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Posted to commits@taverna.apache.org by st...@apache.org on 2015/03/06 17:23:09 UTC
[01/50] incubator-taverna-common-activities git commit:
[maven-release-plugin] prepare release activities-0.7
Repository: incubator-taverna-common-activities
Updated Branches:
refs/heads/master 50dcc955b -> c23952892
[maven-release-plugin] prepare release activities-0.7
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@7965 bf327186-88b3-11dd-a302-d386e5130c1c
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/33df1b5c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/33df1b5c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/33df1b5c
Branch: refs/heads/master
Commit: 33df1b5c8eb249b17fdfa9d21e5e76b1765731a5
Parents: 9f92bc3
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Wed Jun 24 18:04:46 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Wed Jun 24 18:04:46 2009 +0000
----------------------------------------------------------------------
pom.xml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/33df1b5c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 585bce9..2e42c34 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.7-SNAPSHOT</version>
+ <version>0.7</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
@@ -13,12 +13,12 @@
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>workflowmodel-api</artifactId>
- <version>0.6</version>
+ <version>${t2.core.version}</version>
</dependency>
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
<artifactId>workflowmodel-impl</artifactId>
- <version>0.6</version>
+ <version>${t2.core.version}</version>
</dependency>
</dependencies>
</project>
[44/50] incubator-taverna-common-activities git commit:
taverna-dependency-activity
Posted by st...@apache.org.
taverna-dependency-activity
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/a5d4f899
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/a5d4f899
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/a5d4f899
Branch: refs/heads/master
Commit: a5d4f8994853fd6716d2f80886d5c444c450e3ef
Parents: eaa15e2
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:04:55 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:04:55 2015 +0000
----------------------------------------------------------------------
.gitignore | 23 -
.travis.yml | 1 -
README.md | 3 -
pom.xml | 59 ---
.../AbstractAsynchronousDependencyActivity.java | 445 -------------------
.../DependencyActivityConfigurationBean.java | 123 -----
.../dependencyactivity/NewArtifactDialog.java | 207 ---------
src/main/resources/schema.json | 25 --
taverna-dependency-activity/pom.xml | 59 +++
.../AbstractAsynchronousDependencyActivity.java | 445 +++++++++++++++++++
.../DependencyActivityConfigurationBean.java | 123 +++++
.../dependencyactivity/NewArtifactDialog.java | 207 +++++++++
.../src/main/resources/schema.json | 25 ++
13 files changed, 859 insertions(+), 886 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index 6d2ce9e..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,23 +0,0 @@
-# ignore project files #
-.classpath
-.project
-.settings/
-catalog-v001.xml
-# ignore target files #
-target/
-bin/
-build/
-dist/
-apidoc/
-*.swp
-
-# ignore svn files if there
-.svn
-
-# ignore log files #
-*.log
-/logs/*
-*/logs/*
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index dff5f3a..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1 +0,0 @@
-language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
deleted file mode 100644
index abb8c19..0000000
--- a/README.md
+++ /dev/null
@@ -1,3 +0,0 @@
-Taverna Workflow system Dependency Activity: data model and execution implementation
-
-This code was previously hosted at http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 1c138d0..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?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>dependency-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Taverna 2 Activity with Dependencies</name>
- <version>2.0.1-SNAPSHOT</version>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson-databind.version}</version>
- </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>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-dependency-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-dependency-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-dependency-activity</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
deleted file mode 100644
index e2d5143..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ /dev/null
@@ -1,445 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.lang.ref.WeakReference;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.util.HashSet;
-import java.util.WeakHashMap;
-
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
-
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * A parent abstract class for activities that require dependency management, such as
- * API Consumer and Beanshell. Defines dependencies on local JAR files
- * and Raven artifacts.
- *
- * @author Alex Nenadic
- * @author Tom Oinn
- * @author Stian Soiland-Reyes
- */
-public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsynchronousActivity<JsonNode> {
-
- private static final String LOCAL_JARS = "Local jars";
-
- private static final String ARTIFACTS = "Artifacts";
-
- private static Logger logger = Logger.getLogger(AbstractAsynchronousDependencyActivity.class);
-
- /**
- * For persisting class loaders across a whole workflow run (when classloader sharing
- * is set to 'workflow'). The key in the map is the workflow run ID and we are using
- * a WeakHashMap so we don't keep up references to classloaders of old workflow runs.
- */
- private static WeakHashMap<String, ClassLoader> workflowClassLoaders =
- new WeakHashMap<String, ClassLoader>();
-
- /**
- * System classloader, in case when classloader sharing is set to 'system'.
- */
- private static ClassLoader systemClassLoader = null;
-
- /**
- * Classloader to be used for 'executing' this activity, depending on the activity's
- * class loader sharing policy.
- */
- protected ClassLoader classLoader = null;
-
- /**
- * The location of the <code>lib</code> directory in TAVERNA_HOME,
- * where local JAR files the activity depends on should be located.
- */
- public File libDir;
-
- /**
- * Different ways to share a class loader among activities:
- *
- * <dl>
- * <dt>workflow</dt>
- * <dd>Same classloader for all activities using the <code>workflow</code> classloader sharing policy</dd>
- * <dt>system</dt>
- * <dd>System classloader</dd>
- * </dl>
- *
- */
- public static enum ClassLoaderSharing {
- workflow, system;
- public static final ClassLoaderSharing DEFAULT = workflow;
- public static ClassLoaderSharing fromString(String str) {
- if (str == null || str.isEmpty()) {
- return DEFAULT;
- }
- return valueOf(str.toLowerCase());
- }
- }
-
- public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
- if (applicationConfiguration != null) {
- libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
- }
- }
-
- /**
- * Finds or constructs the classloader. The classloader depends on the
- * current classloader sharing policy as defined by {@link #ClassLoaderSharing}.
- * <p>
- * If the classloader sharing is {@link ClassLoaderSharing#workflow}, a
- * common classloader will be used for the whole workflow for all activities
- * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
- * The dependencies will be constructed as union of local and artifact dependencies
- * of all 'workflow' classloader sharing activities at the point of the first
- * call to {@link #getClassLoader()}.
- * <p>
- * If the classloader sharing is {@link ClassLoaderSharing#system}, the
- * system classloader will be used. Note that both local and artifact dependencies
- * configured on the activity will be ignored. Local dependencies can be set by
- * using <code>-classpath</code> when starting the workbench.
- * This is useful in combination with JNI based libraries, which would also
- * require <code>-Djava.library.path</code> and possibly the operating
- * system's PATH / LD_LIBRARY_PATH / DYLD_LIBRARY_PATH environment variable.
- * @param classLoaderSharing
- *
- * @return A new or existing {@link ClassLoader} according to the
- * classloader sharing policy
- */
- protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
-
- if (classLoaderSharing == ClassLoaderSharing.workflow) {
- synchronized (workflowClassLoaders) {
- ClassLoader cl = workflowClassLoaders.get(workflowRunID);
- if (cl == null) {
- cl = makeClassLoader(json, workflowRunID);
- workflowClassLoaders.put(workflowRunID, cl);
- }
- return cl;
- }
- }
- if (classLoaderSharing == ClassLoaderSharing.system) {
-// if (systemClassLoader == null)
-// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
-
-// if (systemClassLoader instanceof BootstrapClassLoader){
-// // Add local and artifact dependencies to the classloader
-// updateBootstrapClassLoader(
-// (BootstrapClassLoader) systemClassLoader,
-// configurationBean, workflowRunID);
-// return systemClassLoader;
-// }
-// else{
- // Local dependencies will have to be set with the -classpath option
- // We cannot have artifact dependencies in this case
- String message = "System classloader is not Taverna's BootstrapClassLoader, so local dependencies " +
- "have to defined with -classpath. Artifact dependencies are ignored completely.";
- logger.warn(message);
- return systemClassLoader;
-// }
- }
- String message = "Unknown classloader sharing policy named '"+ classLoaderSharing+ "' for " + this.getClass();
- logger.error(message);
- throw new RuntimeException(message);
- }
-
- /**
- * Constructs a classloader capable of finding both local jar and artifact dependencies.
- * Called when classloader sharing policy is set to 'workflow'.
- *
- * @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
- */
- private ClassLoader makeClassLoader(JsonNode json, String workflowID) {
- // Find all artifact dependencies
-// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
-
- // Add all local jar dependencies
- HashSet<URL> urls = findDependencies(LOCAL_JARS, json, workflowID);
-
- // Create the classloader capable of loading both local jar and artifact dependencies
- ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
-
- return new URLClassLoader(urls.toArray(new URL[0]), parent) {
-
- // For finding native libraries that have to be stored in TAVERNA_HOME/lib
- @Override
- protected String findLibrary(String libname) {
- String filename = System.mapLibraryName(libname);
- File libraryFile = new File(libDir, filename);
- if (libraryFile.isFile()) {
- logger.info("Found library " + libname + ": " + libraryFile.getAbsolutePath());
- return libraryFile.getAbsolutePath();
- }
- return super.findLibrary(libname);
- }
- };
- }
-
- /**
- * Adds local or artifact dependencies identified by {@link #findDependencies()} to the
- * {@link BootstrapClassLoader} system classloader.
- * Called when classloader sharing policy is set to 'system'.
- *
- * @param loader The augmented BootstrapClassLoader system classloader
- */
-// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
-// DependencyActivityConfigurationBean configurationBean,
-// String workflowRunID) {
-//
-// HashSet<URL> depsURLs = new HashSet<URL>();
-// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
-// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
-//
-// Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
-// for (URL url : depsURLs) {
-// if (exists.contains(url)) {
-// continue;
-// }
-// logger.info("Registering with system classloader: " + url);
-// loader.addURL(url);
-// exists.add(url);
-// }
-// }
-
- /**
- * Finds either local jar or artifact dependencies' URLs for the given classloader
- * sharing policy (passed inside configuration bean) and a workflowRunID (used to
- * retrieve the workflow) that will be added to this activity classloader's list of URLs.
- */
- private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
- // Get the WorkflowInstanceFacade which contains the current workflow
- WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
- WorkflowInstanceFacade wfFacade = null;
- if (wfFacadeRef != null) {
- wfFacade = wfFacadeRef.get();
- }
- Dataflow wf = null;
- if (wfFacade != null) {
- wf = wfFacade.getDataflow();
- }
-
- // Files of dependencies for all activities in the workflow that share the classloading policy
- HashSet<File> dependencies = new HashSet<File>();
- // Urls of all dependencies
- HashSet<URL> dependenciesURLs = new HashSet<URL>();
-
- if (wf != null){
- // Merge in dependencies from all activities that have the same classloader-sharing
- // as this activity
- for (Processor proc : wf.getProcessors()) {
- // Nested workflow case
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
- // Get the nested workflow
- Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedWorkflow));
- }
- else{ // Not nested - go through all of the processor's activities
- Activity<?> activity = proc.getActivityList().get(0);
- if (activity instanceof AbstractAsynchronousDependencyActivity){
- AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
-// if (dependencyType.equals(LOCAL_JARS)){
- // Collect the files of all found local dependencies
- if (dependencyActivity.getConfiguration().has("localDependency")) {
- for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
-// // Get the LocalReposotpry capable of finding artifact jar files
-// LocalRepository rep = (LocalRepository) cl.getRepository();
-// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
-// .getConfiguration())
-// .getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
- }
- }
- }
- } else { // Just add dependencies for this activity since we can't get hold of the whole workflow
-// if (dependencyType.equals(LOCAL_JARS)){
- if (json.has("localDependency")) {
- for (JsonNode jar : json.get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// }
-// else if (dependencyType.equals(ARTIFACTS)){
-// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
-// LocalRepository rep = (LocalRepository)cl.getRepository();
-// if (rep != null){
-// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
-// }
-// else{
-// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
-// // outside Raven so there is nothing we can do about this - some tests
-// // with dependencies will probably fail
-// }
-// }
- }
-
- // Collect the URLs of all found dependencies
- for (File file: dependencies){
- try{
- dependenciesURLs.add(file.toURI().toURL());
- }
- catch(Exception ex){
- logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
- continue;
- }
- }
- return dependenciesURLs;
- }
-
- /**
- * Finds dependencies for a nested workflow.
- */
- private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
-
- // Files of dependencies for all activities in the nested workflow that share the classloading policy
- HashSet<File> dependencies = new HashSet<File>();
- // Urls of all dependencies
- HashSet<URL> dependenciesURLs = new HashSet<URL>();
-
- for (Processor proc : nestedWorkflow.getProcessors()) {
- // Another nested workflow
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
- // Get the nested workflow
- Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedNestedWorkflow));
- }
- else{ // Not nested - go through all of the processor's activities
- Activity<?> activity = proc.getActivityList().get(0);
- if (activity instanceof AbstractAsynchronousDependencyActivity){
- AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
-// if (dependencyType.equals(LOCAL_JARS)){
- // Collect the files of all found local dependencies
- if (dependencyActivity.getConfiguration().has("localDependency")) {
- for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
-// LocalRepository rep = (LocalRepository) cl.getRepository();
-// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
-// .getConfiguration())
-// .getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
- }
- }
- }
-
- // Collect the URLs of all found dependencies
- for (File file: dependencies){
- try{
- dependenciesURLs.add(file.toURI().toURL());
- }
- catch(Exception ex){
- logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
- continue;
- }
- }
- return dependenciesURLs;
- }
-
- /**
- * File filter.
- */
- public static class FileExtFilter implements FilenameFilter {
-
- String ext = null;
-
- public FileExtFilter(String ext) {
- this.ext = ext;
- }
-
- public boolean accept(File dir, String name) {
- return name.endsWith(ext);
- }
- }
-
- /**
- * @param classLoader the classLoader to set
- */
- public void setClassLoader(ClassLoader classLoader) {
- this.classLoader = classLoader;
- }
-
- /**
- * @return the classLoader
- */
- public ClassLoader getClassLoader() {
- return classLoader;
- }
-}
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
deleted file mode 100644
index afe75e2..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.util.LinkedHashSet;
-
-import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Parent configuration bean for activities that have local JAR,
- * such as API Consumer and Beanshell activity.
- *
- * @author Alex Nenadic
- * @author David Withers
- */
-@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
-public class DependencyActivityConfigurationBean extends
- ActivityPortsDefinitionBean {
-
- /**
- * Activity's classloader sharing policy.
- */
- private ClassLoaderSharing classLoaderSharing ;// = ClassLoaderSharing.workflow;
-
- /**
- * Local dependencies, i.e. filenames of JARs the activity depends on.
- * The files should be present in {@link AbstractAsynchronousActivityWithDependencies#libDir},
- * and the paths should be relative.
- */
- private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
-
- /**
- * Constructor.
- */
- public DependencyActivityConfigurationBean(){
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
- localDependencies = new LinkedHashSet<String>();
- }
-
- /**
- * As XStream is not calling the default constructor during deserialization,
- * we have to set the default values here. This method will be called by XStream
- * after instantiating this bean.
- */
- private Object readResolve(){
- if (classLoaderSharing == null)
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
-
- if (localDependencies == null)
- localDependencies = new LinkedHashSet<String>();
-
- return this;
- }
-
- /**
- * @param classLoaderSharing the classLoaderSharing to set
- */
- @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
- public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
- this.classLoaderSharing = classLoaderSharing;
- }
-
- /**
- * @return the classLoaderSharing
- */
- public ClassLoaderSharing getClassLoaderSharing() {
- return classLoaderSharing;
- }
-
- /**
- * @param localDependencies the localDependencies to set
- */
- @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
- public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
- this.localDependencies = localDependencies;
- }
-
- /**
- * @return the localDependencies
- */
- public LinkedHashSet<String> getLocalDependencies() {
- return localDependencies;
- }
-
- /**
- * Adds a dependency to the list of local dependencies.
- * @param dep
- */
- public void addLocalDependency(String dep){
- localDependencies.add(dep);
- }
-
- /**
- * Removes a dependency from the list of local dependencies.
- * @param dep
- */
- public void removeLocalDependency(String dep){
- localDependencies.remove(dep);
- }
-
-}
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
deleted file mode 100644
index 9d04135..0000000
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
+++ /dev/null
@@ -1,207 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.border.EmptyBorder;
-
-/**
- * Dialog used for entering an artifact.
- *
- * @author Alex Nenadic
- */
-@SuppressWarnings("serial")
-public class NewArtifactDialog
- extends JDialog
-{
- private JTextField jtfGroupID;
-
- private JTextField jtfArtifactID;
-
- private JTextField jtfVersion;
-
- /** Stores new group ID entered */
- private String groupID = null;
-
- /** Stores new artifact ID entered */
- private String artifactID = null;
-
- /** Stores new version entered */
- private String version = null;
-
-
- /**
- * Creates new NewArtifactDialog.
- */
- public NewArtifactDialog(String sTitle, boolean bModal)
- {
- super();
- setTitle(sTitle);
- setModal(bModal);
- initComponents();
- }
-
- public String getGroupID()
- {
- return groupID;
- }
-
- public String getArtifatcID()
- {
- return artifactID;
- }
-
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Initialise the dialog's GUI components.
- */
- private void initComponents()
- {
- getContentPane().setLayout(new BorderLayout());
-
- JLabel jlGroupID = new JLabel("Group ID:");
- JLabel jlArtifactID = new JLabel("Artifact ID:");
- JLabel jlVersion = new JLabel("Version");
-
- jtfGroupID = new JTextField(15);
- jtfArtifactID = new JTextField(15);
- jtfVersion = new JTextField(15);
-
- JButton jbOK = new JButton("OK");
- jbOK.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- okPressed();
- }
- });
-
- JButton jbCancel = new JButton("Cancel");
- jbCancel.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- cancelPressed();
- }
- });
-
- JPanel jpPassword = new JPanel(new GridLayout(3, 2, 5, 5));
- jpPassword.add(jlGroupID);
- jpPassword.add(jtfGroupID);
- jpPassword.add(jlArtifactID);
- jpPassword.add(jtfArtifactID);
- jpPassword.add(jlVersion);
- jpPassword.add(jtfVersion);
- jpPassword.setBorder(new EmptyBorder(5, 5, 5, 5));
-
- JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
- jpButtons.add(jbOK);
- jpButtons.add(jbCancel);
-
- getContentPane().add(jpPassword, BorderLayout.CENTER);
- getContentPane().add(jpButtons, BorderLayout.SOUTH);
-
- addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeDialog();
- }
- });
-
- setResizable(false);
-
- getRootPane().setDefaultButton(jbOK);
-
- pack();
- }
-
- private boolean checkFields()
- {
- groupID = jtfGroupID.getText();
- artifactID = jtfArtifactID.getText();
- version = jtfVersion.getText();
-
- if ((!groupID.equals("")) && (!artifactID.equals("")) && (!version.equals(""))){
- return true;
- }
- else {
- JOptionPane.showMessageDialog(this,
- "Field(s) may not be empty",
- "ERROR",
- JOptionPane.ERROR_MESSAGE);
-
- return false;
- }
- }
-
- /**
- * OK button pressed or otherwise activated.
- */
- private void okPressed()
- {
- if (checkFields()) {
- closeDialog();
- }
- }
-
- /**
- * Cancel button pressed or otherwise activated.
- */
- private void cancelPressed()
- {
- // Set the fields to null as it might have changed in the meantime
- // if user entered something previously
- groupID = null;
- artifactID = null;
- version = null;
- closeDialog();
- }
-
- /**
- * Close the dialog.
