http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java deleted file mode 100644 index 194d81e..0000000 --- a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeConfigureMenuAction.java +++ /dev/null @@ -1,77 +0,0 @@ -/********************************************************************** - * Copyright (C) 2007-2009 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.workbench.parallelize; - -import java.awt.event.ActionEvent; -import java.net.URI; - -import javax.swing.AbstractAction; -import javax.swing.Action; - -import net.sf.taverna.t2.ui.menu.AbstractContextualMenuAction; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.selection.SelectionManager; -import uk.org.taverna.scufl2.api.core.Processor; - -public class ParallelizeConfigureMenuAction extends AbstractContextualMenuAction { - - public static final URI configureRunningSection = URI - .create("http://taverna.sf.net/2009/contextMenu/configureRunning";); - - private static final URI PARALLELIZE_CONFIGURE_URI = URI - .create("http://taverna.sf.net/2008/t2workbench/parallelizeConfigure";); - - public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Parallelize";); - - private EditManager editManager; - - private SelectionManager selectionManager; - - public ParallelizeConfigureMenuAction() { - super(configureRunningSection, 10, PARALLELIZE_CONFIGURE_URI); - } - - @SuppressWarnings("serial") - @Override - protected Action createAction() { - return new AbstractAction("Parallel jobs...") { - public void actionPerformed(ActionEvent e) { - Processor processor = (Processor) getContextualSelection().getSelection(); - ParallelizeConfigureAction parallelizeConfigureAction = new ParallelizeConfigureAction( - null, null, processor, editManager, selectionManager); - parallelizeConfigureAction.actionPerformed(e); - } - }; - } - - public boolean isEnabled() { - return super.isEnabled() && (getContextualSelection().getSelection() instanceof Processor); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setSelectionManager(SelectionManager selectionManager) { - this.selectionManager = selectionManager; - } - -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java deleted file mode 100644 index 22d2da1..0000000 --- a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualView.java +++ /dev/null @@ -1,130 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2008 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.workbench.parallelize; - -import java.awt.BorderLayout; -import java.awt.Frame; -import java.util.List; - -import javax.swing.Action; -import javax.swing.JComponent; -import javax.swing.JPanel; -import javax.swing.JTextArea; - -import net.sf.taverna.t2.lang.ui.ReadOnlyTextArea; -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.selection.SelectionManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import uk.org.taverna.scufl2.api.common.Scufl2Tools; -import uk.org.taverna.scufl2.api.configurations.Configuration; -import uk.org.taverna.scufl2.api.core.Processor; - -import com.fasterxml.jackson.databind.JsonNode; - -/** - * View of a processor, including it's iteration stack, activities, etc. - * - * @author Alan R Williams - * - */ -@SuppressWarnings("serial") -public class ParallelizeContextualView extends ContextualView { - - private final Scufl2Tools scufl2Tools = new Scufl2Tools(); - - private Processor processor; - - private JPanel panel; - - private final EditManager editManager; - - private final SelectionManager selectionManager; - - public ParallelizeContextualView(Processor processor, EditManager editManager, SelectionManager selectionManager) { - super(); - this.processor = processor; - this.editManager = editManager; - this.selectionManager = selectionManager; - initialise(); - initView(); - } - - @Override - public void refreshView() { - initialise(); - } - - private void initialise() { - if (panel == null) { - panel = createPanel(); - } else { - panel.removeAll(); - } - - JTextArea textArea = new ReadOnlyTextArea(); - textArea.setEditable(false); - String maxJobs = "1"; - for (Configuration configuration : scufl2Tools.configurationsFor(processor, selectionManager.getSelectedProfile())) { - JsonNode processorConfig = configuration.getJson(); - if (processorConfig.has("parallelize")) { - JsonNode parallelizeConfig = processorConfig.get("parallelize"); - if (parallelizeConfig.has("maximumJobs")) { - maxJobs = parallelizeConfig.get("maximumJobs").asText(); - } - } - } - textArea.setText("The maximum number of jobs is " + maxJobs); - textArea.setBackground(panel.getBackground()); - panel.add(textArea, BorderLayout.CENTER); - revalidate(); - } - - - @Override - public JComponent getMainFrame() { - return panel; - } - - @Override - public String getViewTitle() { - return "Parallel jobs"; - } - - protected JPanel createPanel() { - JPanel result = new