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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:37:18 UTC
[58/70] [abbrv] incubator-taverna-common-activities git commit:
taverna-external-tool-activity/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/java/net/sf/taverna/t2/activities/externaltool/ssh/SshMechanismCreator.java
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diff --git a/src/main/java/net/sf/taverna/t2/activities/externaltool/ssh/SshMechanismCreator.java b/src/main/java/net/sf/taverna/t2/activities/externaltool/ssh/SshMechanismCreator.java
deleted file mode 100644
index 5271b12..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/externaltool/ssh/SshMechanismCreator.java
+++ /dev/null
@@ -1,84 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.externaltool.ssh;
-
-import java.util.ArrayList;
-
-import net.sf.taverna.t2.activities.externaltool.manager.InvocationMechanism;
-import net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator;
-
-import org.apache.log4j.Logger;
-import org.jdom.Element;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation;
-
-/**
- * @author alanrw
- *
- */
-public class SshMechanismCreator extends MechanismCreator {
-
-
- private static Logger logger = Logger.getLogger(SshMechanismCreator.class);
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator#canHandle(java.lang.String)
- */
- @Override
- public boolean canHandle(String mechanismType) {
- return mechanismType.equals(SshUseCaseInvocation.SSH_USE_CASE_INVOCATION_TYPE);
- }
-
-
- @Override
- public InvocationMechanism convert(Element detailsElement,
- String mechanismName) {
- ExternalToolSshInvocationMechanism result = new ExternalToolSshInvocationMechanism();
- result.setName(mechanismName);
- ArrayList<SshNode> nodeList = new ArrayList<SshNode>();
- for (Object nodeObject : detailsElement.getChildren("sshNode")) {
- Element nodeElement = (Element) nodeObject;
- Element hostElement = nodeElement.getChild("host");
- String host;
- int port;
- String directory;
-
- host = hostElement.getText();
-
- Element portElement = nodeElement.getChild("port");
- port = Integer.parseInt(portElement.getText());
-
- Element directoryElement = nodeElement.getChild("directory");
-
- directory = directoryElement.getText();
-
- boolean newNode = !SshNodeFactory.getInstance().containsSshNode(host, port, directory);
-
- SshNode node = SshNodeFactory.getInstance().getSshNode(host, port, directory);
-
- if (newNode) {
-
- Element linkCommandElement = nodeElement.getChild("linkCommand");
- if (linkCommandElement != null) {
- node.setLinkCommand(linkCommandElement.getText());
- }
-
- Element copyCommandElement = nodeElement.getChild("copyCommand");
- if (copyCommandElement != null) {
- node.setCopyCommand(copyCommandElement.getText());
- }
-
- Element retrieveDataElement = nodeElement.getChild("retrieveData");
- node.setRetrieveData(retrieveDataElement != null);
- }
- nodeList.add(node);
-
- }
- result.setNodes(nodeList);
- return result;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.InvocationCreator
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.InvocationCreator b/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.InvocationCreator
deleted file mode 100644
index 3eeef74..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.InvocationCreator
+++ /dev/null
@@ -1,2 +0,0 @@
-net.sf.taverna.t2.activities.externaltool.local.LocalInvocationCreator
-net.sf.taverna.t2.activities.externaltool.ssh.SshInvocationCreator
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister b/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister
deleted file mode 100644
index 4f4b71f..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister
+++ /dev/null
@@ -1,2 +0,0 @@
-net.sf.taverna.t2.activities.externaltool.local.LocalInvocationPersister
-net.sf.taverna.t2.activities.externaltool.ssh.SshInvocationPersister
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator b/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator
deleted file mode 100644
index 2166ed6..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator
+++ /dev/null
@@ -1,2 +0,0 @@
-net.sf.taverna.t2.activities.externaltool.local.LocalMechanismCreator
-net.sf.taverna.t2.activities.externaltool.ssh.SshMechanismCreator
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ExternalReferenceSPI
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ExternalReferenceSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ExternalReferenceSPI
deleted file mode 100644
index 6a18935..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ExternalReferenceSPI
+++ /dev/null
@@ -1,2 +0,0 @@
-# Implementation classes of ExternalReferenceSPI go here, one per line
-de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ValueToReferenceConverterSPI
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ValueToReferenceConverterSPI b/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ValueToReferenceConverterSPI
deleted file mode 100644
index 53ca06c..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.reference.ValueToReferenceConverterSPI
+++ /dev/null
@@ -1,3 +0,0 @@
-# Implementation classes of ValueToReferenceConverterSPI go here, one per line
-de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrlToSshReference
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.RunDeletionListener
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.RunDeletionListener b/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.RunDeletionListener
deleted file mode 100644
index ac84bb3..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.RunDeletionListener
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.externaltool.ExternalToolRunDeletionListener
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
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diff --git a/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index c97a79d..0000000
--- a/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1,2 +0,0 @@
-net.sf.taverna.t2.activities.externaltool.ExternalToolActivityHealthChecker
-net.sf.taverna.t2.activities.externaltool.ExternalToolActivityMimeTypeChecker
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/spring/external-tool-activity-context-osgi.xml
