri="http://purl.org/dc/elements/1.1/description";) - public void setDescription(String description) { - this.description = description; - } - - /** - * @return the description - */ - public String getDescription() { - return description; - } - - /** - * @param executionTimeoutInSeconds the executionTimeoutInSeconds to set - */ - @ConfigurationProperty(name = "executionTimeoutInSeconds", label = "Execution Timeout In Seconds") - public void setExecutionTimeoutInSeconds(int executionTimeoutInSeconds) { - this.executionTimeoutInSeconds = executionTimeoutInSeconds; - } - - /** - * @return the executionTimeoutInSeconds - */ - public int getExecutionTimeoutInSeconds() { - return executionTimeoutInSeconds; - } - - /** - * @param inputs the inputs to set - */ - public void setInputs(Map<String, ScriptInput> inputs) { - this.inputs = inputs; - } - - @ConfigurationProperty(name = "inputs", label = "Inputs", required=false) - public void setInputs(Set<InputMap> inputs) { - if (inputs != null) { - this.inputs = new HashMap<String, ScriptInput>(); - for (InputMap inputMap : inputs) { - this.inputs.put(inputMap.getPort(), inputMap.getInput()); - } - } else { - this.inputs = null; - } - } - - /** - * @return the inputs - */ - public Map<String, ScriptInput> getInputs() { - if (inputs == null) { - inputs = new HashMap<String, ScriptInput>(); - } - return inputs; - } - - /** - * @param outputs the outputs to set - */ - public void setOutputs(Map<String, ScriptOutput> outputs) { - this.outputs = outputs; - } - - @ConfigurationProperty(name = "outputs", label = "Outputs", required=false) - public void setOutputs(Set<OutputMap> outputs) { - if (outputs != null) { - this.outputs = new HashMap<String, ScriptOutput>(); - for (OutputMap outputMap : outputs) { - this.outputs.put(outputMap.getPort(), outputMap.getOutput()); - } - } else { - this.outputs = null; - } - } - - /** - * @return the outputs - */ - public Map<String, ScriptOutput> getOutputs() { - if (outputs == null) { - outputs = new HashMap<String, ScriptOutput>(); - } - return outputs; - } - - /** - * @param preparingTimeoutInSeconds the preparingTimeoutInSeconds to set - */ - @ConfigurationProperty(name = "preparingTimeoutInSeconds", label = "Preparing Timeout In Seconds") - public void setPreparingTimeoutInSeconds(int preparingTimeoutInSeconds) { - this.preparingTimeoutInSeconds = preparingTimeoutInSeconds; - } - - /** - * @return the preparingTimeoutInSeconds - */ - public int getPreparingTimeoutInSeconds() { - return preparingTimeoutInSeconds; - } - - /** - * @param queue_deny the queue_deny to set - */ - public void setQueue_deny(ArrayList<String> queue_deny) { - this.queue_deny = queue_deny; - } - - /** - * @return the queue_deny - */ - public ArrayList<String> getQueue_deny() { - if (queue_deny == null) { - queue_deny = new ArrayList<String>(); - } - return queue_deny; - } - - /** - * @param queue_preferred the queue_preferred to set - */ - public void setQueue_preferred(ArrayList<String> queue_preferred) { - this.queue_preferred = queue_preferred; - } - - /** - * @return the queue_preferred - */ - public ArrayList<String> getQueue_preferred() { - if (queue_preferred == null) { - queue_preferred = new ArrayList<String>(); - } - return queue_preferred; - } - - /** - * @param rEs the rEs to set - */ - public void setREs(List<RuntimeEnvironmentConstraint> rEs) { - REs = rEs; - } - - /** - * @return the rEs - */ - public List<RuntimeEnvironmentConstraint> getREs() { - if (REs == null) { - REs = new ArrayList<RuntimeEnvironmentConstraint>(); - } - return REs; - } - - /** - * @param static_inputs the static_inputs to set - */ - @ConfigurationProperty(name = "staticInputs", label = "Static Inputs", ordering=OrderPolicy.NON_ORDERED, required=false) - public void setStatic_inputs(List<ScriptInputStatic> static_inputs) { - this.static_inputs = static_inputs; - } - - /** - * @return the static_inputs - */ - public List<ScriptInputStatic> getStatic_inputs() { - if (static_inputs == null) { - static_inputs = new ArrayList<ScriptInputStatic>(); - } - return static_inputs; - } - - /** - * @param tags the tags to set - */ - public void setTags(List<String> tags) { - this.tags = tags; - } - - /** - * @return the tags - */ - public List<String> getTags() { - if (tags == null) { - tags = new ArrayList<String>(); - } - return tags; - } - - /** - * @param usecaseid the usecaseid to set - */ - @ConfigurationProperty(name = "usecaseid", label = "Title", uri="http://purl.org/dc/elements/1.1/title";, required=false) - public void setUsecaseid(String usecaseid) { - this.usecaseid = usecaseid; - } - - /** - * @return the usecaseid - */ - public String getUsecaseid() { - return usecaseid; - } - - public boolean isIncludeStdIn() { - return includeStdIn; - } - - @ConfigurationProperty(name = "includeStdIn", label = "Include STDIN") - public void setIncludeStdIn(boolean includeStdIn) { - this.includeStdIn = includeStdIn; - } - - public boolean isIncludeStdOut() { - return