- */
- private void closeDialog()
- {
- setVisible(false);
- dispose();
- }
-}
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/src/main/resources/schema.json b/src/main/resources/schema.json
deleted file mode 100644
index c30459f..0000000
--- a/src/main/resources/schema.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-03/schema#",
- "id": "http://ns.taverna.org.uk/2010/activity/dependency.schema.json",
- "title": "Dependency activity configuration",
- "type": "object",
- "properties": {
- "@context": {
- "description": "JSON-LD context for interpreting the configuration as RDF",
- "required": true,
- "enum": ["http://ns.taverna.org.uk/2010/activity/dependency.context.json"]
- },
- "classLoaderSharing": {
- "title": "ClassLoader Sharing Policy",
- "description": "Policy for sharing class loaders across multiple beanshell activities",
- "default": "workflow",
- "enum": ["workflow", "system"]
- },
- "localDependency": {
- "title": "Local Dependencies",
- "description": "Location of jar files to be added to the beanshell class loader",
- "type": "array",
- "items": { "type" : "string" }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/taverna-dependency-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/pom.xml b/taverna-dependency-activity/pom.xml
new file mode 100644
index 0000000..1c138d0
--- /dev/null
+++ b/taverna-dependency-activity/pom.xml
@@ -0,0 +1,59 @@
+<?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>dependency-activity</artifactId>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 Activity with Dependencies</name>
+ <version>2.0.1-SNAPSHOT</version>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.core</groupId>
+ <artifactId>workflowmodel-api</artifactId>
+ <version>${t2.core.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>${jackson-databind.version}</version>
+ </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>
+ </repositories>
+ <scm>
+ <connection>scm:git:https://github.com/taverna/taverna-dependency-activity.git</connection>
+ <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-dependency-activity.git</developerConnection>
+ <url>https://github.com/taverna/taverna-dependency-activity</url>
+ <tag>HEAD</tag>
+ </scm>
+
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
new file mode 100644
index 0000000..e2d5143
--- /dev/null
+++ b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -0,0 +1,445 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.lang.ref.WeakReference;
+import java.net.URL;
+import java.net.URLClassLoader;
+import java.util.HashSet;
+import java.util.WeakHashMap;
+
+import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.Processor;
+import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * A parent abstract class for activities that require dependency management, such as
+ * API Consumer and Beanshell. Defines dependencies on local JAR files
+ * and Raven artifacts.
+ *
+ * @author Alex Nenadic
+ * @author Tom Oinn
+ * @author Stian Soiland-Reyes
+ */
+public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsynchronousActivity<JsonNode> {
+
+ private static final String LOCAL_JARS = "Local jars";
+
+ private static final String ARTIFACTS = "Artifacts";
+
+ private static Logger logger = Logger.getLogger(AbstractAsynchronousDependencyActivity.class);
+
+ /**
+ * For persisting class loaders across a whole workflow run (when classloader sharing
+ * is set to 'workflow'). The key in the map is the workflow run ID and we are using
+ * a WeakHashMap so we don't keep up references to classloaders of old workflow runs.
+ */
+ private static WeakHashMap<String, ClassLoader> workflowClassLoaders =
+ new WeakHashMap<String, ClassLoader>();
+
+ /**
+ * System classloader, in case when classloader sharing is set to 'system'.
+ */
+ private static ClassLoader systemClassLoader = null;
+
+ /**
+ * Classloader to be used for 'executing' this activity, depending on the activity's
+ * class loader sharing policy.
+ */
+ protected ClassLoader classLoader = null;
+
+ /**
+ * The location of the <code>lib</code> directory in TAVERNA_HOME,
+ * where local JAR files the activity depends on should be located.
+ */
+ public File libDir;
+
+ /**
+ * Different ways to share a class loader among activities:
+ *
+ * <dl>
+ * <dt>workflow</dt>
+ * <dd>Same classloader for all activities using the <code>workflow</code> classloader sharing policy</dd>
+ * <dt>system</dt>
+ * <dd>System classloader</dd>
+ * </dl>
+ *
+ */
+ public static enum ClassLoaderSharing {
+ workflow, system;
+ public static final ClassLoaderSharing DEFAULT = workflow;
+ public static ClassLoaderSharing fromString(String str) {
+ if (str == null || str.isEmpty()) {
+ return DEFAULT;
+ }
+ return valueOf(str.toLowerCase());
+ }
+ }
+
+ public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
+ if (applicationConfiguration != null) {
+ libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
+ }
+ }
+
+ /**
+ * Finds or constructs the classloader. The classloader depends on the
+ * current classloader sharing policy as defined by {@link #ClassLoaderSharing}.
+ * <p>
+ * If the classloader sharing is {@link ClassLoaderSharing#workflow}, a
+ * common classloader will be used for the whole workflow for all activities
+ * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
+ * The dependencies will be constructed as union of local and artifact dependencies
+ * of all 'workflow' classloader sharing activities at the point of the first
+ * call to {@link #getClassLoader()}.
+ * <p>
+ * If the classloader sharing is {@link ClassLoaderSharing#system}, the
+ * system classloader will be used. Note that both local and artifact dependencies
+ * configured on the activity will be ignored. Local dependencies can be set by
+ * using <code>-classpath</code> when starting the workbench.
+ * This is useful in combination with JNI based libraries, which would also
+ * require <code>-Djava.library.path</code> and possibly the operating
+ * system's PATH / LD_LIBRARY_PATH / DYLD_LIBRARY_PATH environment variable.
+ * @param classLoaderSharing
+ *
+ * @return A new or existing {@link ClassLoader} according to the
+ * classloader sharing policy
+ */
+ protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+
+ if (classLoaderSharing == ClassLoaderSharing.workflow) {
+ synchronized (workflowClassLoaders) {
+ ClassLoader cl = workflowClassLoaders.get(workflowRunID);
+ if (cl == null) {
+ cl = makeClassLoader(json, workflowRunID);
+ workflowClassLoaders.put(workflowRunID, cl);
+ }
+ return cl;
+ }
+ }
+ if (classLoaderSharing == ClassLoaderSharing.system) {
+// if (systemClassLoader == null)
+// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
+
+// if (systemClassLoader instanceof BootstrapClassLoader){
+// // Add local and artifact dependencies to the classloader
+// updateBootstrapClassLoader(
+// (BootstrapClassLoader) systemClassLoader,
+// configurationBean, workflowRunID);
+// return systemClassLoader;
+// }
+// else{
+ // Local dependencies will have to be set with the -classpath option
+ // We cannot have artifact dependencies in this case
+ String message = "System classloader is not Taverna's BootstrapClassLoader, so local dependencies " +
+ "have to defined with -classpath. Artifact dependencies are ignored completely.";
+ logger.warn(message);
+ return systemClassLoader;
+// }
+ }
+ String message = "Unknown classloader sharing policy named '"+ classLoaderSharing+ "' for " + this.getClass();
+ logger.error(message);
+ throw new RuntimeException(message);
+ }
+
+ /**
+ * Constructs a classloader capable of finding both local jar and artifact dependencies.
+ * Called when classloader sharing policy is set to 'workflow'.
+ *
+ * @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
+ */
+ private ClassLoader makeClassLoader(JsonNode json, String workflowID) {
+ // Find all artifact dependencies
+// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
+
+ // Add all local jar dependencies
+ HashSet<URL> urls = findDependencies(LOCAL_JARS, json, workflowID);
+
+ // Create the classloader capable of loading both local jar and artifact dependencies
+ ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
+
+ return new URLClassLoader(urls.toArray(new URL[0]), parent) {
+
+ // For finding native libraries that have to be stored in TAVERNA_HOME/lib
+ @Override
+ protected String findLibrary(String libname) {
+ String filename = System.mapLibraryName(libname);
+ File libraryFile = new File(libDir, filename);
+ if (libraryFile.isFile()) {
+ logger.info("Found library " + libname + ": " + libraryFile.getAbsolutePath());
+ return libraryFile.getAbsolutePath();
+ }
+ return super.findLibrary(libname);
+ }
+ };
+ }
+
+ /**
+ * Adds local or artifact dependencies identified by {@link #findDependencies()} to the
+ * {@link BootstrapClassLoader} system classloader.
+ * Called when classloader sharing policy is set to 'system'.
+ *
+ * @param loader The augmented BootstrapClassLoader system classloader
+ */
+// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
+// DependencyActivityConfigurationBean configurationBean,
+// String workflowRunID) {
+//
+// HashSet<URL> depsURLs = new HashSet<URL>();
+// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
+// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
+//
+// Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
+// for (URL url : depsURLs) {
+// if (exists.contains(url)) {
+// continue;
+// }
+// logger.info("Registering with system classloader: " + url);
+// loader.addURL(url);
+// exists.add(url);
+// }
+// }
+
+ /**
+ * Finds either local jar or artifact dependencies' URLs for the given classloader
+ * sharing policy (passed inside configuration bean) and a workflowRunID (used to
+ * retrieve the workflow) that will be added to this activity classloader's list of URLs.
+ */
+ private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+ // Get the WorkflowInstanceFacade which contains the current workflow
+ WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
+ WorkflowInstanceFacade wfFacade = null;
+ if (wfFacadeRef != null) {
+ wfFacade = wfFacadeRef.get();
+ }
+ Dataflow wf = null;
+ if (wfFacade != null) {
+ wf = wfFacade.getDataflow();
+ }
+
+ // Files of dependencies for all activities in the workflow that share the classloading policy
+ HashSet<File> dependencies = new HashSet<File>();
+ // Urls of all dependencies
+ HashSet<URL> dependenciesURLs = new HashSet<URL>();
+
+ if (wf != null){
+ // Merge in dependencies from all activities that have the same classloader-sharing
+ // as this activity
+ for (Processor proc : wf.getProcessors()) {
+ // Nested workflow case
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ // Get the nested workflow
+ Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedWorkflow));
+ }
+ else{ // Not nested - go through all of the processor's activities
+ Activity<?> activity = proc.getActivityList().get(0);
+ if (activity instanceof AbstractAsynchronousDependencyActivity){
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+// if (dependencyType.equals(LOCAL_JARS)){
+ // Collect the files of all found local dependencies
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// // Get the LocalReposotpry capable of finding artifact jar files
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+ }
+ }
+ }
+ } else { // Just add dependencies for this activity since we can't get hold of the whole workflow
+// if (dependencyType.equals(LOCAL_JARS)){
+ if (json.has("localDependency")) {
+ for (JsonNode jar : json.get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// }
+// else if (dependencyType.equals(ARTIFACTS)){
+// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
+// LocalRepository rep = (LocalRepository)cl.getRepository();
+// if (rep != null){
+// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+// }
+// else{
+// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
+// // outside Raven so there is nothing we can do about this - some tests
+// // with dependencies will probably fail
+// }
+// }
+ }
+
+ // Collect the URLs of all found dependencies
+ for (File file: dependencies){
+ try{
+ dependenciesURLs.add(file.toURI().toURL());
+ }
+ catch(Exception ex){
+ logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
+ continue;
+ }
+ }
+ return dependenciesURLs;
+ }
+
+ /**
+ * Finds dependencies for a nested workflow.
+ */
+ private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+
+ // Files of dependencies for all activities in the nested workflow that share the classloading policy
+ HashSet<File> dependencies = new HashSet<File>();
+ // Urls of all dependencies
+ HashSet<URL> dependenciesURLs = new HashSet<URL>();
+
+ for (Processor proc : nestedWorkflow.getProcessors()) {
+ // Another nested workflow
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ // Get the nested workflow
+ Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedNestedWorkflow));
+ }
+ else{ // Not nested - go through all of the processor's activities
+ Activity<?> activity = proc.getActivityList().get(0);
+ if (activity instanceof AbstractAsynchronousDependencyActivity){
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+// if (dependencyType.equals(LOCAL_JARS)){
+ // Collect the files of all found local dependencies
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+ }
+ }
+ }
+
+ // Collect the URLs of all found dependencies
+ for (File file: dependencies){
+ try{
+ dependenciesURLs.add(file.toURI().toURL());
+ }
+ catch(Exception ex){
+ logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
+ continue;
+ }
+ }
+ return dependenciesURLs;
+ }
+
+ /**
+ * File filter.
+ */
+ public static class FileExtFilter implements FilenameFilter {
+
+ String ext = null;
+
+ public FileExtFilter(String ext) {
+ this.ext = ext;
+ }
+
+ public boolean accept(File dir, String name) {
+ return name.endsWith(ext);
+ }
+ }
+
+ /**
+ * @param classLoader the classLoader to set
+ */
+ public void setClassLoader(ClassLoader classLoader) {
+ this.classLoader = classLoader;
+ }
+
+ /**
+ * @return the classLoader
+ */
+ public ClassLoader getClassLoader() {
+ return classLoader;
+ }
+}
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
new file mode 100644
index 0000000..afe75e2
--- /dev/null
+++ b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -0,0 +1,123 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.util.LinkedHashSet;
+
+import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
+import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Parent configuration bean for activities that have local JAR,
+ * such as API Consumer and Beanshell activity.
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
+public class DependencyActivityConfigurationBean extends
+ ActivityPortsDefinitionBean {
+
+ /**
+ * Activity's classloader sharing policy.
+ */
+ private ClassLoaderSharing classLoaderSharing ;// = ClassLoaderSharing.workflow;
+
+ /**
+ * Local dependencies, i.e. filenames of JARs the activity depends on.
+ * The files should be present in {@link AbstractAsynchronousActivityWithDependencies#libDir},
+ * and the paths should be relative.
+ */
+ private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
+
+ /**
+ * Constructor.
+ */
+ public DependencyActivityConfigurationBean(){
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
+ localDependencies = new LinkedHashSet<String>();
+ }
+
+ /**
+ * As XStream is not calling the default constructor during deserialization,
+ * we have to set the default values here. This method will be called by XStream
+ * after instantiating this bean.
+ */
+ private Object readResolve(){
+ if (classLoaderSharing == null)
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
+
+ if (localDependencies == null)
+ localDependencies = new LinkedHashSet<String>();
+
+ return this;
+ }
+
+ /**
+ * @param classLoaderSharing the classLoaderSharing to set
+ */
+ @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
+ public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
+ this.classLoaderSharing = classLoaderSharing;
+ }
+
+ /**
+ * @return the classLoaderSharing
+ */
+ public ClassLoaderSharing getClassLoaderSharing() {
+ return classLoaderSharing;
+ }
+
+ /**
+ * @param localDependencies the localDependencies to set
+ */
+ @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
+ public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
+ this.localDependencies = localDependencies;
+ }
+
+ /**
+ * @return the localDependencies
+ */
+ public LinkedHashSet<String> getLocalDependencies() {
+ return localDependencies;
+ }
+
+ /**
+ * Adds a dependency to the list of local dependencies.
+ * @param dep
+ */
+ public void addLocalDependency(String dep){
+ localDependencies.add(dep);
+ }
+
+ /**
+ * Removes a dependency from the list of local dependencies.
+ * @param dep
+ */
+ public void removeLocalDependency(String dep){
+ localDependencies.remove(dep);
+ }
+
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
new file mode 100644
index 0000000..9d04135
--- /dev/null
+++ b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
@@ -0,0 +1,207 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+/**
+ * Dialog used for entering an artifact.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class NewArtifactDialog
+ extends JDialog
+{
+ private JTextField jtfGroupID;
+
+ private JTextField jtfArtifactID;
+
+ private JTextField jtfVersion;
+
+ /** Stores new group ID entered */
+ private String groupID = null;
+
+ /** Stores new artifact ID entered */
+ private String artifactID = null;
+
+ /** Stores new version entered */
+ private String version = null;
+
+
+ /**
+ * Creates new NewArtifactDialog.
+ */
+ public NewArtifactDialog(String sTitle, boolean bModal)
+ {
+ super();
+ setTitle(sTitle);
+ setModal(bModal);
+ initComponents();
+ }
+
+ public String getGroupID()
+ {
+ return groupID;
+ }
+
+ public String getArtifatcID()
+ {
+ return artifactID;
+ }
+
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Initialise the dialog's GUI components.
+ */
+ private void initComponents()
+ {
+ getContentPane().setLayout(new BorderLayout());
+
+ JLabel jlGroupID = new JLabel("Group ID:");
+ JLabel jlArtifactID = new JLabel("Artifact ID:");
+ JLabel jlVersion = new JLabel("Version");
+
+ jtfGroupID = new JTextField(15);
+ jtfArtifactID = new JTextField(15);
+ jtfVersion = new JTextField(15);
+
+ JButton jbOK = new JButton("OK");
+ jbOK.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ okPressed();
+ }
+ });
+
+ JButton jbCancel = new JButton("Cancel");
+ jbCancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ cancelPressed();
+ }
+ });
+
+ JPanel jpPassword = new JPanel(new GridLayout(3, 2, 5, 5));
+ jpPassword.add(jlGroupID);
+ jpPassword.add(jtfGroupID);
+ jpPassword.add(jlArtifactID);
+ jpPassword.add(jtfArtifactID);
+ jpPassword.add(jlVersion);
+ jpPassword.add(jtfVersion);
+ jpPassword.setBorder(new EmptyBorder(5, 5, 5, 5));
+
+ JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ jpButtons.add(jbOK);
+ jpButtons.add(jbCancel);
+
+ getContentPane().add(jpPassword, BorderLayout.CENTER);
+ getContentPane().add(jpButtons, BorderLayout.SOUTH);
+
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ closeDialog();
+ }
+ });
+
+ setResizable(false);
+
+ getRootPane().setDefaultButton(jbOK);
+
+ pack();
+ }
+
+ private boolean checkFields()
+ {
+ groupID = jtfGroupID.getText();
+ artifactID = jtfArtifactID.getText();
+ version = jtfVersion.getText();
+
+ if ((!groupID.equals("")) && (!artifactID.equals("")) && (!version.equals(""))){
+ return true;
+ }
+ else {
+ JOptionPane.showMessageDialog(this,
+ "Field(s) may not be empty",
+ "ERROR",
+ JOptionPane.ERROR_MESSAGE);
+
+ return false;
+ }
+ }
+
+ /**
+ * OK button pressed or otherwise activated.
+ */
+ private void okPressed()
+ {
+ if (checkFields()) {
+ closeDialog();
+ }
+ }
+
+ /**
+ * Cancel button pressed or otherwise activated.
+ */
+ private void cancelPressed()
+ {
+ // Set the fields to null as it might have changed in the meantime
+ // if user entered something previously
+ groupID = null;
+ artifactID = null;
+ version = null;
+ closeDialog();
+ }
+
+ /**
+ * Close the dialog.
+ */
+ private void closeDialog()
+ {
+ setVisible(false);
+ dispose();
+ }
+}
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a5d4f899/taverna-dependency-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/resources/schema.json b/taverna-dependency-activity/src/main/resources/schema.json
new file mode 100644
index 0000000..c30459f
--- /dev/null
+++ b/taverna-dependency-activity/src/main/resources/schema.json
@@ -0,0 +1,25 @@
+{
+ "$schema": "http://json-schema.org/draft-03/schema#",
+ "id": "http://ns.taverna.org.uk/2010/activity/dependency.schema.json",
+ "title": "Dependency activity configuration",
+ "type": "object",
+ "properties": {
+ "@context": {
+ "description": "JSON-LD context for interpreting the configuration as RDF",
+ "required": true,
+ "enum": ["http://ns.taverna.org.uk/2010/activity/dependency.context.json"]
+ },
+ "classLoaderSharing": {
+ "title": "ClassLoader Sharing Policy",
+ "description": "Policy for sharing class loaders across multiple beanshell activities",
+ "default": "workflow",
+ "enum": ["workflow", "system"]
+ },
+ "localDependency": {
+ "title": "Local Dependencies",
+ "description": "Location of jar files to be added to the beanshell class loader",
+ "type": "array",
+ "items": { "type" : "string" }
+ }
+ }
+}
[33/50] incubator-taverna-common-activities git commit: Added Readme
Posted by st...@apache.org.
Added Readme
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/f5891902
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/f5891902
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/f5891902
Branch: refs/heads/master
Commit: f589190217245176492e24a7f40923fb94dbf754
Parents: 9d230ec
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed May 7 08:03:57 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed May 7 08:03:57 2014 +0100
----------------------------------------------------------------------
README.md | 3 +++
1 file changed, 3 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/f5891902/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..abb8c19
--- /dev/null
+++ b/README.md
@@ -0,0 +1,3 @@
+Taverna Workflow system Dependency Activity: data model and execution implementation
+
+This code was previously hosted at http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/
[34/50] incubator-taverna-common-activities git commit: Added
gutignore
Posted by st...@apache.org.