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diff --git a/src/main/resources/META-INF/spring/external-tool-activity-context-osgi.xml b/src/main/resources/META-INF/spring/external-tool-activity-context-osgi.xml
deleted file mode 100644
index 197f2c0..0000000
--- a/src/main/resources/META-INF/spring/external-tool-activity-context-osgi.xml
+++ /dev/null
@@ -1,42 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="SshReference" interface="net.sf.taverna.t2.reference.ExternalReferenceSPI" />
-
- <service ref="invocationGroupManager" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationGroupManager" />
-
- <service ref="LocalInvocationPersister" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister" />
- <service ref="SshInvocationPersister" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister" />
-
- <service ref="LocalMechanismCreator" interface="net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator" />
- <service ref="SshMechanismCreator" interface="net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator" />
-
- <service ref="ExternalToolRunDeletionListener" interface="net.sf.taverna.t2.workflowmodel.RunDeletionListener" />
-
- <service ref="SshUrlToSshReference" interface="net.sf.taverna.t2.reference.ValueToReferenceConverterSPI" />
-
- <service ref="ExternalToolActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
- <service ref="ExternalToolActivityMimeTypeChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
-
- <service ref="LocalInvocationCreator" interface="net.sf.taverna.t2.activities.externaltool.InvocationCreator" />
- <service ref="SshInvocationCreator" interface="net.sf.taverna.t2.activities.externaltool.InvocationCreator" />
-
- <service ref="externalToolActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
-
- <list id="invocationCreators" interface="net.sf.taverna.t2.activities.externaltool.InvocationCreator" cardinality="0..N" />
-
- <list id="mechanismCreators" interface="net.sf.taverna.t2.activities.externaltool.manager.MechanismCreator" cardinality="0..N" />
-
- <list id="invocationPersisters" interface="net.sf.taverna.t2.activities.externaltool.manager.InvocationPersister" cardinality="0..N" />
-
- <reference id="credentialManager" interface="net.sf.taverna.t2.security.credentialmanager.CredentialManager" />
-
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
-
- <reference id="edits" interface="net.sf.taverna.t2.workflowmodel.Edits" />
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/META-INF/spring/external-tool-activity-context.xml
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diff --git a/src/main/resources/META-INF/spring/external-tool-activity-context.xml b/src/main/resources/META-INF/spring/external-tool-activity-context.xml
deleted file mode 100644
index a3cfdb8..0000000
--- a/src/main/resources/META-INF/spring/external-tool-activity-context.xml
+++ /dev/null
@@ -1,50 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="SshReference" class="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference">
- <property name="credentialManager" ref="credentialManager" />
- </bean>
-
- <bean id="LocalInvocationPersister" class="net.sf.taverna.t2.activities.externaltool.local.LocalInvocationPersister" />
- <bean id="SshInvocationPersister" class="net.sf.taverna.t2.activities.externaltool.ssh.SshInvocationPersister">
- <property name="credentialManager" ref="credentialManager" />
- </bean>
-
- <bean id="LocalMechanismCreator" class="net.sf.taverna.t2.activities.externaltool.local.LocalMechanismCreator" />
- <bean id="SshMechanismCreator" class="net.sf.taverna.t2.activities.externaltool.ssh.SshMechanismCreator" />
-
- <bean id="ExternalToolRunDeletionListener" class="net.sf.taverna.t2.activities.externaltool.ExternalToolRunDeletionListener">
- <property name="invocationGroupManager" ref="invocationGroupManager" />
- </bean>
-
- <bean id="SshUrlToSshReference" class="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrlToSshReference">
- <property name="credentialManager" ref="credentialManager" />
- </bean>
-
- <bean id="ExternalToolActivityHealthChecker" class="net.sf.taverna.t2.activities.externaltool.ExternalToolActivityHealthChecker">
- <property name="invocationGroupManager" ref="invocationGroupManager" />
- </bean>
- <bean id="ExternalToolActivityMimeTypeChecker" class="net.sf.taverna.t2.activities.externaltool.ExternalToolActivityMimeTypeChecker" />
-
- <bean id="LocalInvocationCreator" class="net.sf.taverna.t2.activities.externaltool.local.LocalInvocationCreator" />
- <bean id="SshInvocationCreator" class="net.sf.taverna.t2.activities.externaltool.ssh.SshInvocationCreator">
- <property name="credentialManager" ref="credentialManager" />
- </bean>
-
-
- <bean id="externalToolActivityFactory" class="net.sf.taverna.t2.activities.externaltool.ExternalToolActivityFactory">
- <property name="invocationCreators" ref="invocationCreators" />
- <property name="mechanismCreators" ref="mechanismCreators" />
- <property name="edits" ref="edits" />
- </bean>
-
- <bean id="invocationGroupManager" class="net.sf.taverna.t2.activities.externaltool.manager.impl.InvocationGroupManagerImpl">
- <constructor-arg name="applicationConfiguration" ref="applicationConfiguration" />
- <constructor-arg name="mechanismCreators" ref="mechanismCreators" />
- <constructor-arg name="invocationPersisters" ref="invocationPersisters" />
- </bean>
-
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
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diff --git a/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml b/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
deleted file mode 100644
index 384cb25..0000000
--- a/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<!DOCTYPE hibernate-mapping PUBLIC
- "-//Hibernate/Hibernate Mapping DTD 3.0//EN"
- "http://hibernate.sourceforge.net/hibernate-mapping-3.0.dtd">
-<!-- Hibernate mapping for ssh reference bean -->
-<hibernate-mapping>
- <joined-subclass
- name="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference"
- extends="net.sf.taverna.t2.reference.AbstractExternalReference">
- <!-- Link to primary key from abstract superclass -->
- <key column="bean_id" />
- <!-- SshReference specific properties below here -->
- <property name="host" type="string" />
- <property name="port" type="integer"/>
- <property name="directory" type="string" />
- <property name="subDirectory" type="string" />