includeStdOut; - } - - @ConfigurationProperty(name = "includeStdOut", label = "Include STDOUT") - public void setIncludeStdOut(boolean includeStdOut) { - this.includeStdOut = includeStdOut; - } - - public boolean isIncludeStdErr() { - return includeStdErr; - } - - @ConfigurationProperty(name = "includeStdErr", label = "Include STDERR") - public void setIncludeStdErr(boolean includeStdErr) { - this.includeStdErr = includeStdErr; - } - - /** - * @return the validReturnCodes - */ - public List<Integer> getValidReturnCodes() { - if (validReturnCodes == null) { - validReturnCodes = new ArrayList<Integer>(); - } - if (validReturnCodes.isEmpty()) { - validReturnCodes.add(0); - } - return validReturnCodes; - } - - /** - * @param validReturnCodes the validReturnCodes to set - */ - public void setValidReturnCodes(List<Integer> validReturnCodes) { - this.validReturnCodes = validReturnCodes; - } - - public String getReturnCodesAsText() { - return StringUtils.join(getValidReturnCodes(), ","); - } - - public void setReturnCodesAsText(String text) { - if (getValidReturnCodes() == null) { - validReturnCodes = new ArrayList<Integer>(); - } - validReturnCodes.clear(); - String[] codes = text.split(","); - for (String code : codes) { - try { - Integer codeInt = new Integer(code); - if (!validReturnCodes.contains(codeInt)) { - validReturnCodes.add(codeInt); - } - } - catch (NumberFormatException e) { - logger.error(e); - } - } - if (validReturnCodes.isEmpty()) { - validReturnCodes.add(0); - } - Collections.sort(validReturnCodes); - } - - /** - * @return the group - */ - public String getGroup() { - return group; - } - - /** - * @param group the group to set - */ - public void setGroup(String group) { - this.group = group; - } - - /** - * @return the icon_url - */ - public String getIcon_url() { - return icon_url; - } - - @ConfigurationBean(uri = ExternalToolActivity.URI + "#OutputMap") - public static class OutputMap { - private String port; - - private ScriptOutput output; - - public String getPort() { - return port; - } - - @ConfigurationProperty(name = "port", label = "Port") - public void setPort(String port) { - this.port = port; - } - - public ScriptOutput getOutput() { - return output; - } - - @ConfigurationProperty(name = "output", label = "Output") - public void setOutput(ScriptOutput output) { - this.output = output; - } - } - - @ConfigurationBean(uri = ExternalToolActivity.URI + "#InputMap") - public static class InputMap { - private String port; - - private ScriptInputUser input; - - public String getPort() { - return port; - } - - @ConfigurationProperty(name = "port", label = "Port") - public void setPort(String port) { - this.port = port; - } - - public ScriptInputUser getInput() { - return input; - } - - @ConfigurationProperty(name = "input", label = "Input") - public void setInput(ScriptInputUser input) { - this.input = input; - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java index 1a43461..949ae93 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java @@ -37,9 +37,9 @@ public class UseCaseEnumeration { private static Logger logger = Logger.getLogger(UseCaseEnumeration.class); - public static List<UseCaseDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException { + public static List<ToolDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException { - List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); + List<ToolDescription> ret = new ArrayList<ToolDescription>(); URLConnection con = null; try { URL url = new URL(xmlFileUrl); @@ -61,9 +61,9 @@ public class UseCaseEnumeration { } - public static List<UseCaseDescription> readDescriptionsFromStream(InputStream is) { + public static List<ToolDescription> readDescriptionsFromStream(InputStream is) { - List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); + List<ToolDescription> ret = new ArrayList<ToolDescription>(); SAXBuilder builder = new SAXBuilder(); Document doc = null; @@ -89,7 +89,7 @@ public class UseCaseEnumeration { Element child = (Element) ochild; if (child.getName().equalsIgnoreCase("program")) { try { - ret.add(new UseCaseDescription(child)); + ret.add(new ToolDescription(child)); } catch (DeserializationException e) { logger.error(e); } @@ -98,10 +98,10 @@ public class UseCaseEnumeration { return ret; } - public static UseCaseDescription readDescriptionFromUrl( + public static ToolDescription readDescriptionFromUrl( String repositoryUrl, String id) throws IOException { - List<UseCaseDescription> descriptions = readDescriptionsFromUrl(repositoryUrl); - for (UseCaseDescription usecase : descriptions) { + List<ToolDescription> descriptions = readDescriptionsFromUrl(repositoryUrl); + for (ToolDescription usecase : descriptions) { if (usecase.getUsecaseid().equals(id)) { return usecase; } http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/ToolInvocation.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/ToolInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/ToolInvocation.java index 485f613..2fc56a9 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/ToolInvocation.