Added gutignore
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/4ef07cfc
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/4ef07cfc
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/4ef07cfc
Branch: refs/heads/master
Commit: 4ef07cfc94206a66b8e2b58744c606806103eeb1
Parents: 03671d7
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed May 7 08:12:53 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed May 7 08:12:53 2014 +0100
----------------------------------------------------------------------
.gitignore | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/4ef07cfc/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ebe0e5b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+# ignore project files #
+.classpath
+.project
+.settings/
+catalog-v001.xml
+
+# ignore target files #
+target/
+bin/
+build/
+dist/
+apidoc/
+*.swp
+
+# ignore svn files if there
+.svn
+
+# ignore log files #
+*.log
+/logs/*
+*/logs/*
+
+
+
[42/50] incubator-taverna-common-activities git commit: using
${jackson-databind.version} for T3-1195
Posted by st...@apache.org.
using ${jackson-databind.version} for T3-1195
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/2c3a7d29
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/2c3a7d29
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/2c3a7d29
Branch: refs/heads/master
Commit: 2c3a7d298bbd7900d5f911a0db3cadfa1981013d
Parents: cd37be5
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed Jul 2 15:08:37 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed Jul 2 15:08:37 2014 +0100
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/2c3a7d29/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8fed691..91cbfb4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,7 +25,7 @@
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
- <version>2.2.2</version>
+ <version>${jackson-databind.version}</version>
</dependency>
</dependencies>
<repositories>
[24/50] incubator-taverna-common-activities git commit: Updated trunk
version to snapshot.
Posted by st...@apache.org.
Updated trunk version to snapshot.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@14919 bf327186-88b3-11dd-a302-d386e5130c1c
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/bee5245e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/bee5245e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/bee5245e
Branch: refs/heads/master
Commit: bee5245eca9a920e5ddea16aaa17579a9caed2b4
Parents: 307f70d
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu May 10 21:33:45 2012 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu May 10 21:33:45 2012 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/bee5245e/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8b74160..8481869 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>2.0.0</version>
+ <version>2.0.1-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[45/50] incubator-taverna-common-activities git commit: Merge branch
'taverna-dependency-activity'
Posted by st...@apache.org.
Merge branch 'taverna-dependency-activity'
>From https://github.com/taverna/taverna-dependency-activity/ master
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/e90b6f96
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/e90b6f96
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/e90b6f96
Branch: refs/heads/master
Commit: e90b6f964dbb8d487ac85b585087316b4830323a
Parents: 50dcc95 a5d4f89
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:10:13 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:10:13 2015 +0000
----------------------------------------------------------------------
taverna-dependency-activity/pom.xml | 59 +++
.../AbstractAsynchronousDependencyActivity.java | 445 +++++++++++++++++++
.../DependencyActivityConfigurationBean.java | 123 +++++
.../dependencyactivity/NewArtifactDialog.java | 207 +++++++++
.../src/main/resources/schema.json | 25 ++
5 files changed, 859 insertions(+)
----------------------------------------------------------------------
[11/50] incubator-taverna-common-activities git commit: Undo r10056
Posted by st...@apache.org.
Undo r10056
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@10057 bf327186-88b3-11dd-a302-d386e5130c1c
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/c77f6973
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/c77f6973
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/c77f6973
Branch: refs/heads/master
Commit: c77f6973c40c3f9d5011b35297a95252901961a6
Parents: 0fdfa01
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Apr 29 15:35:12 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Apr 29 15:35:12 2010 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c77f6973/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 69b7190..5b8de22 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.1</version>
+ <version>1.1-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[37/50] incubator-taverna-common-activities git commit: added
and
Posted by st...@apache.org.
added <repository> and <scm>
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/cc39902d
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/cc39902d
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/cc39902d
Branch: refs/heads/master
Commit: cc39902dbfc5e660aab5e4649ac69dbd973ee8c4
Parents: c592d20
Author: Stian Soiland-Reyes <st...@soiland-reyes.com>
Authored: Wed May 14 10:41:44 2014 +0100
Committer: Stian Soiland-Reyes <st...@soiland-reyes.com>
Committed: Wed May 14 10:41:44 2014 +0100
----------------------------------------------------------------------
pom.xml | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cc39902d/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 05037c4..87c9a46 100644
--- a/pom.xml
+++ b/pom.xml
@@ -22,5 +22,32 @@
<version>${t2.core.version}</version>
</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>
+ </repositories>
+ <scm>
+ <connection>scm:git:https://github.com/taverna/taverna-dependency-activity.git</connection>
+ <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-dependency-activity.git</developerConnection>
+ <url>https://github.com/taverna/taverna-dependency-activity</url>
+ <tag>HEAD</tag>
+ </scm>
+
</project>
[27/50] incubator-taverna-common-activities git commit: Assume the
'workflow' as default classLoaderSharing
Posted by st...@apache.org.
Assume the 'workflow' as default classLoaderSharing
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15911 bf327186-88b3-11dd-a302-d386e5130c1c
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/4b383f5b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/4b383f5b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/4b383f5b
Branch: refs/heads/master
Commit: 4b383f5b826951ba3ca2b981462e8c8cbbc969cc
Parents: 10b1750
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Tue Jul 23 12:23:52 2013 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Tue Jul 23 12:23:52 2013 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/4b383f5b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index fbd31d2..4eb4799 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -95,7 +95,14 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
*
*/
public static enum ClassLoaderSharing {
- workflow, system
+ workflow, system;
+ public static final ClassLoaderSharing DEFAULT = workflow;
+ public static ClassLoaderSharing fromString(String str) {
+ if (str == null || str.isEmpty()) {
+ return DEFAULT;
+ }
+ return valueOf(str.toLowerCase());
+ }
}
public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
@@ -128,7 +135,7 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* classloader sharing policy
*/
protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
if (classLoaderSharing == ClassLoaderSharing.workflow) {
synchronized (workflowClassLoaders) {
[23/50] incubator-taverna-common-activities git commit: Release
version 2.0.0
Posted by st...@apache.org.
Release version 2.0.0
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@14917 bf327186-88b3-11dd-a302-d386e5130c1c
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/307f70d3
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/307f70d3
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/307f70d3
Branch: refs/heads/master
Commit: 307f70d3cff2a77fb5d10564fbc424dbb4c4ce44
Parents: ccd8a77
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu May 10 21:20:43 2012 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu May 10 21:20:43 2012 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/307f70d3/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 1eb95aa..8b74160 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>2.0-SNAPSHOT</version>
+ <version>2.0.0</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[15/50] incubator-taverna-common-activities git commit: Changed
packaging type to OSGI bundle
Posted by st...@apache.org.
Changed packaging type to OSGI bundle
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@11937 bf327186-88b3-11dd-a302-d386e5130c1c
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/0c88ecf8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/0c88ecf8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/0c88ecf8
Branch: refs/heads/master
Commit: 0c88ecf869d9df4e3737932b805a3a7fb4ad907b
Parents: 3348187
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Nov 15 16:58:05 2010 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Nov 15 16:58:05 2010 +0000
----------------------------------------------------------------------
pom.xml | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/0c88ecf8/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 560228d..f62bdaa 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,18 +8,23 @@
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
+ <packaging>bundle</packaging>
<name>Taverna 2 Activity with Dependencies</name>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <extensions>true</extensions>
+ </plugin>
+ </plugins>
+ </build>
<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>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
</dependencies>
</project>
[31/50] incubator-taverna-common-activities git commit: Increased
version numbers
Posted by st...@apache.org.
Increased version numbers
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/dependency-activity@16048 bf327186-88b3-11dd-a302-d386e5130c1c
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/b122b1a4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/b122b1a4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/b122b1a4
Branch: refs/heads/master
Commit: b122b1a42817399d30e712ef25ec2134a9db4785
Parents: d2f26b7
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Fri Sep 13 17:01:57 2013 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Fri Sep 13 17:01:57 2013 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/b122b1a4/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 38713d6..238b6d3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.4-SNAPSHOT</version>
+ <version>1.5-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[32/50] incubator-taverna-common-activities git commit: added
.gitignore
Posted by st...@apache.org.
added .gitignore
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/9d230ec8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/9d230ec8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/9d230ec8
Branch: refs/heads/master
Commit: 9d230ec826a4e4661d28f5a75bb3c1283834144d
Parents: b122b1a
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Tue May 6 16:56:02 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Tue May 6 16:56:02 2014 +0100
----------------------------------------------------------------------
.gitignore | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/9d230ec8/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..5a3defb
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+# ignore project files #
+.classpath
+.project
+.settings/
+catalog-v001.xml
+
+# ignore target files #
+target/
+bin/
+build/
+dist/
+apidoc/
+*.swp
+
+# ignore svn files if there
+.svn
+
+# ignore log files #
+*.log
+/logs/*
+*/logs/*
+
+
+
[26/50] incubator-taverna-common-activities git commit: Converted
activities to use JSON configuration. Moved port generation code from
activity configuration to activity factories.
Posted by st...@apache.org.
Converted activities to use JSON configuration.
Moved port generation code from activity configuration to activity factories.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15846 bf327186-88b3-11dd-a302-d386e5130c1c
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/10b17505
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/10b17505
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/10b17505
Branch: refs/heads/master
Commit: 10b17505123da056785e0f4fbf4dc70a600c1094
Parents: 13491a0
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Jul 8 10:00:17 2013 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Jul 8 10:00:17 2013 +0000
----------------------------------------------------------------------
pom.xml | 5 ++
.../AbstractAsynchronousDependencyActivity.java | 67 ++++++++------------
src/main/resources/schema.json | 25 ++++++++
3 files changed, 58 insertions(+), 39 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/10b17505/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index a91b407..3dfe3d8 100644
--- a/pom.xml
+++ b/pom.xml
@@ -21,6 +21,11 @@
<artifactId>taverna-app-configuration-api</artifactId>
<version>${taverna.configuration.version}</version>
</dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.2.2</version>
+ </dependency>
</dependencies>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/10b17505/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index d804b0e..fbd31d2 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -39,6 +39,8 @@ import org.apache.log4j.Logger;
import uk.org.taverna.configuration.app.ApplicationConfiguration;
+import com.fasterxml.jackson.databind.JsonNode;
+
/**
* A parent abstract class for activities that require dependency management, such as
* API Consumer and Beanshell. Defines dependencies on local JAR files
@@ -47,11 +49,8 @@ import uk.org.taverna.configuration.app.ApplicationConfiguration;
* @author Alex Nenadic
* @author Tom Oinn
* @author Stian Soiland-Reyes
- *
- * @param <ConfigType> the configuration type used for this activity
- *
*/
-public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends AbstractAsynchronousActivity<ConfigType>{
+public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsynchronousActivity<JsonNode> {
private static final String LOCAL_JARS = "Local jars";
@@ -78,13 +77,10 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
*/
protected ClassLoader classLoader = null;
- private ApplicationConfiguration applicationConfiguration;
-
/**
* The location of the <code>lib</code> directory in TAVERNA_HOME,
* where local JAR files the activity depends on should be located.
*/
-// public static File libDir = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "lib");
public File libDir;
/**
@@ -131,15 +127,14 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
* @return A new or existing {@link ClassLoader} according to the
* classloader sharing policy
*/
- protected ClassLoader findClassLoader(DependencyActivityConfigurationBean configurationBean, String workflowRunID) throws RuntimeException{
-
- ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
+ protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
if (classLoaderSharing == ClassLoaderSharing.workflow) {
synchronized (workflowClassLoaders) {
ClassLoader cl = workflowClassLoaders.get(workflowRunID);
if (cl == null) {
- cl = makeClassLoader(configurationBean, workflowRunID);
+ cl = makeClassLoader(json, workflowRunID);
workflowClassLoaders.put(workflowRunID, cl);
}
return cl;
@@ -176,15 +171,12 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
*
* @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
*/
- private ClassLoader makeClassLoader(
- DependencyActivityConfigurationBean configurationBean,
- String workflowID) {
-
+ private ClassLoader makeClassLoader(JsonNode json, String workflowID) {
// Find all artifact dependencies
// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
// Add all local jar dependencies
- HashSet<URL> urls = findDependencies(LOCAL_JARS, configurationBean, workflowID);
+ HashSet<URL> urls = findDependencies(LOCAL_JARS, json, workflowID);
// Create the classloader capable of loading both local jar and artifact dependencies
ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
@@ -236,11 +228,8 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
* sharing policy (passed inside configuration bean) and a workflowRunID (used to
* retrieve the workflow) that will be added to this activity classloader's list of URLs.
*/
- private HashSet<URL> findDependencies(String dependencyType,
- DependencyActivityConfigurationBean configurationBean,
- String workflowRunID) {
-
- ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
+ private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
// Get the WorkflowInstanceFacade which contains the current workflow
WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
WorkflowInstanceFacade wfFacade = null;
@@ -265,23 +254,25 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedWorkflow));
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedWorkflow));
}
else{ // Not nested - go through all of the processor's activities
Activity<?> activity = proc.getActivityList().get(0);
if (activity instanceof AbstractAsynchronousDependencyActivity){
- if (((DependencyActivityConfigurationBean) activity
- .getConfiguration()).getClassLoaderSharing() == classLoaderSharing) {
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+ if (ClassLoaderSharing.valueOf(dependencyActivity.getConfiguration().get("classLoaderSharing").textValue()) == classLoaderSharing) {
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
- for (String jar : ((DependencyActivityConfigurationBean)activity.getConfiguration()).getLocalDependencies()) {
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
try {
- dependencies.add(new File(libDir, jar));
+ dependencies.add(new File(libDir, jar.textValue()));
} catch (Exception ex) {
logger.warn("Invalid URL for " + jar, ex);
continue;
}
}
+ }
// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
// // Get the LocalReposotpry capable of finding artifact jar files
@@ -298,14 +289,16 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
}
} else { // Just add dependencies for this activity since we can't get hold of the whole workflow
// if (dependencyType.equals(LOCAL_JARS)){
- for (String jar : configurationBean.getLocalDependencies()) {
+ if (json.has("localDependency")) {
+ for (JsonNode jar : json.get("localDependency")) {
try {
- dependencies.add(new File(libDir, jar));
+ dependencies.add(new File(libDir, jar.textValue()));
} catch (Exception ex) {
logger.warn("Invalid URL for " + jar, ex);
continue;
}
}
+ }
// }
// else if (dependencyType.equals(ARTIFACTS)){
// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
@@ -341,11 +334,8 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
/**
* Finds dependencies for a nested workflow.
*/
- private HashSet<URL> findNestedDependencies(String dependencyType,
- DependencyActivityConfigurationBean configurationBean,
- Dataflow nestedWorkflow) {
-
- ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
+ private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
// Files of dependencies for all activities in the nested workflow that share the classloading policy
HashSet<File> dependencies = new HashSet<File>();
@@ -357,20 +347,19 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedNestedWorkflow));
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedNestedWorkflow));
}
else{ // Not nested - go through all of the processor's activities
Activity<?> activity = proc.getActivityList().get(0);
if (activity instanceof AbstractAsynchronousDependencyActivity){
-
- if (((DependencyActivityConfigurationBean) activity
- .getConfiguration()).getClassLoaderSharing() == classLoaderSharing) {
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+ if (ClassLoaderSharing.valueOf(dependencyActivity.getConfiguration().get("classLoaderSharing").textValue()) == classLoaderSharing) {
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
- for (String jar : ((DependencyActivityConfigurationBean)activity.getConfiguration()).getLocalDependencies()) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
try {
- dependencies.add(new File(libDir, jar));
+ dependencies.add(new File(libDir, jar.textValue()));
} catch (Exception ex) {
logger.warn("Invalid URL for " + jar, ex);
continue;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/10b17505/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/src/main/resources/schema.json b/src/main/resources/schema.json
new file mode 100644
index 0000000..c30459f
--- /dev/null
+++ b/src/main/resources/schema.json
@@ -0,0 +1,25 @@
+{
+ "$schema": "http://json-schema.org/draft-03/schema#",
+ "id": "http://ns.taverna.org.uk/2010/activity/dependency.schema.json",
+ "title": "Dependency activity configuration",
+ "type": "object",
+ "properties": {
+ "@context": {
+ "description": "JSON-LD context for interpreting the configuration as RDF",
+ "required": true,
+ "enum": ["http://ns.taverna.org.uk/2010/activity/dependency.context.json"]
+ },
+ "classLoaderSharing": {
+ "title": "ClassLoader Sharing Policy",
+ "description": "Policy for sharing class loaders across multiple beanshell activities",
+ "default": "workflow",
+ "enum": ["workflow", "system"]
+ },
+ "localDependency": {
+ "title": "Local Dependencies",
+ "description": "Location of jar files to be added to the beanshell class loader",
+ "type": "array",
+ "items": { "type" : "string" }
+ }
+ }
+}
[18/50] incubator-taverna-common-activities git commit: Moved
configuration annotation classes from processor.activity.config to
processor.config as they will be used for dispatch stack layer configurations
too.
Posted by st...@apache.org.
Moved configuration annotation classes from processor.activity.config to processor.config as they will be used for dispatch stack layer configurations too.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@12538 bf327186-88b3-11dd-a302-d386e5130c1c
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/38acc31e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/38acc31e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/38acc31e
Branch: refs/heads/master
Commit: 38acc31e75ffa417d4f07512ca780e8f4e8db276
Parents: 8ae6cbb
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Fri Feb 11 11:24:16 2011 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Fri Feb 11 11:24:16 2011 +0000
----------------------------------------------------------------------
.../dependencyactivity/DependencyActivityConfigurationBean.java | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/38acc31e/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index 5f5e5ed..c0c74eb 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -24,8 +24,8 @@ import java.util.LinkedHashSet;
import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ConfigurationProperty;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
/**
* Parent configuration bean for activities that have local JAR,
[36/50] incubator-taverna-common-activities git commit: Paent changed
to Taverna Parent
Posted by st...@apache.org.
Paent changed to Taverna Parent
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/c592d205
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/c592d205
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/c592d205
Branch: refs/heads/master
Commit: c592d20597905374661ee9dae716d6af64f064df
Parents: f589190
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Mon May 12 12:32:34 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Mon May 12 12:32:34 2014 +0100
----------------------------------------------------------------------
pom.xml | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c592d205/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 238b6d3..05037c4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -2,13 +2,14 @@
<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.t2</groupId>
- <artifactId>activities</artifactId>
- <version>1.5-SNAPSHOT</version>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>2.6-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
<name>Taverna 2 Activity with Dependencies</name>
+ <version>1.6-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
[06/50] incubator-taverna-common-activities git commit: Snapshots for
2.1
Posted by st...@apache.org.
Snapshots for 2.1
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@9320 bf327186-88b3-11dd-a302-d386e5130c1c
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/01c8104c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/01c8104c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/01c8104c
Branch: refs/heads/master
Commit: 01c8104ca53d08cb2b9e6f1f982d0c78488bbc1a
Parents: 42e82d1
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Fri Nov 27 16:46:35 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Fri Nov 27 16:46:35 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/01c8104c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 4ae6965..d97f199 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.9</version>
+ <version>0.10-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[21/50] incubator-taverna-common-activities git commit: Fixed
configuration URI.
Posted by st...@apache.org.
Fixed configuration URI.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@12635 bf327186-88b3-11dd-a302-d386e5130c1c
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/ccd8a773
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/ccd8a773
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/ccd8a773
Branch: refs/heads/master
Commit: ccd8a773e7bd7c827047f46192590aa4239c118e
Parents: 1a2abf0
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Fri Feb 18 15:11:21 2011 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Fri Feb 18 15:11:21 2011 +0000
----------------------------------------------------------------------
.../dependencyactivity/DependencyActivityConfigurationBean.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/ccd8a773/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index ad1fbf2..4e3bc22 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -34,7 +34,7 @@ import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
* @author Alex Nenadic
* @author David Withers
*/
-@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Configuration")
+@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
public class DependencyActivityConfigurationBean extends
ActivityPortsDefinitionBean {
[30/50] incubator-taverna-common-activities git commit: Check for
optional configuration property.
