TAVERNA-963 package taverna.externaltool.*
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/98468d30 Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/98468d30 Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/98468d30 Branch: refs/heads/docker Commit: 98468d304f297b53fc73e80befba8787adabdf53 Parents: 142667c Author: Stian Soiland-Reyes <st...@apache.org> Authored: Wed May 4 00:53:18 2016 +0100 Committer: Stian Soiland-Reyes <st...@apache.org> Committed: Wed May 4 01:00:29 2016 +0100 ---------------------------------------------------------------------- .../inb/knowarc/gui/AskUserForPwPopup.java | 74 -- .../inb/knowarc/gui/PleaseWaitDialog.java | 73 -- .../knowarc/usecases/RuntimeEnvironment.java | 251 ------ .../usecases/RuntimeEnvironmentConstraint.java | 160 ---- .../inb/knowarc/usecases/ScriptInput.java | 134 --- .../inb/knowarc/usecases/ScriptInputStatic.java | 73 -- .../inb/knowarc/usecases/ScriptInputUser.java | 99 -- .../inb/knowarc/usecases/ScriptOutput.java | 88 -- .../knowarc/usecases/UseCaseDescription.java | 897 ------------------- .../knowarc/usecases/UseCaseEnumeration.java | 111 --- .../usecases/invocation/AskUserForPw.java | 32 - .../invocation/InvocationException.java | 36 - .../usecases/invocation/UseCaseInvocation.java | 322 ------- .../local/LocalUseCaseInvocation.java | 561 ------------ .../ssh/SshAutoLoginTrustEveryone.java | 70 -- .../usecases/invocation/ssh/SshNode.java | 157 ---- .../usecases/invocation/ssh/SshNodeFactory.java | 66 -- .../usecases/invocation/ssh/SshPool.java | 158 ---- .../usecases/invocation/ssh/SshReference.java | 222 ----- .../knowarc/usecases/invocation/ssh/SshUrl.java | 163 ---- .../invocation/ssh/SshUrlToSshReference.java | 54 -- .../invocation/ssh/SshUseCaseInvocation.java | 561 ------------ .../externaltool/ExternalToolActivity.java | 13 +- .../ExternalToolActivityConfigurationBean.java | 2 +- .../ExternalToolActivityMimeTypeChecker.java | 5 +- .../externaltool/InvocationCreator.java | 5 +- .../externaltool/RetrieveLoginFromTaverna.java | 2 +- .../externaltool/desc/RuntimeEnvironment.java | 251 ++++++ .../desc/RuntimeEnvironmentConstraint.java | 160 ++++ .../externaltool/desc/ScriptInput.java | 134 +++ .../externaltool/desc/ScriptInputStatic.java | 73 ++ .../externaltool/desc/ScriptInputUser.java | 99 ++ .../externaltool/desc/ScriptOutput.java | 88 ++ .../externaltool/desc/UseCaseDescription.java | 897 +++++++++++++++++++ .../externaltool/desc/UseCaseEnumeration.java | 111 +++ .../externaltool/gui/AskUserForPwPopup.java | 74 ++ .../externaltool/gui/PleaseWaitDialog.java | 73 ++ .../externaltool/invocation/AskUserForPw.java | 32 + .../invocation/InvocationException.java | 36 + .../invocation/UseCaseInvocation.java | 321 +++++++ .../ExternalToolLocalInvocationMechanism.java | 2 - .../local/LocalInvocationCreator.java | 6 +- .../local/LocalInvocationPersister.java | 2 - .../local/LocalMechanismCreator.java | 2 - .../local/LocalUseCaseInvocation.java | 560 ++++++++++++ .../ssh/ExternalToolSshInvocationMechanism.java | 5 - .../ssh/SshAutoLoginTrustEveryone.java | 69 ++ .../externaltool/ssh/SshInvocationCreator.java | 11 +- .../ssh/SshInvocationPersister.java | 4 +- .../externaltool/ssh/SshMechanismCreator.java | 4 - .../activities/externaltool/ssh/SshNode.java | 157 ++++ .../externaltool/ssh/SshNodeFactory.java | 66 ++ .../activities/externaltool/ssh/SshPool.java | 157 ++++ .../externaltool/ssh/SshReference.java | 222 +++++ .../activities/externaltool/ssh/SshUrl.java | 163 ++++ .../externaltool/ssh/SshUrlToSshReference.java | 54 ++ .../externaltool/ssh/SshUseCaseInvocation.java | 560 ++++++++++++ ...pache.taverna.reference.ExternalReferenceSPI | 2 +- ...verna.reference.ValueToReferenceConverterSPI | 2 +- .../spring/external-tool-activity-context.xml | 4 +- .../invocation/ssh/SshReference.hbm.xml | 2 +- 61 files changed, 4379 insertions(+), 4413 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java deleted file mode 100644 index 0ce0460..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java +++ /dev/null @@ -1,74 +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 de.uni_luebeck.inb.knowarc.gui; - -import javax.swing.JOptionPane; - -import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw; -import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode; - -public final class AskUserForPwPopup implements AskUserForPw { - private SshNode ret; - private String pw, pp, kf, us; - - public static String ask(String message, String title) { - return (String) JOptionPane.showInputDialog(null, message, title, JOptionPane.QUESTION_MESSAGE, null, null, ""); - } - - public static boolean askYN(String message, String title) { - return JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION; - } - - public String getPassword() { - getUsername(); - if (pw != null) - return pw; - pw = ask("Please enter your password for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); - return pw; - } - - public String getPassphrase() { - getUsername(); - if (pp != null) - return pp; - pp = ask("Please enter your passphrase for " + kf + " used for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); - return pp; - } - - public String getKeyfile() { - getUsername(); - if (kf != null) - return kf; - kf = ask("Please enter the keyfile for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost()); - return kf; - } - - public String getUsername() { - if (us != null) - return us; - us = ask("Please enter the username for " + ret.getHost(), "Username for " + ret.getHost()); - return us; - } - - public void setSshNode(SshNode sshNode) { - this.ret = sshNode; - } - - public void authenticationSucceeded() { - } -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java deleted file mode 100755 index 2a643eb..