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/ToolInvocation.java @@ -34,7 +34,7 @@ import org.apache.commons.io.IOUtils; import org.apache.taverna.activities.externaltool.desc.ScriptInput; import org.apache.taverna.activities.externaltool.desc.ScriptInputStatic; import org.apache.taverna.activities.externaltool.desc.ScriptInputUser; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.invocation.InvocationContext; import org.apache.taverna.reference.ExternalReferenceSPI; import org.apache.taverna.reference.Identified; @@ -67,7 +67,7 @@ public abstract class ToolInvocation { return actualOsCommand; } - protected UseCaseDescription usecase; + protected ToolDescription usecase; protected final HashMap<String, String> tags = new HashMap<String, String>(); protected int nTempFiles = 0; private static int submissionID = 0; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java index 13154d9..f127049 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java @@ -23,7 +23,7 @@ import java.io.IOException; import java.util.Map; import org.apache.taverna.activities.externaltool.InvocationCreator; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; import org.apache.taverna.activities.externaltool.manager.InvocationMechanism; import org.apache.taverna.reference.ReferenceService; @@ -50,7 +50,7 @@ public final class LocalInvocationCreator implements } @Override - public ToolInvocation convert(InvocationMechanism m, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { + public ToolInvocation convert(InvocationMechanism m, ToolDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { ExternalToolLocalInvocationMechanism mechanism = (ExternalToolLocalInvocationMechanism) m; ToolInvocation result = null; try { http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java index c88f7c8..a6a8d47 100755 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java @@ -49,7 +49,7 @@ import java.util.regex.Matcher; import org.apache.taverna.activities.externaltool.desc.ScriptInput; import org.apache.taverna.activities.externaltool.desc.ScriptOutput; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.InvocationException; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; import org.apache.taverna.activities.externaltool.ssh.SshNode; @@ -93,7 +93,7 @@ public class LocalToolInvocation extends ToolInvocation { private static String LOCAL_INVOCATION_FILE = "localInvocations"; - public LocalToolInvocation(UseCaseDescription desc, boolean retrieveData, String mainTempDirectory, String shellPrefix, String linkCommand) throws IOException { + public LocalToolInvocation(ToolDescription desc, boolean retrieveData, String mainTempDirectory, String shellPrefix, String linkCommand) throws IOException { usecase = desc; setRetrieveData(retrieveData); http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java index 8f1950e..8ebc656 100644 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java @@ -25,7 +25,7 @@ import java.util.Map; import org.apache.taverna.activities.externaltool.InvocationCreator; import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; import org.apache.log4j.Logger; @@ -58,7 +58,7 @@ public final class SshInvocationCreator implements InvocationCreator { } @Override - public ToolInvocation convert(InvocationMechanism m, UseCaseDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { + public ToolInvocation convert(InvocationMechanism m, ToolDescription description, Map<String, T2Reference> data, ReferenceService referenceService) { ExternalToolSshInvocationMechanism mechanism = (ExternalToolSshInvocationMechanism) m; SshToolInvocation result = null; try { http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/59a0dc12/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java index edf9698..a363f8d 100755 --- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java +++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java @@ -45,7 +45,7 @@ import java.util.regex.Matcher; import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna; import org.apache.taverna.activities.externaltool.desc.ScriptInput; import org.apache.taverna.activities.externaltool.desc.ScriptOutput; -import org.apache.taverna.activities.externaltool.desc.UseCaseDescription; +import org.apache.taverna.activities.externaltool.desc.ToolDescription; import org.apache.taverna.activities.externaltool.invocation.AskUserForPw; import org.apache.taverna.activities.externaltool.invocation.InvocationException; import org.apache.taverna.activities.externaltool.invocation.ToolInvocation; @@ -124,7 +124,7 @@ public class SshToolInvocation extends ToolInvocation { return null; } - public SshToolInvocation(UseCaseDescription desc, SshNode workerNodeA, + public SshToolInvocation(ToolDescription desc, SshNode workerNodeA, AskUserForPw askUserForPwA, CredentialManager credentialManager) throws JSchException, SftpException { this.workerNode = workerNodeA;