Posted by st...@apache.org.
Check for optional configuration property.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15956 bf327186-88b3-11dd-a302-d386e5130c1c
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/03671d7b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/03671d7b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/03671d7b
Branch: refs/heads/master
Commit: 03671d7b70487e93317e064f0f62a47741c2e0a2
Parents: 205fd9a
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Jul 25 16:36:50 2013 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Jul 25 16:36:50 2013 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/03671d7b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index 25c56f2..e2d5143 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -375,12 +375,14 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
- for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
}
}
// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
[29/50] incubator-taverna-common-activities git commit: Set value for
option properties.
Posted by st...@apache.org.
Set value for option properties.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15954 bf327186-88b3-11dd-a302-d386e5130c1c
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/205fd9a1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/205fd9a1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/205fd9a1
Branch: refs/heads/master
Commit: 205fd9a1cac245fdb7af3e80fba264774ad2569b
Parents: 76aebac
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Jul 25 15:43:17 2013 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Jul 25 15:43:17 2013 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 21 +++++++++++++++++---
1 file changed, 18 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/205fd9a1/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index 09b6e98..25c56f2 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -135,7 +135,12 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* classloader sharing policy
*/
protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
if (classLoaderSharing == ClassLoaderSharing.workflow) {
synchronized (workflowClassLoaders) {
@@ -236,7 +241,12 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* retrieve the workflow) that will be added to this activity classloader's list of URLs.
*/
private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
// Get the WorkflowInstanceFacade which contains the current workflow
WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
WorkflowInstanceFacade wfFacade = null;
@@ -340,7 +350,12 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* Finds dependencies for a nested workflow.
*/
private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
// Files of dependencies for all activities in the nested workflow that share the classloading policy
HashSet<File> dependencies = new HashSet<File>();
[19/50] incubator-taverna-common-activities git commit: Moved
declaration of maven-bundle plugin and spring repositories to parent pom.
Posted by st...@apache.org.
Moved declaration of maven-bundle plugin and spring repositories to parent pom.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@12590 bf327186-88b3-11dd-a302-d386e5130c1c
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/e999356c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/e999356c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/e999356c
Branch: refs/heads/master
Commit: e999356cc323020630b20bb8addf3d2403d48154
Parents: 38acc31
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Wed Feb 16 11:43:53 2011 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Wed Feb 16 11:43:53 2011 +0000
----------------------------------------------------------------------
pom.xml | 9 ---------
1 file changed, 9 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/e999356c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index f62bdaa..1eb95aa 100644
--- a/pom.xml
+++ b/pom.xml
@@ -10,15 +10,6 @@
<artifactId>dependency-activity</artifactId>
<packaging>bundle</packaging>
<name>Taverna 2 Activity with Dependencies</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <extensions>true</extensions>
- </plugin>
- </plugins>
- </build>
<dependencies>
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
[02/50] incubator-taverna-common-activities git commit:
[maven-release-plugin] prepare for next development iteration
Posted by st...@apache.org.
[maven-release-plugin] prepare for next development iteration
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@7967 bf327186-88b3-11dd-a302-d386e5130c1c
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/1c10f358
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/1c10f358
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/1c10f358
Branch: refs/heads/master
Commit: 1c10f35852c621474cacfd9c60761b6fb8f45467
Parents: 33df1b5
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Wed Jun 24 18:06:00 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Wed Jun 24 18:06:00 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1c10f358/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 2e42c34..1f96afd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.7</version>
+ <version>0.8-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[16/50] incubator-taverna-common-activities git commit: Removed Raven
class loading of artifact dependencies.
Posted by st...@apache.org.
Removed Raven class loading of artifact dependencies.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@11938 bf327186-88b3-11dd-a302-d386e5130c1c
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/f3a8212f
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/f3a8212f
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/f3a8212f
Branch: refs/heads/master
Commit: f3a8212fcb9e88b80b319484c99d305acf0198bc
Parents: 0c88ecf
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Nov 15 16:59:32 2010 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Nov 15 16:59:32 2010 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 156 +++++++++----------
.../DependencyActivityConfigurationBean.java | 58 +------
2 files changed, 78 insertions(+), 136 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/f3a8212f/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index 37a9503..f5fe2ab 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -25,24 +25,15 @@ import java.io.FilenameFilter;
import java.lang.ref.WeakReference;
import java.net.URL;
import java.net.URLClassLoader;
-import java.util.Arrays;
import java.util.HashSet;
-import java.util.Set;
import java.util.WeakHashMap;
-import net.sf.taverna.raven.appconfig.ApplicationRuntime;
-import net.sf.taverna.raven.prelauncher.BootstrapClassLoader;
-import net.sf.taverna.raven.prelauncher.PreLauncher;
-import net.sf.taverna.raven.repository.BasicArtifact;
-import net.sf.taverna.raven.repository.impl.LocalArtifactClassLoader;
-import net.sf.taverna.raven.repository.impl.LocalRepository;
import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
import net.sf.taverna.t2.workflowmodel.Dataflow;
import net.sf.taverna.t2.workflowmodel.Processor;
import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
import org.apache.log4j.Logger;
@@ -89,7 +80,8 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
* The location of the <code>lib</code> directory in TAVERNA_HOME,
* where local JAR files the activity depends on should be located.
*/
- public static File libDir = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "lib");
+// public static File libDir = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "lib");
+ public static File libDir = null;
/**
* Different ways to share a class loader among activities:
@@ -144,24 +136,24 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
}
}
if (classLoaderSharing == ClassLoaderSharing.system) {
- if (systemClassLoader == null)
- systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
+// if (systemClassLoader == null)
+// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
- if (systemClassLoader instanceof BootstrapClassLoader){
- // Add local and artifact dependencies to the classloader
- updateBootstrapClassLoader(
- (BootstrapClassLoader) systemClassLoader,
- configurationBean, workflowRunID);
- return systemClassLoader;
- }
- else{
+// if (systemClassLoader instanceof BootstrapClassLoader){
+// // Add local and artifact dependencies to the classloader
+// updateBootstrapClassLoader(
+// (BootstrapClassLoader) systemClassLoader,
+// configurationBean, workflowRunID);
+// return systemClassLoader;
+// }
+// else{
// Local dependencies will have to be set with the -classpath option
// We cannot have artifact dependencies in this case
String message = "System classloader is not Taverna's BootstrapClassLoader, so local dependencies " +
"have to defined with -classpath. Artifact dependencies are ignored completely.";
logger.warn(message);
return systemClassLoader;
- }
+// }
}
String message = "Unknown classloader sharing policy named '"+ classLoaderSharing+ "' for " + this.getClass();
logger.error(message);
@@ -179,10 +171,10 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
String workflowID) {
// Find all artifact dependencies
- HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
+// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
// Add all local jar dependencies
- urls.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowID));
+ HashSet<URL> urls = findDependencies(LOCAL_JARS, configurationBean, workflowID);
// Create the classloader capable of loading both local jar and artifact dependencies
ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
@@ -210,24 +202,24 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
*
* @param loader The augmented BootstrapClassLoader system classloader
*/
- private void updateBootstrapClassLoader(BootstrapClassLoader loader,
- DependencyActivityConfigurationBean configurationBean,
- String workflowRunID) {
-
- HashSet<URL> depsURLs = new HashSet<URL>();
- depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
- depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
-
- Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
- for (URL url : depsURLs) {
- if (exists.contains(url)) {
- continue;
- }
- logger.info("Registering with system classloader: " + url);
- loader.addURL(url);
- exists.add(url);
- }
- }
+// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
+// DependencyActivityConfigurationBean configurationBean,
+// String workflowRunID) {
+//
+// HashSet<URL> depsURLs = new HashSet<URL>();
+// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
+// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
+//
+// Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
+// for (URL url : depsURLs) {
+// if (exists.contains(url)) {
+// continue;
+// }
+// logger.info("Registering with system classloader: " + url);
+// loader.addURL(url);
+// exists.add(url);
+// }
+// }
/**
* Finds either local jar or artifact dependencies' URLs for the given classloader
@@ -260,7 +252,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
// as this activity
for (Processor proc : wf.getProcessors()) {
// Nested workflow case
- if (Tools.containsNestedWorkflow(proc)){
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedWorkflow));
@@ -270,7 +262,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
if (activity instanceof AbstractAsynchronousDependencyActivity){
if (((DependencyActivityConfigurationBean) activity
.getConfiguration()).getClassLoaderSharing() == classLoaderSharing) {
- if (dependencyType.equals(LOCAL_JARS)){
+// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
for (String jar : ((DependencyActivityConfigurationBean)activity.getConfiguration()).getLocalDependencies()) {
try {
@@ -280,22 +272,22 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
continue;
}
}
- } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
- LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
- // Get the LocalReposotpry capable of finding artifact jar files
- LocalRepository rep = (LocalRepository) cl.getRepository();
- for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
- .getConfiguration())
- .getArtifactDependencies()){
- dependencies.add(rep.jarFile(art));
- }
- }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// // Get the LocalReposotpry capable of finding artifact jar files
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
}
}
}
}
} else { // Just add dependencies for this activity since we can't get hold of the whole workflow
- if (dependencyType.equals(LOCAL_JARS)){
+// if (dependencyType.equals(LOCAL_JARS)){
for (String jar : configurationBean.getLocalDependencies()) {
try {
dependencies.add(new File(libDir, jar));
@@ -304,23 +296,23 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
continue;
}
}
- }
- else if (dependencyType.equals(ARTIFACTS)){
- if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
- LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
- LocalRepository rep = (LocalRepository)cl.getRepository();
- if (rep != null){
- for (BasicArtifact art : configurationBean.getArtifactDependencies()){
- dependencies.add(rep.jarFile(art));
- }
- }
- }
- else{
- // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
- // outside Raven so there is nothing we can do about this - some tests
- // with dependencies will probably fail
- }
- }
+// }
+// else if (dependencyType.equals(ARTIFACTS)){
+// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
+// LocalRepository rep = (LocalRepository)cl.getRepository();
+// if (rep != null){
+// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+// }
+// else{
+// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
+// // outside Raven so there is nothing we can do about this - some tests
+// // with dependencies will probably fail
+// }
+// }
}
// Collect the URLs of all found dependencies
@@ -352,7 +344,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
for (Processor proc : nestedWorkflow.getProcessors()) {
// Another nested workflow
- if (Tools.containsNestedWorkflow(proc)){
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedNestedWorkflow));
@@ -364,7 +356,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
if (((DependencyActivityConfigurationBean) activity
.getConfiguration()).getClassLoaderSharing() == classLoaderSharing) {
- if (dependencyType.equals(LOCAL_JARS)){
+// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
for (String jar : ((DependencyActivityConfigurationBean)activity.getConfiguration()).getLocalDependencies()) {
try {
@@ -373,16 +365,16 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
logger.warn("Invalid URL for " + jar, ex);
continue;
}
- } }
- else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
- LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
- LocalRepository rep = (LocalRepository) cl.getRepository();
- for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
- .getConfiguration())
- .getArtifactDependencies()){
- dependencies.add(rep.jarFile(art));
}
- }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
}
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/f3a8212f/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index 8b63590..aab3a6c 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -20,19 +20,17 @@
******************************************************************************/
package net.sf.taverna.t2.activities.dependencyactivity;
-import java.net.URL;
import java.util.LinkedHashSet;
-import net.sf.taverna.raven.repository.BasicArtifact;
import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
/**
- * Parent configuration bean for activities that have local JAR or artifact dependencies,
+ * Parent configuration bean for activities that have local JAR,
* such as API Consumer and Beanshell activity.
*
* @author Alex Nenadic
- *
+ * @author David Withers
*/
public class DependencyActivityConfigurationBean extends
ActivityPortsDefinitionBean {
@@ -48,28 +46,13 @@ public class DependencyActivityConfigurationBean extends
* and the paths should be relative.
*/
private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
-
- /**
- * Artifact dependencies. These artifacts should be available from
- * the centrally known repositories or from one of the listed repositories in
- * {@link #repositories}.
- */
- private LinkedHashSet<BasicArtifact> artifactDependencies ;//= new LinkedHashSet<BasicArtifact>();
-
- /**
- * Repositoryies to use when searching for artifacts. In addition, the system
- * repositories will be searched.
- */
- @Deprecated
- private LinkedHashSet<URL> repositories ;//= new LinkedHashSet<URL>();
-
+
/**
* Constructor.
*/
public DependencyActivityConfigurationBean(){
classLoaderSharing = ClassLoaderSharing.workflow;
localDependencies = new LinkedHashSet<String>();
- artifactDependencies = new LinkedHashSet<BasicArtifact>();
}
/**
@@ -84,9 +67,6 @@ public class DependencyActivityConfigurationBean extends
if (localDependencies == null)
localDependencies = new LinkedHashSet<String>();
- if (artifactDependencies == null)
- artifactDependencies = new LinkedHashSet<BasicArtifact>();
-
return this;
}
@@ -133,36 +113,6 @@ public class DependencyActivityConfigurationBean extends
public void removeLocalDependency(String dep){
localDependencies.remove(dep);
}
-
- /**
- * @return the artifactDependencies
- */
- public LinkedHashSet<BasicArtifact> getArtifactDependencies() {
- return artifactDependencies;
- }
-
- /**
- * @param artifactDependencies the artifactDependencies to set
- */
- public void setArtifactDependencies(LinkedHashSet<BasicArtifact> artifactDependencies) {
- this.artifactDependencies = artifactDependencies;
- }
-
- /**
- * Adds an artifact dependency to the list of local dependencies.
- * @param dep
- */
- public void addArtifactDependency(BasicArtifact dep){
- artifactDependencies.add(dep);
- }
-
- /**
- * Removes an artifact dependency from the list of local dependencies.
- * @param dep
- */
- public void removeArtifacteDependency(BasicArtifact dep){
- artifactDependencies.remove(dep);
- }
-
+
}
[05/50] incubator-taverna-common-activities git commit: Updated pom
and version-specific files
Posted by st...@apache.org.
Updated pom and version-specific files
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@9216 bf327186-88b3-11dd-a302-d386e5130c1c
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/42e82d1a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/42e82d1a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/42e82d1a
Branch: refs/heads/master
Commit: 42e82d1a4a80938d033867bc46447c2fa6917b26
Parents: 0b00557
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Nov 19 12:28:14 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Nov 19 12:28:14 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/42e82d1a/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 7a732f9..4ae6965 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.9-SNAPSHOT</version>
+ <version>0.9</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[46/50] incubator-taverna-common-activities git commit:
dependency-activity merged into beanshell-activity
Posted by st...@apache.org.
dependency-activity merged into beanshell-activity
.. only one using it
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/a7e6988b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/a7e6988b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/a7e6988b
Branch: refs/heads/master
Commit: a7e6988b9604a4d1fb0d67b142f0505d8fa8456a
Parents: e90b6f9
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:17:36 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:17:36 2015 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 445 +++++++++++++++++++
.../DependencyActivityConfigurationBean.java | 123 +++++
.../dependencyactivity/NewArtifactDialog.java | 207 +++++++++
.../src/main/resources/schema.json | 12 +
taverna-dependency-activity/pom.xml | 59 ---
.../AbstractAsynchronousDependencyActivity.java | 445 -------------------
.../DependencyActivityConfigurationBean.java | 123 -----
.../dependencyactivity/NewArtifactDialog.java | 207 ---------
.../src/main/resources/schema.json | 25 --
9 files changed, 787 insertions(+), 859 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
new file mode 100644
index 0000000..e2d5143
--- /dev/null
+++ b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -0,0 +1,445 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.lang.ref.WeakReference;
+import java.net.URL;
+import java.net.URLClassLoader;
+import java.util.HashSet;
+import java.util.WeakHashMap;
+
+import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
+import net.sf.taverna.t2.workflowmodel.Dataflow;
+import net.sf.taverna.t2.workflowmodel.Processor;
+import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+/**
+ * A parent abstract class for activities that require dependency management, such as
+ * API Consumer and Beanshell. Defines dependencies on local JAR files
+ * and Raven artifacts.
+ *
+ * @author Alex Nenadic
+ * @author Tom Oinn
+ * @author Stian Soiland-Reyes
+ */
+public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsynchronousActivity<JsonNode> {
+
+ private static final String LOCAL_JARS = "Local jars";
+
+ private static final String ARTIFACTS = "Artifacts";
+
+ private static Logger logger = Logger.getLogger(AbstractAsynchronousDependencyActivity.class);
+
+ /**
+ * For persisting class loaders across a whole workflow run (when classloader sharing
+ * is set to 'workflow'). The key in the map is the workflow run ID and we are using
+ * a WeakHashMap so we don't keep up references to classloaders of old workflow runs.
+ */
+ private static WeakHashMap<String, ClassLoader> workflowClassLoaders =
+ new WeakHashMap<String, ClassLoader>();
+
+ /**
+ * System classloader, in case when classloader sharing is set to 'system'.
+ */
+ private static ClassLoader systemClassLoader = null;
+
+ /**
+ * Classloader to be used for 'executing' this activity, depending on the activity's
+ * class loader sharing policy.
+ */
+ protected ClassLoader classLoader = null;
+
+ /**
+ * The location of the <code>lib</code> directory in TAVERNA_HOME,
+ * where local JAR files the activity depends on should be located.
+ */
+ public File libDir;
+
+ /**
+ * Different ways to share a class loader among activities:
+ *
+ * <dl>
+ * <dt>workflow</dt>
+ * <dd>Same classloader for all activities using the <code>workflow</code> classloader sharing policy</dd>
+ * <dt>system</dt>
+ * <dd>System classloader</dd>
+ * </dl>
+ *
+ */
+ public static enum ClassLoaderSharing {
+ workflow, system;
+ public static final ClassLoaderSharing DEFAULT = workflow;
+ public static ClassLoaderSharing fromString(String str) {
+ if (str == null || str.isEmpty()) {
+ return DEFAULT;
+ }
+ return valueOf(str.toLowerCase());
+ }
+ }
+
+ public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
+ if (applicationConfiguration != null) {
+ libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
+ }
+ }
+
+ /**
+ * Finds or constructs the classloader. The classloader depends on the
+ * current classloader sharing policy as defined by {@link #ClassLoaderSharing}.
+ * <p>
+ * If the classloader sharing is {@link ClassLoaderSharing#workflow}, a
+ * common classloader will be used for the whole workflow for all activities
+ * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
+ * The dependencies will be constructed as union of local and artifact dependencies
+ * of all 'workflow' classloader sharing activities at the point of the first
+ * call to {@link #getClassLoader()}.
+ * <p>
+ * If the classloader sharing is {@link ClassLoaderSharing#system}, the
+ * system classloader will be used. Note that both local and artifact dependencies
+ * configured on the activity will be ignored. Local dependencies can be set by
+ * using <code>-classpath</code> when starting the workbench.
+ * This is useful in combination with JNI based libraries, which would also
+ * require <code>-Djava.library.path</code> and possibly the operating
+ * system's PATH / LD_LIBRARY_PATH / DYLD_LIBRARY_PATH environment variable.