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java +++ /dev/null @@ -1,73 +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 de.uni_luebeck.inb.knowarc.gui; - -import java.util.ArrayList; -import java.util.List; - -import javax.swing.JDialog; -import javax.swing.JLabel; - -public class PleaseWaitDialog extends JDialog { - private static final long serialVersionUID = 1L; - - static PleaseWaitDialog instance = new PleaseWaitDialog(); - - public class WaitMessage{ - public WaitMessage() { - } - - String str; - public void set(String newstr) { - synchronized (PleaseWaitDialog.instance) { - if(this.str != null && this.str.equals(newstr)) return; - if(this.str != null) messages.remove(this.str); - this.str = newstr; - if(this.str != null) messages.add(this.str); - } - updateDialog(); - } - public void done() { - set(null); - } - } - - private void updateDialog() { - synchronized (PleaseWaitDialog.instance) { - if(messages.size() > 0) this.setVisible(true); - else this.setVisible(false); - String t = ""; - for (String cur : messages) { - t += cur + "<br>"; - } - l.setText("<html>"+t+"</html>"); - } - } - - List<String> messages = new ArrayList<String>(); - - JLabel l; - private PleaseWaitDialog() { - this.setAlwaysOnTop(true); - this.setTitle("Please wait"); - l = new JLabel(""); - this.add(l); - this.setSize(400, 100); - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java deleted file mode 100644 index c7fd889..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java +++ /dev/null @@ -1,251 +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 de.uni_luebeck.inb.knowarc.usecases; - -import java.util.Arrays; -import java.util.Iterator; -import java.util.List; - -import org.apache.log4j.Logger; - -/** - * Representation of information about a single runtime environment. It is used - * to decide if one runtime environment is possibly compatible with another one - * for the selection of queues to commit to. - * - * To experiment/test these functions, run the following java -cp - * target/taverna-knowarc-processor-0.1.7.jar - * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 foo-1 java -cp - * target/taverna-knowarc-processor-0.1.7.jar - * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 bla-2 java -cp - * target/taverna-knowarc-processor-0.1.7.jar - * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1.2 bla-1 - * - * @author Steffen Moeller - */ -@SuppressWarnings("unchecked") -public class RuntimeEnvironment implements Comparable { - - private static Logger logger = Logger.getLogger(RuntimeEnvironment.class); - - - /** - * Unique identification of the runtime environment - the full name - */ - protected String id; - - /** - * Accessor function for the complete identifier of the runtime environment - */ - public String getID() { - return id; - } - - protected String name; - - /** - * Accessor function for the RE's name - */ - public String getName() { - return name; - } - - protected String version; - - /** - * Accessfor function for the version - */ - public String getVersion() { - return version; - } - - /** - * for those busy fellows who don't have the time to convert the String into - * a RuntimeEnvironment object. - * - * @author Steffen Moeller - */ - public boolean atLeastAsCapableAs(String s) { - RuntimeEnvironment tmpRE = new RuntimeEnvironment(s); - return this.atLeastAsCapableAs(tmpRE); - } - - /** - * Indicates if a runtime environment has the same name, and if so, if the - * given RE has the same or a later version. - * - * @author Steffen Moeller - */ - public boolean atLeastAsCapableAs(RuntimeEnvironment re) { - if (!name.equals(re.name)) - return false; - int c = compareVersions(getVersion(), re.getVersion()); - if (c >= 0) { - return true; - } else { - return false; - } - } - - /** - * Indicates if this runtimeEnvironment is the same version or later as any - * in that list. - * - * @author Steffen Moeller - */ - public boolean atLeastAsCapableAsAnyOf(Iterable<RuntimeEnvironment> res) { - boolean compatibleOneFound = false; - Iterator<RuntimeEnvironment> i = res.iterator(); - while (i.hasNext() && !compatibleOneFound) { - RuntimeEnvironment r = i.next(); - compatibleOneFound = atLeastAsCapableAs(r); - } - return compatibleOneFound; - } - - /** - * Indicates if any of the runtime environments listed is the same version - * as this or later. - * - * @author Steffen Moeller - */ - public boolean