JPanel(); - result.setLayout(new BorderLayout()); - - - return result; - } - - @Override - public int getPreferredPosition() { - return 400; - } - - @Override - public Action getConfigureAction(Frame owner) { - return new ParallelizeConfigureAction(owner, this, processor, editManager, selectionManager); - } - - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java b/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java deleted file mode 100644 index f9ff7e7..0000000 --- a/taverna-workbench-parallelize-ui/src/main/java/net/sf/taverna/t2/workbench/parallelize/ParallelizeContextualViewFactory.java +++ /dev/null @@ -1,56 +0,0 @@ -/******************************************************************************* - * Copyright (C) 2008 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.workbench.parallelize; - -import java.net.URI; -import java.util.Arrays; -import java.util.List; - -import net.sf.taverna.t2.workbench.edits.EditManager; -import net.sf.taverna.t2.workbench.selection.SelectionManager; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView; -import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory; -import uk.org.taverna.scufl2.api.core.Processor; - -public class ParallelizeContextualViewFactory implements ContextualViewFactory<Processor> { - - public static URI TYPE = URI.create("http://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Parallelize";); - - private EditManager editManager; - private SelectionManager selectionManager; - - public boolean canHandle(Object selection) { - return selection instanceof Processor; - } - - public List<ContextualView> getViews(Processor selection) { - return Arrays.asList(new ContextualView[] {new ParallelizeContextualView(selection, editManager, selectionManager)}); - } - - public void setEditManager(EditManager editManager) { - this.editManager = editManager; - } - - public void setSelectionManager(SelectionManager selectionManager) { - this.selectionManager = selectionManager; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent deleted file mode 100644 index edd7b2d..0000000 --- a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent +++ /dev/null @@ -1 +0,0 @@ -net.sf.taverna.t2.workbench.parallelize.ParallelizeConfigureMenuAction http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory deleted file mode 100644 index 8b94f86..0000000 --- a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory +++ /dev/null @@ -1 +0,0 @@ -net.sf.taverna.t2.workbench.parallelize.ParallelizeContextualViewFactory http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml deleted file mode 100644 index 1859672..0000000 --- a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context-osgi.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans:beans xmlns="http://www.springframework.org/schema/osgi"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xmlns:beans="http://www.springframework.org/schema/beans"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd - http://www.springframework.org/schema/osgi - http://www.springframework.org/schema/osgi/spring-osgi.xsd";> - - <service ref="ParallelizeConfigureMenuAction" auto-export="interfaces" /> - - <service ref="ParallelizeContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" /> - - <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" /> - <reference id="selectionManager" interface="net.sf.taverna.t2.workbench.selection.SelectionManager" /> - -</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml ---------------------------------------------------------------------- diff --git a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml b/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml deleted file mode 100644 index 1d1fdd4..0000000 --- a/taverna-workbench-parallelize-ui/src/main/resources/META-INF/spring/parallelize-ui-context.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans xmlns="http://www.springframework.org/schema/beans"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd";> - - <bean id="ParallelizeConfigureMenuAction" class="net.sf.taverna.t2.workbench.parallelize.ParallelizeConfigureMenuAction"> - <property name="editManager" ref="editManager" /> - <property name="selectionManager" ref="selectionManager" /> - </bean> - - <bean id="ParallelizeContextualViewFactory" class="net.sf.taverna.t2.workbench.parallelize.ParallelizeContextualViewFactory"> - <property name="editManager" ref="editManager" /> - <property name="selectionManager" ref="selectionManager" /> - </bean> - -</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat b/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat deleted file mode 100644 index 1c7f299..0000000 --- a/taverna-workbench-perspective-biocatalogue/LocalTestLauncher.bat +++ /dev/null @@ -1,14 +0,0 @@ -@echo off -echo. -echo. -del biocatalogue-perspective-local-launch.jar -echo Deleted old JAR file if it was there. -cd target\classes -jar cfM ..