+ * @param classLoaderSharing
+ *
+ * @return A new or existing {@link ClassLoader} according to the
+ * classloader sharing policy
+ */
+ protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+
+ if (classLoaderSharing == ClassLoaderSharing.workflow) {
+ synchronized (workflowClassLoaders) {
+ ClassLoader cl = workflowClassLoaders.get(workflowRunID);
+ if (cl == null) {
+ cl = makeClassLoader(json, workflowRunID);
+ workflowClassLoaders.put(workflowRunID, cl);
+ }
+ return cl;
+ }
+ }
+ if (classLoaderSharing == ClassLoaderSharing.system) {
+// if (systemClassLoader == null)
+// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
+
+// if (systemClassLoader instanceof BootstrapClassLoader){
+// // Add local and artifact dependencies to the classloader
+// updateBootstrapClassLoader(
+// (BootstrapClassLoader) systemClassLoader,
+// configurationBean, workflowRunID);
+// return systemClassLoader;
+// }
+// else{
+ // Local dependencies will have to be set with the -classpath option
+ // We cannot have artifact dependencies in this case
+ String message = "System classloader is not Taverna's BootstrapClassLoader, so local dependencies " +
+ "have to defined with -classpath. Artifact dependencies are ignored completely.";
+ logger.warn(message);
+ return systemClassLoader;
+// }
+ }
+ String message = "Unknown classloader sharing policy named '"+ classLoaderSharing+ "' for " + this.getClass();
+ logger.error(message);
+ throw new RuntimeException(message);
+ }
+
+ /**
+ * Constructs a classloader capable of finding both local jar and artifact dependencies.
+ * Called when classloader sharing policy is set to 'workflow'.
+ *
+ * @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
+ */
+ private ClassLoader makeClassLoader(JsonNode json, String workflowID) {
+ // Find all artifact dependencies
+// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
+
+ // Add all local jar dependencies
+ HashSet<URL> urls = findDependencies(LOCAL_JARS, json, workflowID);
+
+ // Create the classloader capable of loading both local jar and artifact dependencies
+ ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
+
+ return new URLClassLoader(urls.toArray(new URL[0]), parent) {
+
+ // For finding native libraries that have to be stored in TAVERNA_HOME/lib
+ @Override
+ protected String findLibrary(String libname) {
+ String filename = System.mapLibraryName(libname);
+ File libraryFile = new File(libDir, filename);
+ if (libraryFile.isFile()) {
+ logger.info("Found library " + libname + ": " + libraryFile.getAbsolutePath());
+ return libraryFile.getAbsolutePath();
+ }
+ return super.findLibrary(libname);
+ }
+ };
+ }
+
+ /**
+ * Adds local or artifact dependencies identified by {@link #findDependencies()} to the
+ * {@link BootstrapClassLoader} system classloader.
+ * Called when classloader sharing policy is set to 'system'.
+ *
+ * @param loader The augmented BootstrapClassLoader system classloader
+ */
+// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
+// DependencyActivityConfigurationBean configurationBean,
+// String workflowRunID) {
+//
+// HashSet<URL> depsURLs = new HashSet<URL>();
+// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
+// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
+//
+// Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
+// for (URL url : depsURLs) {
+// if (exists.contains(url)) {
+// continue;
+// }
+// logger.info("Registering with system classloader: " + url);
+// loader.addURL(url);
+// exists.add(url);
+// }
+// }
+
+ /**
+ * Finds either local jar or artifact dependencies' URLs for the given classloader
+ * sharing policy (passed inside configuration bean) and a workflowRunID (used to
+ * retrieve the workflow) that will be added to this activity classloader's list of URLs.
+ */
+ private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+ // Get the WorkflowInstanceFacade which contains the current workflow
+ WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
+ WorkflowInstanceFacade wfFacade = null;
+ if (wfFacadeRef != null) {
+ wfFacade = wfFacadeRef.get();
+ }
+ Dataflow wf = null;
+ if (wfFacade != null) {
+ wf = wfFacade.getDataflow();
+ }
+
+ // Files of dependencies for all activities in the workflow that share the classloading policy
+ HashSet<File> dependencies = new HashSet<File>();
+ // Urls of all dependencies
+ HashSet<URL> dependenciesURLs = new HashSet<URL>();
+
+ if (wf != null){
+ // Merge in dependencies from all activities that have the same classloader-sharing
+ // as this activity
+ for (Processor proc : wf.getProcessors()) {
+ // Nested workflow case
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ // Get the nested workflow
+ Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedWorkflow));
+ }
+ else{ // Not nested - go through all of the processor's activities
+ Activity<?> activity = proc.getActivityList().get(0);
+ if (activity instanceof AbstractAsynchronousDependencyActivity){
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+// if (dependencyType.equals(LOCAL_JARS)){
+ // Collect the files of all found local dependencies
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// // Get the LocalReposotpry capable of finding artifact jar files
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+ }
+ }
+ }
+ } else { // Just add dependencies for this activity since we can't get hold of the whole workflow
+// if (dependencyType.equals(LOCAL_JARS)){
+ if (json.has("localDependency")) {
+ for (JsonNode jar : json.get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// }
+// else if (dependencyType.equals(ARTIFACTS)){
+// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
+// LocalRepository rep = (LocalRepository)cl.getRepository();
+// if (rep != null){
+// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+// }
+// else{
+// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
+// // outside Raven so there is nothing we can do about this - some tests
+// // with dependencies will probably fail
+// }
+// }
+ }
+
+ // Collect the URLs of all found dependencies
+ for (File file: dependencies){
+ try{
+ dependenciesURLs.add(file.toURI().toURL());
+ }
+ catch(Exception ex){
+ logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
+ continue;
+ }
+ }
+ return dependenciesURLs;
+ }
+
+ /**
+ * Finds dependencies for a nested workflow.
+ */
+ private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
+ ClassLoaderSharing classLoaderSharing;
+ if (json.has("classLoaderSharing")) {
+ classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
+ } else {
+ classLoaderSharing = ClassLoaderSharing.workflow;
+ }
+
+ // Files of dependencies for all activities in the nested workflow that share the classloading policy
+ HashSet<File> dependencies = new HashSet<File>();
+ // Urls of all dependencies
+ HashSet<URL> dependenciesURLs = new HashSet<URL>();
+
+ for (Processor proc : nestedWorkflow.getProcessors()) {
+ // Another nested workflow
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ // Get the nested workflow
+ Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
+ dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedNestedWorkflow));
+ }
+ else{ // Not nested - go through all of the processor's activities
+ Activity<?> activity = proc.getActivityList().get(0);
+ if (activity instanceof AbstractAsynchronousDependencyActivity){
+ AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
+// if (dependencyType.equals(LOCAL_JARS)){
+ // Collect the files of all found local dependencies
+ if (dependencyActivity.getConfiguration().has("localDependency")) {
+ for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
+ try {
+ dependencies.add(new File(libDir, jar.textValue()));
+ } catch (Exception ex) {
+ logger.warn("Invalid URL for " + jar, ex);
+ continue;
+ }
+ }
+ }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
+// LocalRepository rep = (LocalRepository) cl.getRepository();
+// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
+// .getConfiguration())
+// .getArtifactDependencies()){
+// dependencies.add(rep.jarFile(art));
+// }
+// }
+ }
+ }
+ }
+
+ // Collect the URLs of all found dependencies
+ for (File file: dependencies){
+ try{
+ dependenciesURLs.add(file.toURI().toURL());
+ }
+ catch(Exception ex){
+ logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
+ continue;
+ }
+ }
+ return dependenciesURLs;
+ }
+
+ /**
+ * File filter.
+ */
+ public static class FileExtFilter implements FilenameFilter {
+
+ String ext = null;
+
+ public FileExtFilter(String ext) {
+ this.ext = ext;
+ }
+
+ public boolean accept(File dir, String name) {
+ return name.endsWith(ext);
+ }
+ }
+
+ /**
+ * @param classLoader the classLoader to set
+ */
+ public void setClassLoader(ClassLoader classLoader) {
+ this.classLoader = classLoader;
+ }
+
+ /**
+ * @return the classLoader
+ */
+ public ClassLoader getClassLoader() {
+ return classLoader;
+ }
+}
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
new file mode 100644
index 0000000..afe75e2
--- /dev/null
+++ b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -0,0 +1,123 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.util.LinkedHashSet;
+
+import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
+import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Parent configuration bean for activities that have local JAR,
+ * such as API Consumer and Beanshell activity.
+ *
+ * @author Alex Nenadic
+ * @author David Withers
+ */
+@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
+public class DependencyActivityConfigurationBean extends
+ ActivityPortsDefinitionBean {
+
+ /**
+ * Activity's classloader sharing policy.
+ */
+ private ClassLoaderSharing classLoaderSharing ;// = ClassLoaderSharing.workflow;
+
+ /**
+ * Local dependencies, i.e. filenames of JARs the activity depends on.
+ * The files should be present in {@link AbstractAsynchronousActivityWithDependencies#libDir},
+ * and the paths should be relative.
+ */
+ private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
+
+ /**
+ * Constructor.
+ */
+ public DependencyActivityConfigurationBean(){
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
+ localDependencies = new LinkedHashSet<String>();
+ }
+
+ /**
+ * As XStream is not calling the default constructor during deserialization,
+ * we have to set the default values here. This method will be called by XStream
+ * after instantiating this bean.
+ */
+ private Object readResolve(){
+ if (classLoaderSharing == null)
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
+
+ if (localDependencies == null)
+ localDependencies = new LinkedHashSet<String>();
+
+ return this;
+ }
+
+ /**
+ * @param classLoaderSharing the classLoaderSharing to set
+ */
+ @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
+ public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
+ this.classLoaderSharing = classLoaderSharing;
+ }
+
+ /**
+ * @return the classLoaderSharing
+ */
+ public ClassLoaderSharing getClassLoaderSharing() {
+ return classLoaderSharing;
+ }
+
+ /**
+ * @param localDependencies the localDependencies to set
+ */
+ @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
+ public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
+ this.localDependencies = localDependencies;
+ }
+
+ /**
+ * @return the localDependencies
+ */
+ public LinkedHashSet<String> getLocalDependencies() {
+ return localDependencies;
+ }
+
+ /**
+ * Adds a dependency to the list of local dependencies.
+ * @param dep
+ */
+ public void addLocalDependency(String dep){
+ localDependencies.add(dep);
+ }
+
+ /**
+ * Removes a dependency from the list of local dependencies.
+ * @param dep
+ */
+ public void removeLocalDependency(String dep){
+ localDependencies.remove(dep);
+ }
+
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
new file mode 100644
index 0000000..9d04135
--- /dev/null
+++ b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
@@ -0,0 +1,207 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.activities.dependencyactivity;
+
+import java.awt.BorderLayout;
+import java.awt.FlowLayout;
+import java.awt.GridLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
+import javax.swing.JButton;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+import javax.swing.border.EmptyBorder;
+
+/**
+ * Dialog used for entering an artifact.
+ *
+ * @author Alex Nenadic
+ */
+@SuppressWarnings("serial")
+public class NewArtifactDialog
+ extends JDialog
+{
+ private JTextField jtfGroupID;
+
+ private JTextField jtfArtifactID;
+
+ private JTextField jtfVersion;
+
+ /** Stores new group ID entered */
+ private String groupID = null;
+
+ /** Stores new artifact ID entered */
+ private String artifactID = null;
+
+ /** Stores new version entered */
+ private String version = null;
+
+
+ /**
+ * Creates new NewArtifactDialog.
+ */
+ public NewArtifactDialog(String sTitle, boolean bModal)
+ {
+ super();
+ setTitle(sTitle);
+ setModal(bModal);
+ initComponents();
+ }
+
+ public String getGroupID()
+ {
+ return groupID;
+ }
+
+ public String getArtifatcID()
+ {
+ return artifactID;
+ }
+
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Initialise the dialog's GUI components.
+ */
+ private void initComponents()
+ {
+ getContentPane().setLayout(new BorderLayout());
+
+ JLabel jlGroupID = new JLabel("Group ID:");
+ JLabel jlArtifactID = new JLabel("Artifact ID:");
+ JLabel jlVersion = new JLabel("Version");
+
+ jtfGroupID = new JTextField(15);
+ jtfArtifactID = new JTextField(15);
+ jtfVersion = new JTextField(15);
+
+ JButton jbOK = new JButton("OK");
+ jbOK.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ okPressed();
+ }
+ });
+
+ JButton jbCancel = new JButton("Cancel");
+ jbCancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ cancelPressed();
+ }
+ });
+
+ JPanel jpPassword = new JPanel(new GridLayout(3, 2, 5, 5));
+ jpPassword.add(jlGroupID);
+ jpPassword.add(jtfGroupID);
+ jpPassword.add(jlArtifactID);
+ jpPassword.add(jtfArtifactID);
+ jpPassword.add(jlVersion);
+ jpPassword.add(jtfVersion);
+ jpPassword.setBorder(new EmptyBorder(5, 5, 5, 5));
+
+ JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
+ jpButtons.add(jbOK);
+ jpButtons.add(jbCancel);
+
+ getContentPane().add(jpPassword, BorderLayout.CENTER);
+ getContentPane().add(jpButtons, BorderLayout.SOUTH);
+
+ addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ closeDialog();
+ }
+ });
+
+ setResizable(false);
+
+ getRootPane().setDefaultButton(jbOK);
+
+ pack();
+ }
+
+ private boolean checkFields()
+ {
+ groupID = jtfGroupID.getText();
+ artifactID = jtfArtifactID.getText();
+ version = jtfVersion.getText();
+
+ if ((!groupID.equals("")) && (!artifactID.equals("")) && (!version.equals(""))){
+ return true;
+ }
+ else {
+ JOptionPane.showMessageDialog(this,
+ "Field(s) may not be empty",
+ "ERROR",
+ JOptionPane.ERROR_MESSAGE);
+
+ return false;
+ }
+ }
+
+ /**
+ * OK button pressed or otherwise activated.
+ */
+ private void okPressed()
+ {
+ if (checkFields()) {
+ closeDialog();
+ }
+ }
+
+ /**
+ * Cancel button pressed or otherwise activated.
+ */
+ private void cancelPressed()
+ {
+ // Set the fields to null as it might have changed in the meantime
+ // if user entered something previously
+ groupID = null;
+ artifactID = null;
+ version = null;
+ closeDialog();
+ }
+
+ /**
+ * Close the dialog.
+ */
+ private void closeDialog()
+ {
+ setVisible(false);
+ dispose();
+ }
+}
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-beanshell-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/resources/schema.json b/taverna-beanshell-activity/src/main/resources/schema.json
index fcf07b2..a9d195b 100644
--- a/taverna-beanshell-activity/src/main/resources/schema.json
+++ b/taverna-beanshell-activity/src/main/resources/schema.json
@@ -17,5 +17,17 @@
"required": true,
"default": ""
}
+ "classLoaderSharing": {
+ "title": "ClassLoader Sharing Policy",
+ "description": "Policy for sharing class loaders across multiple beanshell activities",
+ "default": "workflow",
+ "enum": ["workflow", "system"]
+ },
+ "localDependency": {
+ "title": "Local Dependencies",
+ "description": "Location of jar files to be added to the beanshell class loader",
+ "type": "array",
+ "items": { "type" : "string" }
+ }
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-dependency-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/pom.xml b/taverna-dependency-activity/pom.xml
deleted file mode 100644
index 1c138d0..0000000
--- a/taverna-dependency-activity/pom.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<?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>dependency-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Taverna 2 Activity with Dependencies</name>
- <version>2.0.1-SNAPSHOT</version>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson-databind.version}</version>
- </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>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-dependency-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-dependency-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-dependency-activity</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
deleted file mode 100644
index e2d5143..0000000
--- a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ /dev/null
@@ -1,445 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.io.File;
-import java.io.FilenameFilter;
-import java.lang.ref.WeakReference;
-import java.net.URL;
-import java.net.URLClassLoader;
-import java.util.HashSet;
-import java.util.WeakHashMap;
-
-import net.sf.taverna.t2.facade.WorkflowInstanceFacade;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
-
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * A parent abstract class for activities that require dependency management, such as
- * API Consumer and Beanshell. Defines dependencies on local JAR files
- * and Raven artifacts.
- *
- * @author Alex Nenadic
- * @author Tom Oinn
- * @author Stian Soiland-Reyes
- */
-public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsynchronousActivity<JsonNode> {
-
- private static final String LOCAL_JARS = "Local jars";
-
- private static final String ARTIFACTS = "Artifacts";
-
- private static Logger logger = Logger.getLogger(AbstractAsynchronousDependencyActivity.class);
-
- /**
- * For persisting class loaders across a whole workflow run (when classloader sharing
- * is set to 'workflow'). The key in the map is the workflow run ID and we are using
- * a WeakHashMap so we don't keep up references to classloaders of old workflow runs.
- */
- private static WeakHashMap<String, ClassLoader> workflowClassLoaders =
- new WeakHashMap<String, ClassLoader>();
-
- /**
- * System classloader, in case when classloader sharing is set to 'system'.
- */
- private static ClassLoader systemClassLoader = null;
-
- /**
- * Classloader to be used for 'executing' this activity, depending on the activity's
- * class loader sharing policy.
- */
- protected ClassLoader classLoader = null;
-
- /**
- * The location of the <code>lib</code> directory in TAVERNA_HOME,
- * where local JAR files the activity depends on should be located.
- */
- public File libDir;
-
- /**
- * Different ways to share a class loader among activities:
- *
- * <dl>
- * <dt>workflow</dt>
- * <dd>Same classloader for all activities using the <code>workflow</code> classloader sharing policy</dd>
- * <dt>system</dt>
- * <dd>System classloader</dd>
- * </dl>
- *
- */
- public static enum ClassLoaderSharing {
- workflow, system;
- public static final ClassLoaderSharing DEFAULT = workflow;
- public static ClassLoaderSharing fromString(String str) {
- if (str == null || str.isEmpty()) {
- return DEFAULT;
- }
- return valueOf(str.toLowerCase());
- }
- }
-
- public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
- if (applicationConfiguration != null) {
- libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
- }
- }
-
- /**
- * Finds or constructs the classloader. The classloader depends on the
- * current classloader sharing policy as defined by {@link #ClassLoaderSharing}.
- * <p>
- * If the classloader sharing is {@link ClassLoaderSharing#workflow}, a
- * common classloader will be used for the whole workflow for all activities
- * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
- * The dependencies will be constructed as union of local and artifact dependencies
- * of all 'workflow' classloader sharing activities at the point of the first
- * call to {@link #getClassLoader()}.
- * <p>
- * If the classloader sharing is {@link ClassLoaderSharing#system}, the
- * system classloader will be used. Note that both local and artifact dependencies
- * configured on the activity will be ignored. Local dependencies can be set by
- * using <code>-classpath</code> when starting the workbench.
- * This is useful in combination with JNI based libraries, which would also
- * require <code>-Djava.library.path</code> and possibly the operating
- * system's PATH / LD_LIBRARY_PATH / DYLD_LIBRARY_PATH environment variable.
- * @param classLoaderSharing
- *
- * @return A new or existing {@link ClassLoader} according to the
- * classloader sharing policy
- */
- protected ClassLoader findClassLoader(JsonNode json, String workflowRunID) throws RuntimeException{
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
-
- if (classLoaderSharing == ClassLoaderSharing.workflow) {
- synchronized (workflowClassLoaders) {
- ClassLoader cl = workflowClassLoaders.get(workflowRunID);
- if (cl == null) {
- cl = makeClassLoader(json, workflowRunID);
- workflowClassLoaders.put(workflowRunID, cl);
- }
- return cl;
- }
- }
- if (classLoaderSharing == ClassLoaderSharing.system) {
-// if (systemClassLoader == null)
-// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
-
-// if (systemClassLoader instanceof BootstrapClassLoader){
-// // Add local and artifact dependencies to the classloader
-// updateBootstrapClassLoader(
-// (BootstrapClassLoader) systemClassLoader,
-// configurationBean, workflowRunID);
-// return systemClassLoader;
-// }
-// else{
- // Local dependencies will have to be set with the -classpath option
- // We cannot have artifact dependencies in this case
- String message = "System classloader is not Taverna's BootstrapClassLoader, so local dependencies " +
- "have to defined with -classpath. Artifact dependencies are ignored completely.";
- logger.warn(message);
- return systemClassLoader;
-// }
- }
- String message = "Unknown classloader sharing policy named '"+ classLoaderSharing+ "' for " + this.getClass();
- logger.error(message);
- throw new RuntimeException(message);
- }
-
- /**
- * Constructs a classloader capable of finding both local jar and artifact dependencies.