isInferiorToAtLeastOneIn(Iterable<RuntimeEnvironment> res) { - boolean compatibleOneFound = false; - Iterator<RuntimeEnvironment> i = res.iterator(); - while (i.hasNext() && !compatibleOneFound) { - RuntimeEnvironment r = i.next(); - compatibleOneFound = r.atLeastAsCapableAs(this); - } - return compatibleOneFound; - } - - /** - * Parses a string as commonly presented by the infosystem - * - * @author Steffen Moeller - */ - public RuntimeEnvironment(String raw) { - id = raw; - int dashpos = raw.indexOf("-"); - if (-1 == dashpos) { - version = ""; - name = raw; - } else { - name = raw.substring(0, dashpos); - if (dashpos + 1 <= raw.length()) { - version = raw.substring(dashpos + 1, raw.length()); - } else { - version = ""; - } - } - } - - /** - * to make it behave like a string at time, as it was originally implemented - */ - @Override - public String toString() { - return id; - } - - /** - * Implementation of Comparable interface. It comes handy albeit this - * function says nothing about the compatibility of two runtime environments - * unless their names are identical and the relation of the constraint was - * taken into account. It just sorts them in lists. - */ - public int compareTo(Object o) throws ClassCastException { - RuntimeEnvironment r = (RuntimeEnvironment) o; - if (getName().equals(r.getName())) { - return RuntimeEnvironment.compareVersions(getVersion(), r.getVersion()); - } else { - return id.compareTo(r.getID()); - } - } - - /** - * FIXME: For the sake of simplicity, this implementation makes an error in - * treating . and - in the versions equally. Versions, if numerical, are - * treated numerically. Otherwise it is lexicographical, which is error - * prone, though. Should the 'Scanner' class should be tapped into? - * - * @author Steffen Moeller - */ - public static int compareVersions(String a, String b) { - - // null pointer exceptions are not risked .. we are nice - if (null == a) - a = ""; - if (null == b) - b = ""; - - // catching the dumb case first - if (a.equals(b)) - return 0; - - List as = Arrays.asList(a.split("[.-]")); - List bs = Arrays.asList(b.split("[.-]")); - - // both lists have the empty element as members at least - Iterator aIterator = as.iterator(); - Iterator bIterator = bs.iterator(); - - while (aIterator.hasNext()) { - String aa = (String) aIterator.next(); - if (!bIterator.hasNext()) { - // a is longer while equal so far - return 1; // a > b - } - String bb = (String) bIterator.next(); - if (!aa.equals(bb)) { - // a and b differ - try { - Integer aInt = Integer.parseInt(aa); - Integer bInt = Integer.parseInt(bb); - return aInt.compareTo(bInt); - } catch (Exception e) { - return aa.compareTo(bb); - } - } - } - if (bIterator.hasNext()) { - // b is longer while equal so far - return -1; // a < b - } - return 0; // a == b - } - - /** - * For testing purposes - */ - public static void main(String argv[]) { - if ("compare".equals(argv[0])) { - RuntimeEnvironment r1 = new RuntimeEnvironment(argv[1]); - RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]); - logger.info("r1.getName(): " + r1.getName()); - logger.info("r1.getVersion(): " + r1.getVersion()); - logger.info("r2.getName(): " + r2.getName()); - logger.info("r2.getVersion(): " + r2.getVersion()); - logger.info("r1.atLeastAsCapableAs(r2): " + String.valueOf(r1.atLeastAsCapableAs(r2))); - } else { - logger.info("Don't know how to '" + argv[0] + "'"); - } - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java deleted file mode 100644 index ce7e055..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java +++ /dev/null @@ -1,160 +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 de.uni_luebeck.inb.knowarc.usecases; - -import java.util.Collection; -import java.util.Iterator; - -import org.apache.log4j.Logger; - - -/** - * When use cases present a runtime environment, then they don't want to express - * that these would provide such, but that these request such, i.e. they constrain - * lists of potentially eligible queues. - * @author Steffen Moeller - * @since 2008 - */ -public class RuntimeEnvironmentConstraint extends RuntimeEnvironment { - - private static Logger logger = Logger.getLogger(RuntimeEnvironmentConstraint.class); - - private static String[] ACCEPTED_RELATIONS = new String[] {"=", ">=", "<=", ">", "<"}; - /** - * If there is no relation specified, presume >= - */ - private static String DEFAULT_RELATION = ">="; - - public static String[] getAcceptedRelations() { - return ACCEPTED_RELATIONS; - } - - public static String getDefaultRelation() { - return DEFAULT_RELATION; - } - - /** - * Identifies the relation between runtime environments to be tested - */ - protected String relation; - - /** - * Accessor function for relation - */ - public String getRelation() { - return this.relation; - } - - /** - * Tests of a relation is supported - * @param relation - * @return true iff in <, > , <=, >=, = - */ - public static boolean acceptedRelation(String relation) { - if ((null == relation) || relation.equals("")) { - return false; - } - return relation.equals("=")||relation.equals(">=")||relation.equals("<=")||relation.equals(">")||relation.equals("<"); - } - - /** - * Constructor - * @param id - expects the name of the runtime environment together with the version to which the - * @param relation - relates to (">","<","=",">=","<=") - */ - public RuntimeEnvironmentConstraint(String id, String relation) { - super(id); - if (null == relation || relation.equals("")) { - relation=RuntimeEnvironmentConstraint.getDefaultRelation(); - } - if (relation.equals("==")) { - relation="="; - } - else if (relation.equals("=<")) { - relation="<="; - } - else if (!RuntimeEnvironmentConstraint.acceptedRelation(relation)) { - logger.warn("Unknown relation '"+relation+"', presuming '"+RuntimeEnvironmentConstraint.getDefaultRelation()+"'"); - relation=RuntimeEnvironmentConstraint.getDefaultRelation(); - } - this.relation=relation; - } - - /** - * Perfoms test if the RuntimeEnvironment (RE) passed as argument fulfills the requirements set by the constraint. - * @param re - RE to test - * @return true iff the RE fulfills this REconstraint. - */ - public boolean isFulfilledBy(RuntimeEnvironment re) { - logger.info(re.getID()+" " + this.getRelation() + " "+this.getID() + " ?"); - if (this.getRelation().equals("=")) { - logger.info("="); - return re.getID().equals(this.getID()); - } - if (!re.getName().equals(this.getName())) { - logger.warn("Name match failed"); - return false; - } - int c = RuntimeEnvironment.compareVersions(re.getVersion(),this.getVersion()); - logger.info("c="+c); - if (this.getRelation().equals(">")) return c>0; - if (this.getRelation().equals(">=")) return c>=0; - if (this.getRelation().equals("<=")) return c<=0; - if (this.getRelation().equals("<")) return c<0; - throw new RuntimeException("Unknown/untreated releation '"+this.getRelation()+"'"); - } - - /** - * Iterates over all the RuntimeEnvironments passed as argument. - * @param REs - list of RuntimeEnvironments, mostly those offered at a particular queue - * @return true iff any RE among the REs passed as argument are fulfilling the constraint - */ - public boolean isFulfilledByAtLeastOneIn(Collection<RuntimeEnvironment> REs) { - boolean fulfilled = false; - Iterator<RuntimeEnvironment> i = REs.iterator(); - while(i.hasNext() && !fulfilled) { - RuntimeEnvironment r = i.next(); - fulfilled = this.isFulfilledBy(r); - } - return fulfilled; - } - /** - * For testing purposes - */ - public static void main(String argv[]) { - try { - if (argv[0].equals("--help") || argv.length != 3) { - logger.error("Expecting arguments (<|>|=|<=|>=) runtime1-version runtime2-version"); - } - else { - RuntimeEnvironmentConstraint r1 = new RuntimeEnvironmentConstraint(argv[1], argv[0]); - RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]); - logger.info("r1.getName(): "+r1.getName()); - logger.info("r1.getVersion(): "+r1.getVersion()); - logger.info("r1.getRelation(): "+r1.getRelation()); - logger.info("r2.getName(): "+r2.getName()); - logger.info("r2.getVersion(): "+r2.getVersion()); - logger.info("r1.isFulfilledBy(r2): "+String.valueOf(r1.isFulfilledBy(r2))); - } - } - catch (Exception e) { - logger.error(e); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java deleted file mode 100644 index 50747b5..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java +++ /dev/null @@ -1,134 +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 de.uni_luebeck.inb.knowarc.usecases; - -import java.nio.charset.Charset; - -import org.apache.taverna.activities.externaltool.ExternalToolActivity; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; - -/** - * Integrates inputs to the grid that come from the use case descriptions - * with those that are fed through the workflow. - * - * this class controls name and data storage of one input, - * no matter where the data comes from - */ -@ConfigurationBean(uri = ExternalToolActivity.URI + "#AbstractScriptInput") -public abstract class ScriptInput { - /** - * This input can be referenced under the name 'tag'. - */ - private String tag = null; - /** - * In most cases, the data will be stored under a specific - * filename. - */ - private boolean file = false; - /** - * Set, if the name of the file to be executed is not - * explicitly set but prepared by some automatism and referenced - * via the tagging principle. - */ - private boolean tempFile = false; - /** - * True if (!) the data is binary. (Text otherwise) - */ - private boolean binary = false; - - private String charsetName = Charset.defaultCharset().name(); - private boolean forceCopy = false; - - /** - * @return the tag - */ - public final String getTag() { - return tag; - } - /** - * @param tag the tag to set - */ - @ConfigurationProperty(name = "tag", label = "Tag") - public final void setTag(String tag) { - this.tag = tag; - } - /** - * @return the file - */ - public final boolean isFile() { - return file; - } - /** - * @param file the file to set - */ - @ConfigurationProperty(name = "file", label = "File") - public final void setFile(boolean file) { - this.file = file; - } - /** - * @return the tempFile - */ - public final boolean isTempFile() { - return tempFile; - } - /** - * @param