\..\biocatalogue-perspective-local-launch.jar *.* -cd ..\.. -echo JAR assembly done, launching app... - -java -cp .;.\biocatalogue-perspective-local-launch.jar;c:/Users/Sergey/.m2/repository/net/sf/taverna/t2/workbench/ui-api/0.2/ui-api-0.2.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\lang\ui\1.0\ui-1.0.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\ui-components\workflow-view\1.0\workflow-view-1.0.jar;c:\Users\Sergey\.m2\repository\net\sf\taverna\t2\ui-activities\wsdl-activity-ui\0.7\wsdl-activity-ui-0.7.jar;C:\Users\Sergey\.m2\repository\log4j\log4j\1.2.13\log4j-1.2.13.jar;C:\Users\Sergey\.m2\repository\net\sf\taverna\t2\workbench\commons-icons\0.2\commons-icons-0.2.jar;c:\Users\Sergey\.m2\repository\BrowserLauncher2\BrowserLauncher2\1.3\BrowserLauncher2-1.3.jar;C:\Users\Sergey\.m2\repository\jdom\jdom\1.0\jdom-1.0.jar;"c:\Program Files\Java\xmlbeans-2.4.0\lib\xbean.jar";"c:\Program Files\Java\xmlbeans-2.4.0\lib\jsr173_1.0_api.jar";.\lib\lablib-checkboxtree-3.1.jar;.\lib\core-renderer.jar;.\lib\commons-lang-2.4.jar net.sf.taverna.t2.ui.perspectives.biocatalogue.TestJFra meForLocalLaunch - -del biocatalogue-perspective-local-launch.jar -echo Cleanup done - deleted old the JAR file that was used for the current launch. \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar b/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar deleted file mode 100644 index 871fabf..0000000 Binary files a/taverna-workbench-perspective-biocatalogue/lib/core-renderer.jar and /dev/null differ http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/log4j.properties ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/log4j.properties b/taverna-workbench-perspective-biocatalogue/log4j.properties deleted file mode 100644 index fcd1d0c..0000000 --- a/taverna-workbench-perspective-biocatalogue/log4j.properties +++ /dev/null @@ -1,4 +0,0 @@ -log4j.rootLogger=DEBUG, A1 -log4j.appender.A1=org.apache.log4j.ConsoleAppender -log4j.appender.A1.layout=org.apache.log4j.PatternLayout -log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/pom.xml b/taverna-workbench-perspective-biocatalogue/pom.xml deleted file mode 100644 index 3f5457a..0000000 --- a/taverna-workbench-perspective-biocatalogue/pom.xml +++ /dev/null @@ -1,183 +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.t2</groupId> - <artifactId>ui-exts</artifactId> - <version>2.0-SNAPSHOT</version> - </parent> - <groupId>net.sf.taverna.t2.ui-exts</groupId> - <artifactId>perspective-biocatalogue</artifactId> - <name>BioCatalogue Perspective</name> - <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 /> - <snapshots> - <enabled>false</enabled> - </snapshots> - <id>fuse</id> - <name>fuseRepository</name> - <url>http://repo.fusesource.com/maven2-all/</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> - - <dependencies> - <!-- <dependency> <groupId>net.sf.taverna.t2.ui-api</groupId> <artifactId>perspective-core</artifactId> - <version>${t2.ui.api.version}</version> </dependency> --> - <dependency> - <groupId>net.sf.taverna.t2.core</groupId> - <artifactId>workflowmodel-impl</artifactId> - <version>${t2.core.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>menu-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>file-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.lang</groupId> - <artifactId>ui</artifactId> - <version>${t2.lang.version}</version> - </dependency> - <!-- required for providing contextual views in the bottom-left area of - Design perspective --> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>contextual-views-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <!-- required for inserting a SOAP processor into the current workflow --> - <dependency> - <groupId>net.sf.taverna.t2.ui-activities</groupId> - <artifactId>wsdl-activity-ui</artifactId> - <version>${t2.ui.activities.version}</version> - </dependency> - <!-- required for importing REST processors into the current workflow --> - <dependency> - <groupId>net.sf.taverna.t2.ui-activities</groupId> - <artifactId>rest-activity-ui</artifactId> - <version>${t2.ui.activities.version}</version> - </dependency> - <!-- required for inserting a processor into the current workflow --> - <dependency> - <groupId>net.sf.taverna.t2.ui-components</groupId> - <artifactId>workflow-view</artifactId> - <version>${t2.ui.components.version}</version> - </dependency> - <!-- required registering with and opening help window --> - <dependency> - <groupId>net.sf.taverna.t2.ui-impl</groupId> - <artifactId>helper</artifactId> - <version>${t2.ui.impl.version}</version> - </dependency> - <dependency> - <groupId>uk.org.taverna.configuration</groupId> - <artifactId>taverna-app-configuration-api</artifactId> - <version>${taverna.configuration.version}</version> - </dependency> - - <dependency> - <groupId>org.jdom</groupId> - <artifactId>com.springsource.org.jdom</artifactId> - <version>${jdom.version}</version> - </dependency> - <dependency> - <groupId>org.apache.log4j</groupId> - <artifactId>com.springsource.org.apache.log4j</artifactId> - </dependency> - <dependency> - <groupId>org.apache.xmlbeans</groupId> - <artifactId>xmlbeans</artifactId> - <version>2.5.0</version> - </dependency> - - <!