- * Called when classloader sharing policy is set to 'workflow'.
- *
- * @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
- */
- private ClassLoader makeClassLoader(JsonNode json, String workflowID) {
- // Find all artifact dependencies
-// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
-
- // Add all local jar dependencies
- HashSet<URL> urls = findDependencies(LOCAL_JARS, json, workflowID);
-
- // Create the classloader capable of loading both local jar and artifact dependencies
- ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
-
- return new URLClassLoader(urls.toArray(new URL[0]), parent) {
-
- // For finding native libraries that have to be stored in TAVERNA_HOME/lib
- @Override
- protected String findLibrary(String libname) {
- String filename = System.mapLibraryName(libname);
- File libraryFile = new File(libDir, filename);
- if (libraryFile.isFile()) {
- logger.info("Found library " + libname + ": " + libraryFile.getAbsolutePath());
- return libraryFile.getAbsolutePath();
- }
- return super.findLibrary(libname);
- }
- };
- }
-
- /**
- * Adds local or artifact dependencies identified by {@link #findDependencies()} to the
- * {@link BootstrapClassLoader} system classloader.
- * Called when classloader sharing policy is set to 'system'.
- *
- * @param loader The augmented BootstrapClassLoader system classloader
- */
-// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
-// DependencyActivityConfigurationBean configurationBean,
-// String workflowRunID) {
-//
-// HashSet<URL> depsURLs = new HashSet<URL>();
-// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
-// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
-//
-// Set<URL> exists = new HashSet<URL>(Arrays.asList(loader.getURLs()));
-// for (URL url : depsURLs) {
-// if (exists.contains(url)) {
-// continue;
-// }
-// logger.info("Registering with system classloader: " + url);
-// loader.addURL(url);
-// exists.add(url);
-// }
-// }
-
- /**
- * Finds either local jar or artifact dependencies' URLs for the given classloader
- * sharing policy (passed inside configuration bean) and a workflowRunID (used to
- * retrieve the workflow) that will be added to this activity classloader's list of URLs.
- */
- private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
- // Get the WorkflowInstanceFacade which contains the current workflow
- WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
- WorkflowInstanceFacade wfFacade = null;
- if (wfFacadeRef != null) {
- wfFacade = wfFacadeRef.get();
- }
- Dataflow wf = null;
- if (wfFacade != null) {
- wf = wfFacade.getDataflow();
- }
-
- // Files of dependencies for all activities in the workflow that share the classloading policy
- HashSet<File> dependencies = new HashSet<File>();
- // Urls of all dependencies
- HashSet<URL> dependenciesURLs = new HashSet<URL>();
-
- if (wf != null){
- // Merge in dependencies from all activities that have the same classloader-sharing
- // as this activity
- for (Processor proc : wf.getProcessors()) {
- // Nested workflow case
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
- // Get the nested workflow
- Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedWorkflow));
- }
- else{ // Not nested - go through all of the processor's activities
- Activity<?> activity = proc.getActivityList().get(0);
- if (activity instanceof AbstractAsynchronousDependencyActivity){
- AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
-// if (dependencyType.equals(LOCAL_JARS)){
- // Collect the files of all found local dependencies
- if (dependencyActivity.getConfiguration().has("localDependency")) {
- for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
-// // Get the LocalReposotpry capable of finding artifact jar files
-// LocalRepository rep = (LocalRepository) cl.getRepository();
-// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
-// .getConfiguration())
-// .getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
- }
- }
- }
- } else { // Just add dependencies for this activity since we can't get hold of the whole workflow
-// if (dependencyType.equals(LOCAL_JARS)){
- if (json.has("localDependency")) {
- for (JsonNode jar : json.get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// }
-// else if (dependencyType.equals(ARTIFACTS)){
-// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
-// LocalRepository rep = (LocalRepository)cl.getRepository();
-// if (rep != null){
-// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
-// }
-// else{
-// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
-// // outside Raven so there is nothing we can do about this - some tests
-// // with dependencies will probably fail
-// }
-// }
- }
-
- // Collect the URLs of all found dependencies
- for (File file: dependencies){
- try{
- dependenciesURLs.add(file.toURI().toURL());
- }
- catch(Exception ex){
- logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
- continue;
- }
- }
- return dependenciesURLs;
- }
-
- /**
- * Finds dependencies for a nested workflow.
- */
- private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
- ClassLoaderSharing classLoaderSharing;
- if (json.has("classLoaderSharing")) {
- classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
- } else {
- classLoaderSharing = ClassLoaderSharing.workflow;
- }
-
- // Files of dependencies for all activities in the nested workflow that share the classloading policy
- HashSet<File> dependencies = new HashSet<File>();
- // Urls of all dependencies
- HashSet<URL> dependenciesURLs = new HashSet<URL>();
-
- for (Processor proc : nestedWorkflow.getProcessors()) {
- // Another nested workflow
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
- // Get the nested workflow
- Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
- dependenciesURLs.addAll(findNestedDependencies(dependencyType, json, nestedNestedWorkflow));
- }
- else{ // Not nested - go through all of the processor's activities
- Activity<?> activity = proc.getActivityList().get(0);
- if (activity instanceof AbstractAsynchronousDependencyActivity){
- AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
-// if (dependencyType.equals(LOCAL_JARS)){
- // Collect the files of all found local dependencies
- if (dependencyActivity.getConfiguration().has("localDependency")) {
- for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
- try {
- dependencies.add(new File(libDir, jar.textValue()));
- } catch (Exception ex) {
- logger.warn("Invalid URL for " + jar, ex);
- continue;
- }
- }
- }
-// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
-// LocalRepository rep = (LocalRepository) cl.getRepository();
-// for (BasicArtifact art : ((DependencyActivityConfigurationBean) activity
-// .getConfiguration())
-// .getArtifactDependencies()){
-// dependencies.add(rep.jarFile(art));
-// }
-// }
- }
- }
- }
-
- // Collect the URLs of all found dependencies
- for (File file: dependencies){
- try{
- dependenciesURLs.add(file.toURI().toURL());
- }
- catch(Exception ex){
- logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
- continue;
- }
- }
- return dependenciesURLs;
- }
-
- /**
- * File filter.
- */
- public static class FileExtFilter implements FilenameFilter {
-
- String ext = null;
-
- public FileExtFilter(String ext) {
- this.ext = ext;
- }
-
- public boolean accept(File dir, String name) {
- return name.endsWith(ext);
- }
- }
-
- /**
- * @param classLoader the classLoader to set
- */
- public void setClassLoader(ClassLoader classLoader) {
- this.classLoader = classLoader;
- }
-
- /**
- * @return the classLoader
- */
- public ClassLoader getClassLoader() {
- return classLoader;
- }
-}
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
deleted file mode 100644
index afe75e2..0000000
--- a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.util.LinkedHashSet;
-
-import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Parent configuration bean for activities that have local JAR,
- * such as API Consumer and Beanshell activity.
- *
- * @author Alex Nenadic
- * @author David Withers
- */
-@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
-public class DependencyActivityConfigurationBean extends
- ActivityPortsDefinitionBean {
-
- /**
- * Activity's classloader sharing policy.
- */
- private ClassLoaderSharing classLoaderSharing ;// = ClassLoaderSharing.workflow;
-
- /**
- * Local dependencies, i.e. filenames of JARs the activity depends on.
- * The files should be present in {@link AbstractAsynchronousActivityWithDependencies#libDir},
- * and the paths should be relative.
- */
- private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
-
- /**
- * Constructor.
- */
- public DependencyActivityConfigurationBean(){
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
- localDependencies = new LinkedHashSet<String>();
- }
-
- /**
- * As XStream is not calling the default constructor during deserialization,
- * we have to set the default values here. This method will be called by XStream
- * after instantiating this bean.
- */
- private Object readResolve(){
- if (classLoaderSharing == null)
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
-
- if (localDependencies == null)
- localDependencies = new LinkedHashSet<String>();
-
- return this;
- }
-
- /**
- * @param classLoaderSharing the classLoaderSharing to set
- */
- @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
- public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
- this.classLoaderSharing = classLoaderSharing;
- }
-
- /**
- * @return the classLoaderSharing
- */
- public ClassLoaderSharing getClassLoaderSharing() {
- return classLoaderSharing;
- }
-
- /**
- * @param localDependencies the localDependencies to set
- */
- @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
- public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
- this.localDependencies = localDependencies;
- }
-
- /**
- * @return the localDependencies
- */
- public LinkedHashSet<String> getLocalDependencies() {
- return localDependencies;
- }
-
- /**
- * Adds a dependency to the list of local dependencies.
- * @param dep
- */
- public void addLocalDependency(String dep){
- localDependencies.add(dep);
- }
-
- /**
- * Removes a dependency from the list of local dependencies.
- * @param dep
- */
- public void removeLocalDependency(String dep){
- localDependencies.remove(dep);
- }
-
-}
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java b/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
deleted file mode 100644
index 9d04135..0000000
--- a/taverna-dependency-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
+++ /dev/null
@@ -1,207 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.border.EmptyBorder;
-
-/**
- * Dialog used for entering an artifact.
- *
- * @author Alex Nenadic
- */
-@SuppressWarnings("serial")
-public class NewArtifactDialog
- extends JDialog
-{
- private JTextField jtfGroupID;
-
- private JTextField jtfArtifactID;
-
- private JTextField jtfVersion;
-
- /** Stores new group ID entered */
- private String groupID = null;
-
- /** Stores new artifact ID entered */
- private String artifactID = null;
-
- /** Stores new version entered */
- private String version = null;
-
-
- /**
- * Creates new NewArtifactDialog.
- */
- public NewArtifactDialog(String sTitle, boolean bModal)
- {
- super();
- setTitle(sTitle);
- setModal(bModal);
- initComponents();
- }
-
- public String getGroupID()
- {
- return groupID;
- }
-
- public String getArtifatcID()
- {
- return artifactID;
- }
-
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Initialise the dialog's GUI components.
- */
- private void initComponents()
- {
- getContentPane().setLayout(new BorderLayout());
-
- JLabel jlGroupID = new JLabel("Group ID:");
- JLabel jlArtifactID = new JLabel("Artifact ID:");
- JLabel jlVersion = new JLabel("Version");
-
- jtfGroupID = new JTextField(15);
- jtfArtifactID = new JTextField(15);
- jtfVersion = new JTextField(15);
-
- JButton jbOK = new JButton("OK");
- jbOK.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- okPressed();
- }
- });
-
- JButton jbCancel = new JButton("Cancel");
- jbCancel.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- cancelPressed();
- }
- });
-
- JPanel jpPassword = new JPanel(new GridLayout(3, 2, 5, 5));
- jpPassword.add(jlGroupID);
- jpPassword.add(jtfGroupID);
- jpPassword.add(jlArtifactID);
- jpPassword.add(jtfArtifactID);
- jpPassword.add(jlVersion);
- jpPassword.add(jtfVersion);
- jpPassword.setBorder(new EmptyBorder(5, 5, 5, 5));
-
- JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
- jpButtons.add(jbOK);
- jpButtons.add(jbCancel);
-
- getContentPane().add(jpPassword, BorderLayout.CENTER);
- getContentPane().add(jpButtons, BorderLayout.SOUTH);
-
- addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeDialog();
- }
- });
-
- setResizable(false);
-
- getRootPane().setDefaultButton(jbOK);
-
- pack();
- }
-
- private boolean checkFields()
- {
- groupID = jtfGroupID.getText();
- artifactID = jtfArtifactID.getText();
- version = jtfVersion.getText();
-
- if ((!groupID.equals("")) && (!artifactID.equals("")) && (!version.equals(""))){
- return true;
- }
- else {
- JOptionPane.showMessageDialog(this,
- "Field(s) may not be empty",
- "ERROR",
- JOptionPane.ERROR_MESSAGE);
-
- return false;
- }
- }
-
- /**
- * OK button pressed or otherwise activated.
- */
- private void okPressed()
- {
- if (checkFields()) {
- closeDialog();
- }
- }
-
- /**
- * Cancel button pressed or otherwise activated.
- */
- private void cancelPressed()
- {
- // Set the fields to null as it might have changed in the meantime
- // if user entered something previously
- groupID = null;
- artifactID = null;
- version = null;
- closeDialog();
- }
-
- /**
- * Close the dialog.
- */
- private void closeDialog()
- {
- setVisible(false);
- dispose();
- }
-}
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a7e6988b/taverna-dependency-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-dependency-activity/src/main/resources/schema.json b/taverna-dependency-activity/src/main/resources/schema.json
deleted file mode 100644
index c30459f..0000000
--- a/taverna-dependency-activity/src/main/resources/schema.json
+++ /dev/null
@@ -1,25 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-03/schema#",
- "id": "http://ns.taverna.org.uk/2010/activity/dependency.schema.json",
- "title": "Dependency activity configuration",
- "type": "object",
- "properties": {
- "@context": {
- "description": "JSON-LD context for interpreting the configuration as RDF",
- "required": true,
- "enum": ["http://ns.taverna.org.uk/2010/activity/dependency.context.json"]
- },
- "classLoaderSharing": {
- "title": "ClassLoader Sharing Policy",
- "description": "Policy for sharing class loaders across multiple beanshell activities",
- "default": "workflow",
- "enum": ["workflow", "system"]
- },
- "localDependency": {
- "title": "Local Dependencies",
- "description": "Location of jar files to be added to the beanshell class loader",
- "type": "array",
- "items": { "type" : "string" }
- }
- }
-}
[50/50] incubator-taverna-common-activities git commit: ARTIFACTS not
used
Posted by st...@apache.org.
ARTIFACTS not used
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/c2395289
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/c2395289
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/c2395289
Branch: refs/heads/master
Commit: c23952892343a0d839d7f321f92935c4bd22b385
Parents: a413395
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:23:03 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:23:03 2015 +0000
----------------------------------------------------------------------
.../dependencyactivity/AbstractAsynchronousDependencyActivity.java | 2 --
1 file changed, 2 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c2395289/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index e2d5143..a4f7e84 100644
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -54,8 +54,6 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
private static final String LOCAL_JARS = "Local jars";
- private static final String ARTIFACTS = "Artifacts";
-
private static Logger logger = Logger.getLogger(AbstractAsynchronousDependencyActivity.class);
/**
[17/50] incubator-taverna-common-activities git commit: Added
configuration bean annotations
Posted by st...@apache.org.
Added configuration bean annotations
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@12216 bf327186-88b3-11dd-a302-d386e5130c1c
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/8ae6cbb2
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/8ae6cbb2
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/8ae6cbb2
Branch: refs/heads/master
Commit: 8ae6cbb2e8cd4c27fe682d9659e0d6d3ff12ee81
Parents: f3a8212
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Wed Jan 19 16:41:43 2011 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Wed Jan 19 16:41:43 2011 +0000
----------------------------------------------------------------------
.../dependencyactivity/DependencyActivityConfigurationBean.java | 5 +++++
1 file changed, 5 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/8ae6cbb2/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index aab3a6c..5f5e5ed 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -24,6 +24,8 @@ import java.util.LinkedHashSet;
import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+import net.sf.taverna.t2.workflowmodel.processor.activity.config.ConfigurationBean;
+import net.sf.taverna.t2.workflowmodel.processor.activity.config.ConfigurationProperty;
/**
* Parent configuration bean for activities that have local JAR,
@@ -32,6 +34,7 @@ import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDe
* @author Alex Nenadic
* @author David Withers
*/
+@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency/Configuration")
public class DependencyActivityConfigurationBean extends
ActivityPortsDefinitionBean {
@@ -73,6 +76,7 @@ public class DependencyActivityConfigurationBean extends
/**
* @param classLoaderSharing the classLoaderSharing to set
*/
+ @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
this.classLoaderSharing = classLoaderSharing;
}
@@ -87,6 +91,7 @@ public class DependencyActivityConfigurationBean extends
/**
* @param localDependencies the localDependencies to set
*/
+ @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
this.localDependencies = localDependencies;
}
[13/50] incubator-taverna-common-activities git commit: Maintenance
branch
Posted by st...@apache.org.
Maintenance branch
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/dependency-activity@11411 bf327186-88b3-11dd-a302-d386e5130c1c
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/9d0bda21
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/9d0bda21
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/9d0bda21
Branch: refs/heads/master
Commit: 9d0bda215cae97d4f92b53170644356002e8635d
Parents: e3c74ab
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Sep 6 12:53:25 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Sep 6 12:53:25 2010 +0000
----------------------------------------------------------------------
----------------------------------------------------------------------
[49/50] incubator-taverna-common-activities git commit: Wrong javadoc
Posted by st...@apache.org.
Wrong javadoc
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/a413395e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/a413395e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/a413395e
Branch: refs/heads/master
Commit: a413395ec04b377af82e9c0ce53b51434e328e0a
Parents: d00b4c1
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:20:41 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:20:41 2015 +0000
----------------------------------------------------------------------
.../main/java/net/sf/taverna/t2/activities/beanshell/package.html | 3 ---
1 file changed, 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/a413395e/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
deleted file mode 100644
index 8b6e7a5..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/package.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<body>
-Contains the activity classes required to include String constants within a DataFlow.
-</body>
\ No newline at end of file
[39/50] incubator-taverna-common-activities git commit: Changed
taverna parent.
Posted by st...@apache.org.
Changed taverna parent.
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/96b8c3a4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/96b8c3a4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/96b8c3a4
Branch: refs/heads/master
Commit: 96b8c3a4180d43a9fe5b9e21910e0485919ec562
Parents: 85a02f4
Author: Aleksandra Nenadic <an...@cs.man.ac.uk>
Authored: Thu May 29 15:08:17 2014 +0100
Committer: Aleksandra Nenadic <an...@cs.man.ac.uk>
Committed: Thu May 29 15:08:17 2014 +0100
----------------------------------------------------------------------
pom.xml | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/96b8c3a4/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 3dfe3d8..8b183d7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -2,9 +2,9 @@
<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.t2</groupId>
- <artifactId>activities</artifactId>
- <version>2.0.1-SNAPSHOT</version>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[08/50] incubator-taverna-common-activities git commit: T2-936 bump
trunk version number of t2infrastructure to 2.1-SNAPSHOT
Posted by st...@apache.org.
T2-936 bump trunk version number of t2infrastructure to 2.1-SNAPSHOT
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@9619 bf327186-88b3-11dd-a302-d386e5130c1c
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/8b4e5bca
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/8b4e5bca
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/8b4e5bca
Branch: refs/heads/master
Commit: 8b4e5bca206e864ed88bd91ed1defd9514735fba
Parents: bff0f8e
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Tue Jan 5 12:39:50 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Tue Jan 5 12:39:50 2010 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/8b4e5bca/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index e26106d..5b8de22 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.0</version>
+ <version>1.1-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[10/50] incubator-taverna-common-activities git commit: merged to
trunk, T2-847
Posted by st...@apache.org.
merged to trunk, T2-847
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@10056 bf327186-88b3-11dd-a302-d386e5130c1c
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/0fdfa016
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/0fdfa016
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/0fdfa016
Branch: refs/heads/master
Commit: 0fdfa016100dd28ed2f2c6f8db31d74cf96e863c
Parents: 73a6807
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Apr 29 15:24:47 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Apr 29 15:24:47 2010 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/0fdfa016/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 5b8de22..69b7190 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.1-SNAPSHOT</version>
+ <version>1.1</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[43/50] incubator-taverna-common-activities git commit: Merge branch
'master' of git@github.com:taverna/taverna-dependency-activity.git
Posted by st...@apache.org.