tempFile the tempFile to set - */ - @ConfigurationProperty(name = "tempFile", label = "Temporary File") - public final void setTempFile(boolean tempFile) { - this.tempFile = tempFile; - } - /** - * @return the binary - */ - public final boolean isBinary() { - return binary; - } - /** - * @param binary the binary to set - */ - @ConfigurationProperty(name = "binary", label = "Binary") - public final void setBinary(boolean binary) { - this.binary = binary; - } - - public String getCharsetName() { - return this.charsetName; - } - /** - * @param charsetName the charsetName to set - */ - @ConfigurationProperty(name = "charsetName", label = "Chararter Set") - public void setCharsetName(String charsetName) { - this.charsetName = charsetName; - } - - @ConfigurationProperty(name = "forceCopy", label = "Force Copy") - public final void setForceCopy(boolean forceCopy) { - this.forceCopy = forceCopy; - - } - /** - * @return the forceCopy - */ - public boolean isForceCopy() { - return forceCopy; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java deleted file mode 100644 index 749e104..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java +++ /dev/null @@ -1,73 +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 de.uni_luebeck.inb.knowarc.usecases; - -import org.apache.taverna.activities.externaltool.ExternalToolActivity; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; - -/** - * This subclass of script input is used to manage static content - * which is embedded into the use case description. - */ -@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInputStatic") -public class ScriptInputStatic extends ScriptInput { - - public ScriptInputStatic() { - } - - private String url = null; //if this is set, load content from remote URL - private String content = null; - - @Override - public String toString() { - return "InputStatic[tag: " + - getTag() + (isFile() ? ", file" : "") + (isTempFile() ? ", tempfile" : "") + (isBinary() ? ", binary" : "") + ", content: " + content + "]"; - } - - /** - * @return the url - */ - public final String getUrl() { - return url; - } - - /** - * @param url the url to set - */ - @ConfigurationProperty(name = "url", label = "URL", required=false) - public final void setUrl(String url) { - this.url = url; - } - - /** - * @return the content - */ - public final String getContent() { - return content; - } - - /** - * @param content the content to set - */ - @ConfigurationProperty(name = "content", label = "Content", required=false) - public final void setContent(String content) { - this.content = content; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java deleted file mode 100644 index 715c13e..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java +++ /dev/null @@ -1,99 +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 de.uni_luebeck.inb.knowarc.usecases; -import java.util.ArrayList; - -import org.apache.taverna.activities.externaltool.ExternalToolActivity; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; - -/** - * Internal description of output - */ -@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInput") -public class ScriptInputUser extends ScriptInput { - - /** - * This input may be fed from multiple ouputs. - */ - private boolean list = false; - /** - * True if the data from a list input in taverna is concatenated into one single input file. - */ - private boolean concatenate = false; - - private ArrayList<String> mime = new ArrayList<String>(); - - @Override - public String toString() { - return "Input[tag: " + getTag() + (isFile() ? ", file" : "") - + (isTempFile() ? ", tempfile" : "") - + (isBinary() ? ", binary" : "") + (list ? ", list" : "") - + (concatenate ? ", concatenate" : "") - + " mime: " + mime.toString() + "]"; - } - - /** - * @return the list - */ - public final boolean isList() { - return list; - } - - /** - * @param list the list to set - */ - @ConfigurationProperty(name = "list", label = "List") - public final void setList(boolean list) { - this.list = list; - } - - /** - * @return the concatenate - */ - public final boolean isConcatenate() { - return concatenate; - } - - /** - * @param concatenate the concatenate to set - */ - @ConfigurationProperty(name = "concatenate", label = "Concatenate") - public final void setConcatenate(boolean concatenate) { - this.concatenate = concatenate; - } - - /** - * @return the mime - */ - public final ArrayList<String> getMime() { - if (mime == null) { - mime = new ArrayList<String>(); - } - return mime; - } - - /** - * @param mime the mime to set - */ - @ConfigurationProperty(name = "mime", label = "Mime Types", required=false) - public final void setMime(ArrayList<String> mime) { - this.mime = mime; - } -}; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java deleted file mode 100644 index d824ad4..