-- FlyingSaucer XHTML Renderer --> - <!-- (it is critical to use version R8, not any earlier ones - e.g. R8pre2, - etc.) --> - <dependency> - <groupId>org.xhtmlrenderer</groupId> - <artifactId>core-renderer</artifactId> - <version>${org.xhtmlrenderer.core-renderer.version}</version> - <exclusions> - <exclusion> - <groupId>bouncycastle</groupId> - <artifactId>bcprov-jdk14</artifactId> - </exclusion> - <exclusion> - <groupId>bouncycastle</groupId> - <artifactId>bcmail-jdk14</artifactId> - </exclusion> - </exclusions> - </dependency> - - <!-- At least StringEscapeUtils class is used from this library --> - <dependency> - <groupId>org.apache.commons</groupId> - <artifactId>com.springsource.org.apache.commons.lang</artifactId> - <version>${commons.lang.version}</version> - </dependency> - - <!-- Gson: Java to Json conversion --> - <dependency> - <groupId>com.google.code.gson</groupId> - <artifactId>gson</artifactId> - <version>${gson.version}</version> - </dependency> - </dependencies> - - <build> - <!-- Adds "xmlbeans:xmlbeans" Maven2 goal to compile the API binding classes - from XSD schema. --> - <plugins> - <plugin> - <groupId>org.codehaus.mojo</groupId> - <artifactId>xmlbeans-maven-plugin</artifactId> - <version>2.3.3</version> - <executions> - <execution> - <goals> - <goal>xmlbeans</goal> - </goals> - </execution> - </executions> - <inherited>true</inherited> - <configuration> - <!-- "javaSource=1.5" is required to make use of generics and have getXXXList() - methods available, not just getXXXArrray() --> - <javaSource>1.5</javaSource> - <download>true</download> - <schemaDirectory>src/main/xsd</schemaDirectory> - <!-- Default is target/generated-sources/xmlbeans - which the Maven - plugin should be able to add to the Project classpath --> - <!-- <sourceGenerationDirectory>src/main/java</sourceGenerationDirectory> --> - </configuration> - </plugin> - </plugins> - </build> -</project> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat deleted file mode 100644 index 3786d7c..0000000 --- a/taverna-workbench-perspective-biocatalogue/schema_compilation/move_scomp_results_into_project.bat +++ /dev/null @@ -1,29 +0,0 @@ -@echo off - -echo This will replace the JAR file with compiled API classes -pause -del ..\lib\biocatalogue_api_classes.jar -move biocatalogue_api_classes.jar ..\lib\ -echo JAR file replaced -echo. - -REM replace the sources of API classes -echo This will delete *ALL* files in \src\main\java\org\biocatalogue -echo \src\main\java\org\purl -echo \src\main\java\org\w3 -pause - -rd /S /Q ..\src\main\java\org\biocatalogue -rd /S /Q ..\src\main\java\org\purl -rd /S /Q ..\src\main\java\org\w3 - -move /Y org\biocatalogue ..\src\main\java\org -move /Y org\purl ..\src\main\java\org -move /Y org\w3 ..\src\main\java\org -rd org - -echo Sources of API classes replaced -echo. - -echo Done! -pause \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat deleted file mode 100644 index ee10a50..0000000 --- a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web.bat +++ /dev/null @@ -1,9 +0,0 @@ -@echo off - -REM -src . -- put source files here -REM -srconly -- only sources, no compiling of java classes, no jar bundling -REM -compiler -- where to find javac -REM -javasource -- which JAVA version to aim for (1.5 uses generics) -REM -dl -- allows download of referenced schemas - -scomp -src . -srconly -compiler "%JAVA_HOME%\bin\javac.exe" -javasource 1.5 -dl http://www.biocatalogue.org/2009/xml/rest/schema-v1.xsd \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat b/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat deleted file mode 100644 index dd66206..0000000 --- a/taverna-workbench-perspective-biocatalogue/schema_compilation/scomp_compile_from_web_to_jar.bat +++ /dev/null @@ -1,9 +0,0 @@ -@echo off - -REM -src . -- put source files here -REM -compiler -- where to find javac -REM -javasource -- which JAVA version to aim for (1.5 uses generics) -REM -out -- specifies the name of the target JAR file -REM -dl -- allows download of referenced schemas - -scomp -src . -compiler "%JAVA_HOME%\bin\javac.exe" -javasource 1.5 -out biocatalogue_api_classes.jar -dl http://www.biocatalogue.org/2009/xml/rest/schema-v1.xsd \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt b/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt deleted file mode 100644 index 85056d7..0000000 Binary files a/taverna-workbench-perspective-biocatalogue/src/main/doc/BioCatalogue Plugin Documentation.odt and /dev/null differ http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt b/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt deleted file mode 100644 index 8d6c953..