Merge branch 'master' of git@github.com:taverna/taverna-dependency-activity.git
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/eaa15e21
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/eaa15e21
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/eaa15e21
Branch: refs/heads/master
Commit: eaa15e216d6cae6138e985b4af86a1cc8788e073
Parents: 2c3a7d2 458a3e7
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed Jul 2 15:09:04 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed Jul 2 15:09:04 2014 +0100
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/eaa15e21/pom.xml
----------------------------------------------------------------------
[28/50] incubator-taverna-common-activities git commit: class loader
sharing workflow by default
Posted by st...@apache.org.
class loader sharing workflow by default
Removed strange self-checks of classLoaderSharing ==
classLoaderSharing..
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15912 bf327186-88b3-11dd-a302-d386e5130c1c
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/76aebac4
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/76aebac4
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/76aebac4
Branch: refs/heads/master
Commit: 76aebac486a0c1b80485b345c0f66d438cd037ef
Parents: 4b383f5
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Tue Jul 23 12:24:16 2013 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Tue Jul 23 12:24:16 2013 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 9 ++-------
.../DependencyActivityConfigurationBean.java | 4 ++--
2 files changed, 4 insertions(+), 9 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/76aebac4/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index 4eb4799..09b6e98 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -236,7 +236,7 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* retrieve the workflow) that will be added to this activity classloader's list of URLs.
*/
private HashSet<URL> findDependencies(String dependencyType, JsonNode json, String workflowRunID) {
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
// Get the WorkflowInstanceFacade which contains the current workflow
WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
WorkflowInstanceFacade wfFacade = null;
@@ -267,7 +267,6 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
Activity<?> activity = proc.getActivityList().get(0);
if (activity instanceof AbstractAsynchronousDependencyActivity){
AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
- if (ClassLoaderSharing.valueOf(dependencyActivity.getConfiguration().get("classLoaderSharing").textValue()) == classLoaderSharing) {
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
if (dependencyActivity.getConfiguration().has("localDependency")) {
@@ -290,7 +289,6 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
// dependencies.add(rep.jarFile(art));
// }
// }
- }
}
}
}
@@ -342,7 +340,7 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
* Finds dependencies for a nested workflow.
*/
private HashSet<URL> findNestedDependencies(String dependencyType, JsonNode json, Dataflow nestedWorkflow) {
- ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.valueOf(json.get("classLoaderSharing").textValue());
+ ClassLoaderSharing classLoaderSharing = ClassLoaderSharing.fromString(json.get("classLoaderSharing").textValue());
// Files of dependencies for all activities in the nested workflow that share the classloading policy
HashSet<File> dependencies = new HashSet<File>();
@@ -360,8 +358,6 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
Activity<?> activity = proc.getActivityList().get(0);
if (activity instanceof AbstractAsynchronousDependencyActivity){
AbstractAsynchronousDependencyActivity dependencyActivity = (AbstractAsynchronousDependencyActivity) activity;
- if (ClassLoaderSharing.valueOf(dependencyActivity.getConfiguration().get("classLoaderSharing").textValue()) == classLoaderSharing) {
-
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
for (JsonNode jar : dependencyActivity.getConfiguration().get("localDependency")) {
@@ -381,7 +377,6 @@ public abstract class AbstractAsynchronousDependencyActivity extends AbstractAsy
// dependencies.add(rep.jarFile(art));
// }
// }
- }
}
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/76aebac4/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index 4e3bc22..afe75e2 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -54,7 +54,7 @@ public class DependencyActivityConfigurationBean extends
* Constructor.
*/
public DependencyActivityConfigurationBean(){
- classLoaderSharing = ClassLoaderSharing.workflow;
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
localDependencies = new LinkedHashSet<String>();
}
@@ -65,7 +65,7 @@ public class DependencyActivityConfigurationBean extends
*/
private Object readResolve(){
if (classLoaderSharing == null)
- classLoaderSharing = ClassLoaderSharing.workflow;
+ classLoaderSharing = ClassLoaderSharing.DEFAULT;
if (localDependencies == null)
localDependencies = new LinkedHashSet<String>();
[07/50] incubator-taverna-common-activities git commit: Updated
version numbers
Posted by st...@apache.org.
Updated version numbers
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@9508 bf327186-88b3-11dd-a302-d386e5130c1c
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/bff0f8ec
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/bff0f8ec
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/bff0f8ec
Branch: refs/heads/master
Commit: bff0f8eca81d58f4430f56cefcf71aaa3d0bef3e
Parents: 01c8104
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Sun Dec 13 16:09:35 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Sun Dec 13 16:09:35 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/bff0f8ec/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index d97f199..e26106d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.10-SNAPSHOT</version>
+ <version>1.0</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[41/50] incubator-taverna-common-activities git commit: Update pom.xml
Posted by st...@apache.org.
Update pom.xml
Corrected version number
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/458a3e7c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/458a3e7c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/458a3e7c
Branch: refs/heads/master
Commit: 458a3e7c4ece9e0bf1feb3bd65a9165a731d4d42
Parents: cd37be5
Author: alaninmcr <al...@manchester.ac.uk>
Authored: Fri May 30 12:48:14 2014 +0100
Committer: alaninmcr <al...@manchester.ac.uk>
Committed: Fri May 30 12:48:14 2014 +0100
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/458a3e7c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8fed691..fe92714 100644
--- a/pom.xml
+++ b/pom.xml
@@ -10,7 +10,7 @@
<artifactId>dependency-activity</artifactId>
<packaging>bundle</packaging>
<name>Taverna 2 Activity with Dependencies</name>
- <version>1.6-SNAPSHOT</version>
+ <version>2.0.1-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
[09/50] incubator-taverna-common-activities git commit: T2-1135 use
weak references to the facades to avoid facade memory leak.
Posted by st...@apache.org.
T2-1135 use weak references to the facades to avoid facade memory leak.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@9653 bf327186-88b3-11dd-a302-d386e5130c1c
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/73a68072
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/73a68072
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/73a68072
Branch: refs/heads/master
Commit: 73a6807242ea3d9b9208dc6168f337ce25a10b12
Parents: 8b4e5bc
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Feb 1 16:03:40 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Feb 1 16:03:40 2010 +0000
----------------------------------------------------------------------
.../AbstractAsynchronousDependencyActivity.java | 16 +++++++++++-----
1 file changed, 11 insertions(+), 5 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/73a68072/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index 1e75e13..37a9503 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -22,6 +22,7 @@ package net.sf.taverna.t2.activities.dependencyactivity;
import java.io.File;
import java.io.FilenameFilter;
+import java.lang.ref.WeakReference;
import java.net.URL;
import java.net.URLClassLoader;
import java.util.Arrays;
@@ -29,8 +30,6 @@ import java.util.HashSet;
import java.util.Set;
import java.util.WeakHashMap;
-import org.apache.log4j.Logger;
-
import net.sf.taverna.raven.appconfig.ApplicationRuntime;
import net.sf.taverna.raven.prelauncher.BootstrapClassLoader;
import net.sf.taverna.raven.prelauncher.PreLauncher;
@@ -45,6 +44,8 @@ import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
import net.sf.taverna.t2.workflowmodel.utils.Tools;
+import org.apache.log4j.Logger;
+
/**
* A parent abstract class for activities that require dependency management, such as
* API Consumer and Beanshell. Defines dependencies on local JAR files
@@ -239,10 +240,15 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
// Get the WorkflowInstanceFacade which contains the current workflow
- WorkflowInstanceFacade wfFacade = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
+ WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
+ WorkflowInstanceFacade wfFacade = null;
+ if (wfFacadeRef != null) {
+ wfFacade = wfFacadeRef.get();
+ }
Dataflow wf = null;
- if (wfFacade != null)
- wf = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID).getDataflow();
+ if (wfFacade != null) {
+ wf = wfFacade.getDataflow();
+ }
// Files of dependencies for all activities in the workflow that share the classloading policy
HashSet<File> dependencies = new HashSet<File>();
[40/50] incubator-taverna-common-activities git commit: Merge branch
'maintenance'.
Posted by st...@apache.org.
Merge branch 'maintenance'.
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/cd37be57
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/cd37be57
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/cd37be57
Branch: refs/heads/master
Commit: cd37be575c3407839e177c657b7fa16d2385566e
Parents: 96b8c3a cc39902
Author: Aleksandra Nenadic <an...@cs.man.ac.uk>
Authored: Thu May 29 15:11:15 2014 +0100
Committer: Aleksandra Nenadic <an...@cs.man.ac.uk>
Committed: Thu May 29 15:11:15 2014 +0100
----------------------------------------------------------------------
.gitignore | 1 -
pom.xml | 28 ++++++++++++++++++++++++++++
2 files changed, 28 insertions(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cd37be57/.gitignore
----------------------------------------------------------------------
diff --cc .gitignore
index ebe0e5b,5a3defb..6d2ce9e
--- a/.gitignore
+++ b/.gitignore
@@@ -3,7 -3,7 +3,6 @@@
.project
.settings/
catalog-v001.xml
-
-
# ignore target files #
target/
bin/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/cd37be57/pom.xml
----------------------------------------------------------------------
diff --cc pom.xml
index 8b183d7,87c9a46..8fed691
--- a/pom.xml
+++ b/pom.xml
@@@ -8,8 -8,8 +8,9 @@@
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
+ <packaging>bundle</packaging>
<name>Taverna 2 Activity with Dependencies</name>
+ <version>1.6-SNAPSHOT</version>
<dependencies>
<dependency>
<groupId>net.sf.taverna.t2.core</groupId>
@@@ -17,15 -17,37 +18,42 @@@
<version>${t2.core.version}</version>
</dependency>
<dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-impl</artifactId>
- <version>${t2.core.version}</version>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.2.2</version>
</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>
+ </repositories>
+ <scm>
+ <connection>scm:git:https://github.com/taverna/taverna-dependency-activity.git</connection>
+ <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-dependency-activity.git</developerConnection>
+ <url>https://github.com/taverna/taverna-dependency-activity</url>
+ <tag>HEAD</tag>
+ </scm>
+
</project>
[14/50] incubator-taverna-common-activities git commit: Bumped
versions numbers. 1.3-SNAPSHOT -> 2.0-SNAPSHOT, 2.3-SNAPSHOT -> 3.0-SNAPSHOT
Posted by st...@apache.org.
Bumped versions numbers. 1.3-SNAPSHOT -> 2.0-SNAPSHOT, 2.3-SNAPSHOT -> 3.0-SNAPSHOT
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@11464 bf327186-88b3-11dd-a302-d386e5130c1c
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/3348187c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/3348187c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/3348187c
Branch: refs/heads/master
Commit: 3348187c0d915c59558574d513375fb10ad59845
Parents: e3c74ab
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Sep 6 14:13:56 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Sep 6 14:13:56 2010 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/3348187c/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index a360771..560228d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.3-SNAPSHOT</version>
+ <version>2.0-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[47/50] incubator-taverna-common-activities git commit:
NewArtifactDialog not relevant in T3
Posted by st...@apache.org.
NewArtifactDialog not relevant in T3
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/31ee601a
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/31ee601a
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/31ee601a
Branch: refs/heads/master
Commit: 31ee601aa6aeb29be25ca699e40a7a910c93a5e5
Parents: a7e6988
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:19:43 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:19:43 2015 +0000
----------------------------------------------------------------------
.../dependencyactivity/NewArtifactDialog.java | 207 -------------------
1 file changed, 207 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/31ee601a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
deleted file mode 100644
index 9d04135..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/NewArtifactDialog.java
+++ /dev/null
@@ -1,207 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-
-import javax.swing.JButton;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.border.EmptyBorder;
-
-/**
- * Dialog used for entering an artifact.
- *
- * @author Alex Nenadic
- */
-@SuppressWarnings("serial")
-public class NewArtifactDialog
- extends JDialog
-{
- private JTextField jtfGroupID;
-
- private JTextField jtfArtifactID;
-
- private JTextField jtfVersion;
-
- /** Stores new group ID entered */
- private String groupID = null;
-
- /** Stores new artifact ID entered */
- private String artifactID = null;
-
- /** Stores new version entered */
- private String version = null;
-
-
- /**
- * Creates new NewArtifactDialog.
- */
- public NewArtifactDialog(String sTitle, boolean bModal)
- {
- super();
- setTitle(sTitle);
- setModal(bModal);
- initComponents();
- }
-
- public String getGroupID()
- {
- return groupID;
- }
-
- public String getArtifatcID()
- {
- return artifactID;
- }
-
- public String getVersion()
- {
- return version;
- }
-
- /**
- * Initialise the dialog's GUI components.
- */
- private void initComponents()
- {
- getContentPane().setLayout(new BorderLayout());
-
- JLabel jlGroupID = new JLabel("Group ID:");
- JLabel jlArtifactID = new JLabel("Artifact ID:");
- JLabel jlVersion = new JLabel("Version");
-
- jtfGroupID = new JTextField(15);
- jtfArtifactID = new JTextField(15);
- jtfVersion = new JTextField(15);
-
- JButton jbOK = new JButton("OK");
- jbOK.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- okPressed();
- }
- });
-
- JButton jbCancel = new JButton("Cancel");
- jbCancel.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent evt)
- {
- cancelPressed();
- }
- });
-
- JPanel jpPassword = new JPanel(new GridLayout(3, 2, 5, 5));
- jpPassword.add(jlGroupID);
- jpPassword.add(jtfGroupID);
- jpPassword.add(jlArtifactID);
- jpPassword.add(jtfArtifactID);
- jpPassword.add(jlVersion);
- jpPassword.add(jtfVersion);
- jpPassword.setBorder(new EmptyBorder(5, 5, 5, 5));
-
- JPanel jpButtons = new JPanel(new FlowLayout(FlowLayout.CENTER));
- jpButtons.add(jbOK);
- jpButtons.add(jbCancel);
-
- getContentPane().add(jpPassword, BorderLayout.CENTER);
- getContentPane().add(jpButtons, BorderLayout.SOUTH);
-
- addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- closeDialog();
- }
- });
-
- setResizable(false);
-
- getRootPane().setDefaultButton(jbOK);
-
- pack();
- }
-
- private boolean checkFields()
- {
- groupID = jtfGroupID.getText();
- artifactID = jtfArtifactID.getText();
- version = jtfVersion.getText();
-
- if ((!groupID.equals("")) && (!artifactID.equals("")) && (!version.equals(""))){
- return true;
- }
- else {
- JOptionPane.showMessageDialog(this,
- "Field(s) may not be empty",
- "ERROR",
- JOptionPane.ERROR_MESSAGE);
-
- return false;
- }
- }
-
- /**
- * OK button pressed or otherwise activated.
- */
- private void okPressed()
- {
- if (checkFields()) {
- closeDialog();
- }
- }
-
- /**
- * Cancel button pressed or otherwise activated.
- */
- private void cancelPressed()
- {
- // Set the fields to null as it might have changed in the meantime
- // if user entered something previously
- groupID = null;
- artifactID = null;
- version = null;
- closeDialog();
- }
-
- /**
- * Close the dialog.
- */
- private void closeDialog()
- {
- setVisible(false);
- dispose();
- }
-}
-
-
-
[22/50] incubator-taverna-common-activities git commit: Attempt to
correct version numbers
Posted by st...@apache.org.
Attempt to correct version numbers
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/branches/maintenance/dependency-activity@14303 bf327186-88b3-11dd-a302-d386e5130c1c
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/d2f26b7e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/d2f26b7e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/d2f26b7e
Branch: refs/heads/master
Commit: d2f26b7e8a78c147a2dc19e90f0f98218c3b5ac1
Parents: 9d0bda2
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Dec 5 15:11:30 2011 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Dec 5 15:11:30 2011 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/d2f26b7e/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index a360771..38713d6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.3-SNAPSHOT</version>
+ <version>1.4-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[48/50] incubator-taverna-common-activities git commit: Configuration
beans not relevant in Taverna 3
Posted by st...@apache.org.
Configuration beans not relevant in Taverna 3
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/d00b4c16
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/d00b4c16
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/d00b4c16
Branch: refs/heads/master
Commit: d00b4c16e88289c2db3e5b1e4416dc567fb2d9cf
Parents: 31ee601
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Fri Mar 6 16:20:23 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Fri Mar 6 16:20:23 2015 +0000
----------------------------------------------------------------------
.../activities/beanshell/BeanshellActivity.java | 2 -
.../BeanshellActivityConfigurationBean.java | 86 -------------
.../DependencyActivityConfigurationBean.java | 123 -------------------
3 files changed, 211 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/d00b4c16/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
index 134d3fe..9f0f938 100644
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
+++ b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivity.java
@@ -53,8 +53,6 @@ public class BeanshellActivity extends AbstractAsynchronousDependencyActivity {
public static final String URI = "http://ns.taverna.org.uk/2010/activity/beanshell";
- protected BeanshellActivityConfigurationBean configurationBean;
-
private static Logger logger = Logger.getLogger(BeanshellActivity.class);
private Interpreter interpreter;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/d00b4c16/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
deleted file mode 100644
index 8a5f06f..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/beanshell/BeanshellActivityConfigurationBean.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.beanshell;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.dependencyactivity.DependencyActivityConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to a Beanshell activity; provides details
- * about the Beanshell script and its local and artifact dependencies.
- *
- * @author Stuart Owen
- * @author David Withers
- * @author Alex Nenadic
- */
-@ConfigurationBean(uri = BeanshellActivity.URI + "#Config")
-public class BeanshellActivityConfigurationBean extends DependencyActivityConfigurationBean {
-
- private String script;
-
- public BeanshellActivityConfigurationBean() {
- super();
- this.script = "";
- }
-
- /**
- * @return the Beanshell script
- */
- public String getScript() {
- return script;
- }
-
- /**
- * @param script the Beanshell script
- */
- @ConfigurationProperty(name = "script", label = "Beanshell Script", description = "The beanshell script to be executed")
- public void setScript(String script) {
- this.script = script;
- }
-
- ///////////// From old code //////////
- @Deprecated
- private List<String> dependencies = new ArrayList<String>();
-
- /**
- * Returns the dependencies.
- *
- * @return the dependencies
- */
- public List<String> getDependencies() {
- return dependencies;
- }
-
- /**
- * Sets the dependencies.
- *
- * @param dependencies the new dependencies
- */
- public void setDependencies(List<String> dependencies) {
- this.dependencies = dependencies;
- }
- ///////////// From old code //////////
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/d00b4c16/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
deleted file mode 100644
index afe75e2..0000000
--- a/taverna-beanshell-activity/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ /dev/null
@@ -1,123 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.dependencyactivity;
-
-import java.util.LinkedHashSet;
-
-import net.sf.taverna.t2.activities.dependencyactivity.AbstractAsynchronousDependencyActivity.ClassLoaderSharing;
-import net.sf.taverna.t2.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Parent configuration bean for activities that have local JAR,
- * such as API Consumer and Beanshell activity.
- *
- * @author Alex Nenadic
- * @author David Withers
- */
-@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Config")
-public class DependencyActivityConfigurationBean extends
- ActivityPortsDefinitionBean {
-
- /**
- * Activity's classloader sharing policy.
- */
- private ClassLoaderSharing classLoaderSharing ;// = ClassLoaderSharing.workflow;
-
- /**
- * Local dependencies, i.e. filenames of JARs the activity depends on.
- * The files should be present in {@link AbstractAsynchronousActivityWithDependencies#libDir},
- * and the paths should be relative.
- */
- private LinkedHashSet<String> localDependencies ;//= new LinkedHashSet<String>();
-
- /**
- * Constructor.
- */
- public DependencyActivityConfigurationBean(){
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
- localDependencies = new LinkedHashSet<String>();
- }
-
- /**
- * As XStream is not calling the default constructor during deserialization,
- * we have to set the default values here. This method will be called by XStream
- * after instantiating this bean.