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java +++ /dev/null @@ -1,88 +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 de.uni_luebeck.inb.knowarc.usecases; -import java.util.ArrayList; - -import org.apache.taverna.activities.externaltool.ExternalToolActivity; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean; -import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty; - -/** - * Internal description of input - */ -@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptOutput") -public class ScriptOutput { - private String path; - private boolean binary; - private ArrayList<String> mime = new ArrayList<String>(); - - @Override - public String toString() { - return "Output[path: " + path + (binary ? ", binary" : "") - + " mime: " + mime.toString() + "]"; - } - - /** - * @return the path - */ - public final String getPath() { - return path; - } - - /** - * @param path the path to set - */ - @ConfigurationProperty(name = "path", label = "Path") - public final void setPath(String path) { - this.path = path; - } - - /** - * @return the binary - */ - public final boolean isBinary() { - return binary; - } - - /** - * @param binary the binary to set - */ - @ConfigurationProperty(name = "binary", label = "Binary") - public final void setBinary(boolean binary) { - this.binary = binary; - } - - /** - * @return the mime - */ - public final ArrayList<String> getMime() { - if (mime == null) { - mime = new ArrayList<String>(); - } - return mime; - } - - /** - * @param mime the mime to set - */ - @ConfigurationProperty(name = "mime", label = "Mime Types", required=false) - public final void setMime(ArrayList<String> mime) { - this.mime = mime; - } -}; http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java deleted file mode 100644 index 1c5914e..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/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 de.uni_luebeck.inb.knowarc.usecases; - -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/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java deleted file mode 100644 index d5c5d2c..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java +++ /dev/null @@ -1,111 +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 de.uni_luebeck.inb.knowarc.usecases; - -import java.io.IOException; -import java.io.InputStream; -import java.net.URL; -import java.net.URLConnection; -import java.util.ArrayList; -import java.util.List; - -import org.apache.taverna.workflowmodel.serialization.DeserializationException; - -import org.apache.log4j.Logger; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.input.SAXBuilder; - -public class UseCaseEnumeration { - - private static Logger logger = Logger.getLogger(UseCaseEnumeration.class); - - public static List<UseCaseDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException { - - List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); - URLConnection con = null; - try { - URL url = new URL(xmlFileUrl); - - con = url.openConnection(); - con.setConnectTimeout(4000); - ret = readDescriptionsFromStream(con.getInputStream()); - - } catch (IOException ioe) { - logger.error("Problem retrieving from " + xmlFileUrl); - logger.error(ioe); - throw ioe; - } - finally { - - } - - return ret; - - } - - public static List<UseCaseDescription> readDescriptionsFromStream(InputStream is) { - - List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>(); - - SAXBuilder builder = new SAXBuilder(); - Document doc = null; - try { - doc = builder.build(is); - is.close(); - } catch (JDOMException e1) { - logger.error(e1); - return ret; - } catch (IOException e1) { - logger.error(e1); - return ret; - } finally { - try { - is.close(); - } catch (IOException e) { - logger.error(e); - } - } - - Element usecases = doc.getRootElement(); - for (Object ochild : usecases.getChildren()) { - Element child = (Element) ochild; - if (child.getName().equalsIgnoreCase("program")) { - try { - ret.add(new UseCaseDescription(child)); - } catch (DeserializationException e) { - logger.error(e); - } - } - } - return ret; - } - - public static UseCaseDescription readDescriptionFromUrl( - String repositoryUrl, String id) throws IOException { - List<UseCaseDescription> descriptions = readDescriptionsFromUrl(repositoryUrl); - for (UseCaseDescription usecase : descriptions) { - if (usecase.getUsecaseid().equals(id)) { - return usecase; - } - } - return null; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java deleted file mode 100644 index e912db1..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java +++ /dev/null @@ -1,32 +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 de.uni_luebeck.inb.knowarc.usecases.invocation; - -public interface AskUserForPw { - - // we will try keyfile first - public String getKeyfile(); - public String getPassphrase(); - - // then username+password - public String getUsername(); - public String getPassword(); - - public void authenticationSucceeded(); -} \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java deleted file mode 100644 index 2f4485f..