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/help/Index-TOC-Map-Additions.txt +++ /dev/null @@ -1,20 +0,0 @@ -/* http://www.mygrid.org.uk/taverna2_1/helpset/toc.xml */ - -<tocitem text="BioCatalogue Plugin" target="biocatalogue-plugin" expand="false"> - <tocitem text="Feature Overview" target="biocatalogue-plugin-features"/> - <tocitem text="Feedback" target="biocatalogue-plugin-feedback"/> -</tocitem> - - - -/* http://www.mygrid.org.uk/taverna2_1/helpset/index.xml */ - -<indexitem text="BioCatalogue Plugin" target="biocatalogue-plugin"/> - - - -/* http://www.mygrid.org.uk/taverna2_1/helpset/map.xml */ - -<mapID target="biocatalogue-plugin" url="html/biocatalogue-plugin.html"/> -<mapID target="biocatalogue-plugin-features" url="html/biocatalogue-plugin-features.html"/> -<mapID target="biocatalogue-plugin-feedback" url="html/biocatalogue-plugin-feedback.html"/> \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html deleted file mode 100644 index ece2949..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-features.html +++ /dev/null @@ -1,113 +0,0 @@ -<html> - <head> - <meta content="text/html; charset=MacRoman" http-equiv="Content-Type"> - <link rel="stylesheet" href="./basic.css" type="text/css"> - <meta name="generator" content="Helen"> - <title>BioCatalogue Plugin - Features</title> - </head> - <body> - <h2> - BioCatalogue Plugin - Features - </h2> - - <h3> - BioCatalogue Perspective - </h3> - <p> - This perspective is designed for searching and browsing the BioCatalogue - data. It aids with discovery of Processors that may be used in a workflow. - </p> - - <p> - In the BioCatalogue perspective you may: - <ul> - <li>Search for Web Services by free text queries of by tags;</li> - <li>Filter search results by the same set of criteria as available on the BioCatalogue website;</li> - <li>Save favourite filters and search queries for re-use at a later point;</li> - <li>View search history;</li> - <li>Immediately see the types and monitoring statuses of all found Web - Services directly in the results listings;</li> - <li>Preview Web Services.</li> - </ul> - </p> - - <p> - Web Service previews display a similar set of information to - that shown on the BioCatalogue website: service description, - type, location, provider and other details are shown. Listing - of all operations and their descriptions within that Web Service - is shown. Any operation may be added directly into the current - workflow or into the Service Panel in the Design Perspective - for later use. - </p> - - <h3> - Integration into Design Perspective - </h3> - - <p> - <ul> - <li>Any Web Service operations added to the Service Panel from the BioCatalogue - perspective can be dragged into the Workflow Diagram like any other Processors. - They are saved by the plugin, so that when Taverna is restarted, those services - can still be found in the Service Panel. - </li> - <li>Right mouse click on a Processor in the Workflow Explorer or Workflow Diagram - will display options provided by the plugin - for all WSDL Processors it is - possible to check their monitoring status or launch the Processor Preview. - </li> - <li>Right mouse click on an empty space in the Workflow Diagram will let to launch - the workflow "health check" - currently this feature will identify a list of all - WSDL activities in a workflow and will fetch the latest monitoring data about - each of the from BioCatalogue. - </li> - <li>"Details" tab in the contextual view area (bottom-left corner of the Design - Perspective) will display information about the WSDL Processors and their - input or output ports (if they are registered in BioCatalogue). These contextual - views are only shown if BioCatalogue knows how to handle the selected type of - workflow element. - </li> - </ul> - </p> - - - <h3> - Choosing the BioCatalogue Instance to Work With - </h3> - - <p> - The BioCatalogue is an open-source project and anyone can setup their - own instance of the BioCatalogue software. By default, the plugin is - configured to use the main BioCatalogue website - (at <font color="blue">http://www.biocatalogue.org</font>) as a source - of data. - </p> - <p> - Should this be necessary, the plugin can be configured to use another - instance of BioCatalogue. This can be done through the Preferences dialog - of Taverna by going to: <pre>File -> Preferences -> BioCatalogue</pre> - </p> - - - <h3> - Known Issues and Missing Functionality - </h3> - - <p> - Below are the most important known issues. These will be fixed in the later releases. - </p> - - <p> - <ul> - <li>Previews are only available for SOAP services, but not REST services - or users, registries, service providers. - </li> - <li>Search history, favourite search queries and filters are not persisted. - This means that this data will only be available for the current working - session and will be lost after Taverna is switched off. - </li> - <li>Only read access to the BioCatalogue data is currently provided.