- */
- private Object readResolve(){
- if (classLoaderSharing == null)
- classLoaderSharing = ClassLoaderSharing.DEFAULT;
-
- if (localDependencies == null)
- localDependencies = new LinkedHashSet<String>();
-
- return this;
- }
-
- /**
- * @param classLoaderSharing the classLoaderSharing to set
- */
- @ConfigurationProperty(name = "classLoaderSharing", label = "ClassLoader Sharing Policy", required = false)
- public void setClassLoaderSharing(ClassLoaderSharing classLoaderSharing) {
- this.classLoaderSharing = classLoaderSharing;
- }
-
- /**
- * @return the classLoaderSharing
- */
- public ClassLoaderSharing getClassLoaderSharing() {
- return classLoaderSharing;
- }
-
- /**
- * @param localDependencies the localDependencies to set
- */
- @ConfigurationProperty(name = "localDependency", label = "Local Dependencies", required = false)
- public void setLocalDependencies(LinkedHashSet<String> localDependencies) {
- this.localDependencies = localDependencies;
- }
-
- /**
- * @return the localDependencies
- */
- public LinkedHashSet<String> getLocalDependencies() {
- return localDependencies;
- }
-
- /**
- * Adds a dependency to the list of local dependencies.
- * @param dep
- */
- public void addLocalDependency(String dep){
- localDependencies.add(dep);
- }
-
- /**
- * Removes a dependency from the list of local dependencies.
- * @param dep
- */
- public void removeLocalDependency(String dep){
- localDependencies.remove(dep);
- }
-
-}
-
[38/50] incubator-taverna-common-activities git commit: travis
Posted by st...@apache.org.
travis
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/85a02f4e
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/85a02f4e
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/85a02f4e
Branch: refs/heads/master
Commit: 85a02f4e68e443f03f7212cac3588a3d43b4a697
Parents: 536a7fc
Author: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Authored: Thu May 15 15:10:32 2014 +0100
Committer: Stian Soiland-Reyes <so...@cs.manchester.ac.uk>
Committed: Thu May 15 15:10:32 2014 +0100
----------------------------------------------------------------------
.travis.yml | 1 +
1 file changed, 1 insertion(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/85a02f4e/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..dff5f3a
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1 @@
+language: java
[03/50] incubator-taverna-common-activities git commit:
[maven-release-plugin] prepare release activities-0.8
Posted by st...@apache.org.
[maven-release-plugin] prepare release activities-0.8
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@7982 bf327186-88b3-11dd-a302-d386e5130c1c
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/c3c05192
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/c3c05192
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/c3c05192
Branch: refs/heads/master
Commit: c3c051925a6d682eb8dbf441788271bc06c48250
Parents: 1c10f35
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Jun 25 10:11:50 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Jun 25 10:11:50 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/c3c05192/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 1f96afd..8090a8a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.8-SNAPSHOT</version>
+ <version>0.8</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[25/50] incubator-taverna-common-activities git commit: Added
application configuration which is used to determine directory containing
dependency jars.
Posted by st...@apache.org.
Added application configuration which is used to determine directory containing dependency jars.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@15004 bf327186-88b3-11dd-a302-d386e5130c1c
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/13491a07
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/13491a07
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/13491a07
Branch: refs/heads/master
Commit: 13491a07183d0af44379cb37a47b84f053e48986
Parents: bee5245
Author: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Tue Jun 12 11:28:01 2012 +0000
Committer: david@mygrid.org.uk <da...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Tue Jun 12 11:28:01 2012 +0000
----------------------------------------------------------------------
pom.xml | 5 +
.../AbstractAsynchronousDependencyActivity.java | 132 ++++++++++---------
2 files changed, 76 insertions(+), 61 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/13491a07/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8481869..a91b407 100644
--- a/pom.xml
+++ b/pom.xml
@@ -16,6 +16,11 @@
<artifactId>workflowmodel-api</artifactId>
<version>${t2.core.version}</version>
</dependency>
+ <dependency>
+ <groupId>uk.org.taverna.configuration</groupId>
+ <artifactId>taverna-app-configuration-api</artifactId>
+ <version>${taverna.configuration.version}</version>
+ </dependency>
</dependencies>
</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/13491a07/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
index f5fe2ab..d804b0e 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/AbstractAsynchronousDependencyActivity.java
@@ -1,19 +1,19 @@
/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
+ * Copyright (C) 2007 The University of Manchester
+ *
* Modifications to the initial code base are copyright of their
* respective authors, or their employers as appropriate.
- *
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1 of
* the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
- *
+ *
* You should have received a copy of the GNU Lesser General Public
* License along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
@@ -37,20 +37,22 @@ import net.sf.taverna.t2.workflowmodel.processor.activity.NestedDataflow;
import org.apache.log4j.Logger;
+import uk.org.taverna.configuration.app.ApplicationConfiguration;
+
/**
* A parent abstract class for activities that require dependency management, such as
- * API Consumer and Beanshell. Defines dependencies on local JAR files
+ * API Consumer and Beanshell. Defines dependencies on local JAR files
* and Raven artifacts.
- *
+ *
* @author Alex Nenadic
* @author Tom Oinn
* @author Stian Soiland-Reyes
- *
+ *
* @param <ConfigType> the configuration type used for this activity
*
*/
public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends AbstractAsynchronousActivity<ConfigType>{
-
+
private static final String LOCAL_JARS = "Local jars";
private static final String ARTIFACTS = "Artifacts";
@@ -59,12 +61,12 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
/**
* For persisting class loaders across a whole workflow run (when classloader sharing
- * is set to 'workflow'). The key in the map is the workflow run ID and we are using
+ * is set to 'workflow'). The key in the map is the workflow run ID and we are using
* a WeakHashMap so we don't keep up references to classloaders of old workflow runs.
*/
private static WeakHashMap<String, ClassLoader> workflowClassLoaders =
new WeakHashMap<String, ClassLoader>();
-
+
/**
* System classloader, in case when classloader sharing is set to 'system'.
*/
@@ -75,56 +77,64 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
* class loader sharing policy.
*/
protected ClassLoader classLoader = null;
-
+
+ private ApplicationConfiguration applicationConfiguration;
+
/**
* The location of the <code>lib</code> directory in TAVERNA_HOME,
* where local JAR files the activity depends on should be located.
*/
// public static File libDir = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "lib");
- public static File libDir = null;
+ public File libDir;
/**
* Different ways to share a class loader among activities:
- *
+ *
* <dl>
* <dt>workflow</dt>
* <dd>Same classloader for all activities using the <code>workflow</code> classloader sharing policy</dd>
* <dt>system</dt>
* <dd>System classloader</dd>
* </dl>
- *
+ *
*/
public static enum ClassLoaderSharing {
workflow, system
}
-
+
+ public AbstractAsynchronousDependencyActivity(ApplicationConfiguration applicationConfiguration) {
+ if (applicationConfiguration != null) {
+ libDir = new File(applicationConfiguration.getApplicationHomeDir(), "lib");
+ }
+ }
+
/**
* Finds or constructs the classloader. The classloader depends on the
* current classloader sharing policy as defined by {@link #ClassLoaderSharing}.
* <p>
* If the classloader sharing is {@link ClassLoaderSharing#workflow}, a
* common classloader will be used for the whole workflow for all activities
- * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
- * The dependencies will be constructed as union of local and artifact dependencies
- * of all 'workflow' classloader sharing activities at the point of the first
+ * with the same (i.e. {@link ClassLoaderSharing#workflow}) policy.
+ * The dependencies will be constructed as union of local and artifact dependencies
+ * of all 'workflow' classloader sharing activities at the point of the first
* call to {@link #getClassLoader()}.
* <p>
* If the classloader sharing is {@link ClassLoaderSharing#system}, the
- * system classloader will be used. Note that both local and artifact dependencies
- * configured on the activity will be ignored. Local dependencies can be set by
+ * system classloader will be used. Note that both local and artifact dependencies
+ * configured on the activity will be ignored. Local dependencies can be set by
* using <code>-classpath</code> when starting the workbench.
* This is useful in combination with JNI based libraries, which would also
* require <code>-Djava.library.path</code> and possibly the operating
* system's PATH / LD_LIBRARY_PATH / DYLD_LIBRARY_PATH environment variable.
- * @param classLoaderSharing
- *
+ * @param classLoaderSharing
+ *
* @return A new or existing {@link ClassLoader} according to the
* classloader sharing policy
*/
protected ClassLoader findClassLoader(DependencyActivityConfigurationBean configurationBean, String workflowRunID) throws RuntimeException{
-
+
ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
-
+
if (classLoaderSharing == ClassLoaderSharing.workflow) {
synchronized (workflowClassLoaders) {
ClassLoader cl = workflowClassLoaders.get(workflowRunID);
@@ -138,7 +148,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
if (classLoaderSharing == ClassLoaderSharing.system) {
// if (systemClassLoader == null)
// systemClassLoader = PreLauncher.getInstance().getLaunchingClassLoader();
-
+
// if (systemClassLoader instanceof BootstrapClassLoader){
// // Add local and artifact dependencies to the classloader
// updateBootstrapClassLoader(
@@ -163,24 +173,24 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
/**
* Constructs a classloader capable of finding both local jar and artifact dependencies.
* Called when classloader sharing policy is set to 'workflow'.
- *
+ *
* @return A {@link ClassLoader} capable of accessing all the dependencies (both local jar and artifact)
*/
private ClassLoader makeClassLoader(
DependencyActivityConfigurationBean configurationBean,
String workflowID) {
-
+
// Find all artifact dependencies
// HashSet<URL> urls = findDependencies(ARTIFACTS, configurationBean, workflowID);
-
+
// Add all local jar dependencies
HashSet<URL> urls = findDependencies(LOCAL_JARS, configurationBean, workflowID);
-
+
// Create the classloader capable of loading both local jar and artifact dependencies
ClassLoader parent = this.getClass().getClassLoader(); // this will be a LocalArtifactClassLoader
-
+
return new URLClassLoader(urls.toArray(new URL[0]), parent) {
-
+
// For finding native libraries that have to be stored in TAVERNA_HOME/lib
@Override
protected String findLibrary(String libname) {
@@ -194,18 +204,18 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
}
};
}
-
+
/**
* Adds local or artifact dependencies identified by {@link #findDependencies()} to the
* {@link BootstrapClassLoader} system classloader.
* Called when classloader sharing policy is set to 'system'.
- *
+ *
* @param loader The augmented BootstrapClassLoader system classloader
*/
// private void updateBootstrapClassLoader(BootstrapClassLoader loader,
// DependencyActivityConfigurationBean configurationBean,
// String workflowRunID) {
-//
+//
// HashSet<URL> depsURLs = new HashSet<URL>();
// depsURLs.addAll(findDependencies(LOCAL_JARS, configurationBean, workflowRunID));
// depsURLs.addAll(findDependencies(ARTIFACTS, configurationBean, workflowRunID));
@@ -218,12 +228,12 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
// logger.info("Registering with system classloader: " + url);
// loader.addURL(url);
// exists.add(url);
-// }
+// }
// }
/**
- * Finds either local jar or artifact dependencies' URLs for the given classloader
- * sharing policy (passed inside configuration bean) and a workflowRunID (used to
+ * Finds either local jar or artifact dependencies' URLs for the given classloader
+ * sharing policy (passed inside configuration bean) and a workflowRunID (used to
* retrieve the workflow) that will be added to this activity classloader's list of URLs.
*/
private HashSet<URL> findDependencies(String dependencyType,
@@ -233,7 +243,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
// Get the WorkflowInstanceFacade which contains the current workflow
WeakReference<WorkflowInstanceFacade> wfFacadeRef = WorkflowInstanceFacade.workflowRunFacades.get(workflowRunID);
- WorkflowInstanceFacade wfFacade = null;
+ WorkflowInstanceFacade wfFacade = null;
if (wfFacadeRef != null) {
wfFacade = wfFacadeRef.get();
}
@@ -252,7 +262,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
// as this activity
for (Processor proc : wf.getProcessors()) {
// Nested workflow case
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedWorkflow));
@@ -271,8 +281,8 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
logger.warn("Invalid URL for " + jar, ex);
continue;
}
- }
-// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
+ }
+// } else if (dependencyType.equals(ARTIFACTS) && this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){
// LocalArtifactClassLoader cl = (LocalArtifactClassLoader) this.getClass().getClassLoader(); // this class is always loaded with LocalArtifactClassLoader
// // Get the LocalReposotpry capable of finding artifact jar files
// LocalRepository rep = (LocalRepository) cl.getRepository();
@@ -295,26 +305,26 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
logger.warn("Invalid URL for " + jar, ex);
continue;
}
- }
+ }
// }
// else if (dependencyType.equals(ARTIFACTS)){
// if (this.getClass().getClassLoader() instanceof LocalArtifactClassLoader){ // This should normally be the case
-// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
+// LocalArtifactClassLoader cl = (LocalArtifactClassLoader)this.getClass().getClassLoader();
// LocalRepository rep = (LocalRepository)cl.getRepository();
-// if (rep != null){
+// if (rep != null){
// for (BasicArtifact art : configurationBean.getArtifactDependencies()){
// dependencies.add(rep.jarFile(art));
// }
// }
// }
// else{
-// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
+// // Tests will not be loaded using the LocalArtifactClassLoader as athey are loaded
// // outside Raven so there is nothing we can do about this - some tests
// // with dependencies will probably fail
// }
// }
}
-
+
// Collect the URLs of all found dependencies
for (File file: dependencies){
try{
@@ -324,38 +334,38 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
continue;
}
- }
- return dependenciesURLs;
+ }
+ return dependenciesURLs;
}
/**
- * Finds dependencies for a nested workflow.
+ * Finds dependencies for a nested workflow.
*/
private HashSet<URL> findNestedDependencies(String dependencyType,
DependencyActivityConfigurationBean configurationBean,
Dataflow nestedWorkflow) {
-
+
ClassLoaderSharing classLoaderSharing = configurationBean.getClassLoaderSharing();
// Files of dependencies for all activities in the nested workflow that share the classloading policy
HashSet<File> dependencies = new HashSet<File>();
// Urls of all dependencies
HashSet<URL> dependenciesURLs = new HashSet<URL>();
-
+
for (Processor proc : nestedWorkflow.getProcessors()) {
// Another nested workflow
- if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
+ if (!proc.getActivityList().isEmpty() && proc.getActivityList().get(0) instanceof NestedDataflow){
// Get the nested workflow
Dataflow nestedNestedWorkflow = ((NestedDataflow) proc.getActivityList().get(0)).getNestedDataflow();
dependenciesURLs.addAll(findNestedDependencies(dependencyType, configurationBean, nestedNestedWorkflow));
}
else{ // Not nested - go through all of the processor's activities
Activity<?> activity = proc.getActivityList().get(0);
- if (activity instanceof AbstractAsynchronousDependencyActivity){
-
+ if (activity instanceof AbstractAsynchronousDependencyActivity){
+
if (((DependencyActivityConfigurationBean) activity
.getConfiguration()).getClassLoaderSharing() == classLoaderSharing) {
-
+
// if (dependencyType.equals(LOCAL_JARS)){
// Collect the files of all found local dependencies
for (String jar : ((DependencyActivityConfigurationBean)activity.getConfiguration()).getLocalDependencies()) {
@@ -374,12 +384,12 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
// .getArtifactDependencies()){
// dependencies.add(rep.jarFile(art));
// }
-// }
+// }
}
}
}
}
-
+
// Collect the URLs of all found dependencies
for (File file: dependencies){
try{
@@ -389,10 +399,10 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
logger.warn("Invalid URL for " + file.getAbsolutePath(), ex);
continue;
}
- }
+ }
return dependenciesURLs;
}
-
+
/**
* File filter.
*/
@@ -408,7 +418,7 @@ public abstract class AbstractAsynchronousDependencyActivity<ConfigType> extends
return name.endsWith(ext);
}
}
-
+
/**
* @param classLoader the classLoader to set
*/
[35/50] incubator-taverna-common-activities git commit: Added readme
Posted by st...@apache.org.
Added readme
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/536a7fcf
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/536a7fcf
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/536a7fcf
Branch: refs/heads/master
Commit: 536a7fcf18127ec11401df78ea47e3413ff9dbe8
Parents: 4ef07cf
Author: Christian-B <br...@cs.man.ac.uk>
Authored: Wed May 7 08:13:02 2014 +0100
Committer: Christian-B <br...@cs.man.ac.uk>
Committed: Wed May 7 08:13:02 2014 +0100
----------------------------------------------------------------------
README.md | 3 +++
1 file changed, 3 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/536a7fcf/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..abb8c19
--- /dev/null
+++ b/README.md
@@ -0,0 +1,3 @@
+Taverna Workflow system Dependency Activity: data model and execution implementation
+
+This code was previously hosted at http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/
[20/50] incubator-taverna-common-activities git commit: Support
subclassed configuration beans Bean URIs now resolved by URI of bean class
where the method is defined (not by activity URI) Updated URIs for
configuration beans to match t2flow parsing SVN
Posted by st...@apache.org.
Support subclassed configuration beans
Bean URIs now resolved by URI of bean class where the method is defined (not by activity URI)
Updated URIs for configuration beans to match t2flow parsing
SVN is stupid. No more 500 Server errors, please.
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@12625 bf327186-88b3-11dd-a302-d386e5130c1c
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/1a2abf03
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/1a2abf03
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/1a2abf03
Branch: refs/heads/master
Commit: 1a2abf03ee1373c8872eef88c5cb7d14efa43541
Parents: e999356
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Feb 17 17:14:30 2011 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Feb 17 17:14:30 2011 +0000
----------------------------------------------------------------------
.../dependencyactivity/DependencyActivityConfigurationBean.java | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1a2abf03/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
index c0c74eb..ad1fbf2 100644
--- a/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
+++ b/src/main/java/net/sf/taverna/t2/activities/dependencyactivity/DependencyActivityConfigurationBean.java
@@ -34,7 +34,7 @@ import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
* @author Alex Nenadic
* @author David Withers
*/
-@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency/Configuration")
+@ConfigurationBean(uri = "http://ns.taverna.org.uk/2010/activity/dependency#Configuration")
public class DependencyActivityConfigurationBean extends
ActivityPortsDefinitionBean {
[04/50] incubator-taverna-common-activities git commit:
[maven-release-plugin] prepare for next development iteration
Posted by st...@apache.org.
[maven-release-plugin] prepare for next development iteration
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@7984 bf327186-88b3-11dd-a302-d386e5130c1c
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/0b005575
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/0b005575
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/0b005575
Branch: refs/heads/master
Commit: 0b0055759b696d5bac027bf26c5264ec545a2d61
Parents: c3c0519
Author: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Thu Jun 25 10:14:57 2009 +0000
Committer: alan@mygrid.org.uk <al...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Thu Jun 25 10:14:57 2009 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/0b005575/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 8090a8a..7a732f9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>0.8</version>
+ <version>0.9-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>
[12/50] incubator-taverna-common-activities git commit: T2-1388
bumped trunk to 1.3-SNAPSHOT / 2.3-SNAPSHOT
Posted by st...@apache.org.
T2-1388 bumped trunk to 1.3-SNAPSHOT / 2.3-SNAPSHOT
git-svn-id: http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/trunk/dependency-activity@10906 bf327186-88b3-11dd-a302-d386e5130c1c
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/e3c74ab0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/e3c74ab0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/e3c74ab0
Branch: refs/heads/master
Commit: e3c74ab0ad7a749f8773fcdf0324544c86206c33
Parents: c77f697
Author: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Authored: Mon Jun 14 12:48:50 2010 +0000
Committer: stian@mygrid.org.uk <st...@bf327186-88b3-11dd-a302-d386e5130c1c>
Committed: Mon Jun 14 12:48:50 2010 +0000
----------------------------------------------------------------------
pom.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/e3c74ab0/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 5b8de22..a360771 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
<parent>
<groupId>net.sf.taverna.t2</groupId>
<artifactId>activities</artifactId>
- <version>1.1-SNAPSHOT</version>
+ <version>1.3-SNAPSHOT</version>
</parent>
<groupId>net.sf.taverna.t2.activities</groupId>
<artifactId>dependency-activity</artifactId>