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java +++ /dev/null @@ -1,36 +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 de.uni_luebeck.inb.knowarc.usecases.invocation; - -public class InvocationException extends Exception { - - /** - * - */ - private static final long serialVersionUID = 437316164959631591L; - - public InvocationException(String string) { - super(string); - } - - public InvocationException(Exception e) { - super(e); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/98468d30/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java ---------------------------------------------------------------------- diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java deleted file mode 100644 index d6b2502..0000000 --- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java +++ /dev/null @@ -1,322 +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 de.uni_luebeck.inb.knowarc.usecases.invocation; - -import java.io.BufferedWriter; -import java.io.ByteArrayOutputStream; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.HashMap; -import java.util.List; -import java.util.Set; - -import org.apache.commons.io.IOUtils; - -import org.apache.taverna.invocation.InvocationContext; -import org.apache.taverna.reference.ExternalReferenceSPI; -import org.apache.taverna.reference.Identified; -import org.apache.taverna.reference.IdentifiedList; -import org.apache.taverna.reference.ReferenceService; -import org.apache.taverna.reference.ReferenceServiceException; -import org.apache.taverna.reference.ReferenceSet; -import org.apache.taverna.reference.T2Reference; -import org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder; -import org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder; -import de.uni_luebeck.inb.knowarc.usecases.ScriptInput; -import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic; -import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser; -import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription; - -/** - * An abstraction of various forms to bring job using the software that is - * referenced as a use case towards their execution. - * - * @author Hajo Nils Krabbenhoeft with some contribution by - * @author Steffen Moeller - */ -public abstract class UseCaseInvocation { - - private String runId; - - - protected static String getActualOsCommand(String osCommand, String pathToOriginal, - String targetName, String pathTarget) { - String actualOsCommand = osCommand; - actualOsCommand = actualOsCommand.replace("%%PATH_TO_ORIGINAL%%", pathToOriginal); - actualOsCommand = actualOsCommand.replace("%%TARGET_NAME%%", targetName); - actualOsCommand = actualOsCommand.replace("%%PATH_TO_TARGET%%", pathTarget); - return actualOsCommand; - } - - protected UseCaseDescription usecase; - protected final HashMap<String, String> tags = new HashMap<String, String>(); - protected int nTempFiles = 0; - private static int submissionID = 0; - protected static InlineByteArrayReferenceBuilder inlineByteArrayReferenceBuilder = new InlineByteArrayReferenceBuilder(); - protected static InlineStringReferenceBuilder inlineStringReferenceBuilder = new InlineStringReferenceBuilder(); - private InvocationContext invocationContext; - private boolean retrieveData; - - /* - * get the class of the data we expect for a given input - */ - @SuppressWarnings("unchecked") - public Class getType(String inputName) { - if (!usecase.getInputs().containsKey(inputName)) - return null; - ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName); - if (input.isList()) { - if (input.isBinary()) - return List.class; - else - return List.class; - } else { - if (input.isBinary()) - return byte[].class; - else - return String.class; - } - } - - /* - * get a list of all the input port names - */ - public Set<String> getInputs() { - return usecase.getInputs().keySet(); - } - - - /* - * get a id, incremented with each job. thus, this should be thread-wide - * unique - */ - public synchronized int getSubmissionID() { - return submissionID++; - } - - /* - * set the data for the input port with given name - */ - @SuppressWarnings("unchecked") - public void setInput(String inputName, ReferenceService referenceService, T2Reference t2Reference) throws InvocationException { - if (t2Reference == null) { - throw new InvocationException("No input specified for " + inputName); - } - ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName); - if (input.isList()) { - IdentifiedList<T2Reference> listOfReferences = (IdentifiedList<T2Reference>) referenceService - .getListService().getList(t2Reference); - - if (!input.isConcatenate()) { - // this is a list input (not concatenated) - // so write every element to its own temporary file - // and create a filelist file - - // we need to write the list elements to temporary files - ScriptInputUser listElementTemp = new ScriptInputUser(); - listElementTemp.setBinary(input.isBinary()); - listElementTemp.setTempFile(true); - - String lineEndChar = "\n"; - if (!input.isFile() && !input.isTempFile()) { - lineEndChar = " "; - } - - String listFileContent = ""; - String filenamesFileContent = ""; - // create a list of all temp file names - for (T2Reference cur : listOfReferences) { - String tmp = setOneInput(referenceService, cur, - listElementTemp); - listFileContent += tmp + lineEndChar; - int ind = tmp.lastIndexOf('/'); - if (ind == -1) { - ind = tmp.lastIndexOf('\\'); - } - if (ind != -1) { - tmp = tmp.substring(ind + 1); - } - filenamesFileContent += tmp + lineEndChar; - } - - // how do we want the listfile to be stored? - ScriptInputUser listFile = new ScriptInputUser(); - listFile.setBinary(false); // since its a list file - listFile.setFile(input.isFile()); - listFile.setTempFile(input.isTempFile()); - listFile.setTag(input.getTag()); - T2Reference listFileContentReference = referenceService - .register(listFileContent, 0, true, invocationContext); - - tags.put(listFile.getTag(), setOneInput(referenceService, - listFileContentReference, listFile)); - - listFile.setTag(input.getTag() + "_NAMES"); - T2Reference filenamesFileContentReference = referenceService - .register(filenamesFileContent, 0, true, null); - tags.put(listFile.getTag(), setOneInput(referenceService, - filenamesFileContentReference, listFile)); - } else { - try { - // first, concatenate all data - if (input.isBinary()) { - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - BufferedWriter outputWriter = new BufferedWriter( - new OutputStreamWriter(outputStream)); - for (T2Reference cur : listOfReferences) { - InputStreamReader inputReader = new InputStreamReader( - getAsStream(referenceService, cur)); - IOUtils.copyLarge(inputReader, outputWriter); - inputReader.close(); - } - outputWriter.close(); - T2Reference binaryReference = referenceService - .register(outputStream.toByteArray(), 0, true, - invocationContext); - tags.put(input.getTag(), setOneInput(referenceService, - binaryReference, input)); - } else { - ByteArrayOutputStream outputStream = new ByteArrayOutputStream(); - BufferedWriter outputWriter = new BufferedWriter( - new OutputStreamWriter(outputStream)); - for (T2Reference cur : listOfReferences) { - InputStreamReader inputReader = new InputStreamReader( - getAsStream(referenceService, cur)); - IOUtils.copyLarge(inputReader, outputWriter); - outputWriter.write(" "); - inputReader.close(); - } - outputWriter.close(); - T2Reference binaryReference = referenceService - .register(outputStream.toByteArray(), 0, true, - invocationContext); - tags.put(input.getTag(), setOneInput(referenceService, - binaryReference, input)); - } - } catch (IOException e) { - throw new InvocationException(e); - } - } - } else { - tags.put(input.getTag(), setOneInput(referenceService, t2Reference, - input)); - } - } - - /* - * submit a grid job and wait for it to finish, then get the result as - * on-demand downloads or directly as data (in case of local execution) - */ - public HashMap<String, Object> Submit(ReferenceService referenceService) throws InvocationException { - submit_generate_job(referenceService); - return submit_wait_fetch_results(referenceService); - } - - /* - * just submit the job. useful if you want to wait for it to finish later on - * - * Can the statics be made more static? - */ - public void submit_generate_job(ReferenceService referenceService) throws InvocationException { - for (ScriptInputStatic input : usecase.getStatic_inputs()) { - T2Reference ref; - if (input.getUrl() != null) { - // Does this work OK with binary - try { - ref = referenceService.register(new URL(input.getUrl()), 0, true, null); - } catch (ReferenceServiceException e) { - throw new InvocationException(e); - } catch (MalformedURLException e) { - throw new InvocationException(e); - } - } else { - ref = referenceService.register((String) input.getContent(), 0, true, null); - } - tags.put(input.getTag(), setOneInput(referenceService, ref, input)); - - } - submit_generate_job_inner(); - } - - protected abstract void submit_generate_job_inner() throws InvocationException; - - /* - * wait for a submitted job to finish and fetch the results - */ - public abstract HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException; - - public abstract String setOneInput(ReferenceService referenceService, T2Reference t2Reference, ScriptInput input) throws InvocationException; - - protected InputStream getAsStream(ReferenceService referenceService, T2Reference t2Reference) { - Identified identified = referenceService.resolveIdentifier(t2Reference, null, null); - if (identified instanceof ReferenceSet) { - ExternalReferenceSPI ref = ((ReferenceSet) identified).getExternalReferences().iterator().next(); - return ref.openStream(invocationContext); - } - return null; - } - - public void setContext(InvocationContext context) { - this.invocationContext = context; - - } - - public InvocationContext getContext() { - return this.invocationContext; - } - - public abstract void setStdIn(ReferenceService referenceService, - T2Reference t2Reference); - - public abstract void rememberRun(String runId); - - /** - * @return the runId - */ - protected String getRunId() { - return runId; - } - - /** - * @param runId the runId to set - */ - protected void setRunId(String runId) { - this.runId = runId; - } - - /** - * @return the retrieveData - */ - protected boolean isRetrieveData() { - return retrieveData; - } - - /** - * @param retrieveData the retrieveData to set - */ - protected void setRetrieveData(boolean retrieveData) { - this.retrieveData = retrieveData; - } - - -}