- <property name="fileName" type="string" />
- <property name="dataNatureInteger" type="integer"/>
-
- <property name="charset" type="string" />
- </joined-subclass>
-</hibernate-mapping>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/taverna-external-tool-activity/pom.xml
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diff --git a/taverna-external-tool-activity/pom.xml b/taverna-external-tool-activity/pom.xml
new file mode 100644
index 0000000..17c551f
--- /dev/null
+++ b/taverna-external-tool-activity/pom.xml
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>external-tool-activity</artifactId>
+ <version>2.0.1-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 External Tool Activity</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-api</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-api</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>reference-core-extensions</artifactId>
+ <version>${t2.reference-core-extensions.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.security</groupId>
+ <artifactId>credential-manager</artifactId>
+ <version>${t2.security.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.jdom</groupId>
+ <artifactId>com.springsource.org.jdom</artifactId>
+ <version>${jdom.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.commons</groupId>
+ <artifactId>com.springsource.org.apache.commons.lang</artifactId>
+ <version>${commons.lang.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.openengsb.wrapped</groupId>
+ <artifactId>com.jcraft.jsch-all</artifactId>
+ <version>${jsch.version}</version>
+ </dependency>
+ <!--dependency>
+ <groupId>com.jcraft.jsch</groupId>
+ <artifactId>com.springsource.com.jcraft.jsch</artifactId>
+ <version>${jsch.version}</version>
+ </dependency-->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>activity-test-utils</artifactId>
+ <version>${t2.activities.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository</url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ <repository>
+ <id>repository.springframework.maven.release</id>
+ <name>Spring Framework Maven Release Repository</name>
+ <url>http://maven.springframework.org/release</url>
+ </repository>
+ </repositories>
+ <scm>
+ <connection>scm:git:https://github.com/taverna/taverna-external-tool-activity.git</connection>
+ <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-external-tool-activity.git</developerConnection>
+ <url>https://github.com/taverna/taverna-external-tool-activity/</url>
+ <tag>HEAD</tag>
+ </scm>
+
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/6bc470a3/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
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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
new file mode 100644
index 0000000..e2ae7e1
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
@@ -0,0 +1,77 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.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/6bc470a3/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
new file mode 100755
index 0000000..a6bf707
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
@@ -0,0 +1,75 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.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/6bc470a3/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
new file mode 100644
index 0000000..ea49079
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
@@ -0,0 +1,253 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+
+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/6bc470a3/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
new file mode 100644
index 0000000..baa68d2
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
@@ -0,0 +1,162 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+
+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/6bc470a3/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
new file mode 100644
index 0000000..a9f97b0
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
@@ -0,0 +1,136 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+
+import java.nio.charset.Charset;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.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/6bc470a3/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
new file mode 100644
index 0000000..4e108b9
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
@@ -0,0 +1,75 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.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/6bc470a3/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
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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
new file mode 100644
index 0000000..858b7fa
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
@@ -0,0 +1,101 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+import java.util.ArrayList;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.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/6bc470a3/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
new file mode 100644
index 0000000..fe63cc9
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
@@ -0,0 +1,90 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+import java.util.ArrayList;
+
+import net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.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/6bc470a3/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
new file mode 100644
index 0000000..217eae5
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
@@ -0,0 +1,899 @@
+/* Part of the KnowARC Janitor Use-case processor for taverna
+ * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
+ * University of Luebeck, Institute for Neuro- and Bioinformatics
+ * University of Luebeck, Institute for Dermatolgy
+ *
+ * This package is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This package is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this package; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+
+package de.uni_luebeck.inb.knowarc.usecases;
+
+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 net.sf.taverna.t2.activities.externaltool.ExternalToolActivity;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy;
+import net.sf.taverna.t2.workflowmodel.serialization.DeserializationException;
+import net.sf.taverna.t2.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;
+ }
+ }
+
+}