</li> - </ul> - </p> - </body> -</html> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html deleted file mode 100644 index b2c48b4..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin-feedback.html +++ /dev/null @@ -1,28 +0,0 @@ -<html> - <head> - <meta content="text/html; charset=MacRoman" http-equiv="Content-Type"> - <link rel="stylesheet" href="./basic.css" type="text/css"> - <meta name="generator" content="Helen"> - <title>BioCatalogue Plugin - Feedback</title> - </head> - <body> - <h2> - BioCatalogue Plugin - Feedback - </h2> - <p> - Please provide us with your feedback to help improve the BioCatalogue plugin. - In order to do so, please go to <em>About</em> tab in the <em>BioCatalogue perspective</em> - and click the "Leave feedback" button - you will be taken to a web page with a form - to fill in and submit your comments. - </p> - <p> - Developers are very interested to hear: - <ul> - <li>suggestions regarding the existing functionality;</li> - <li>new feature requests;</li> - <li>ideas for improving the user interfaces;</li> - <li>any other feedback you may have.</li> - </ul> - </p> - </body> -</html> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html b/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html deleted file mode 100644 index 152b935..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/help/biocatalogue-plugin.html +++ /dev/null @@ -1,54 +0,0 @@ -<html> - <head> - <meta content="text/html; charset=MacRoman" http-equiv="Content-Type"> - <link rel="stylesheet" href="./basic.css" type="text/css"> - <meta name="generator" content="Helen"> - <title>BioCatalogue Plugin</title> - </head> - <body> - <h2> - BioCatalogue Plugin - </h2> - <h3><small>Version: 0.1.1 (alpha)</small></h3> - <p> - The <em>BioCatalogue plugin</em> is intended to provide access to the data held - in the <em>BioCatalogue Web Services Registry</em> directly from <em>Taverna Workbench</em>. - </p> - <p> - In its current state the plugin is designed to: - <ul> - <li>display the integration capabilities with both BioCatalogue and Taverna;</li> - <li>provide a general idea of the kinds of data that can be fetched - from the Biocatalogue through its REST API; - </li> - <li>attempt to make the workflow composition process easier and provide useful - contextual data to help with understanding of existing workflows. - </li> - </ul> - </p> - <p> - This release has made the plugin compatible with the latest version of - Taverna - 2.2. Several important bugs were also fixed, however more new - functionality will be added soon. - </p> - <p> - To learn more about the available functionality, please see the <a href= - "./biocatalogue-plugin-features.html">feature list</a>. - </p> - <p><b> - Please note that this is an incomplete version of the BioCatalogue plugin. - You may see notifications that certain pieces of functionality have not been - implemented yet; some features are not yet fully stable, which means that - occasionally you may see unexpected error messages. - </b></p> - <p> - Any <a href="./biocatalogue-plugin-feedback.html">feedback</a> will be greatly apppreciated - it - will help to understand the true needs of the user community and develop - a complete version of this plugin later in the year. - </p> - <p> - This version of the plugin was developed by Sergejs Aleksejevs as part of his - final year project on the undergraduate Computer Science course at the University of Manchester. - </p> - </body> -</html> http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java deleted file mode 100644 index 791b544..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/BioCataloguePluginConstants.java +++ /dev/null @@ -1,77 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -import java.io.File; - - -/** - * This class contains the collection of important constants, - * which are used throughout the BioCatalogue plugin. - * - * @author Sergejs Aleksejevs - */ -public class BioCataloguePluginConstants -{ - public static final String APP_VISIBLE_NAME = "Service Catalogue Plugin"; - public static final String APP_PREFIX = "T2ServiceCataloguePlugin:"; - - - public static final boolean PERFORM_API_RESPONSE_TIME_LOGGING = true; - public static final boolean PERFORM_API_XML_DATA_BINDING_TIME_LOGGING = true; - public static final String API_OPERATION_LOG_FILENAME = "service_catalogue_api.log"; - - - public static final int DEFAULT_SCROLL = 15; // default vertical scroll increment to be used in all JScrollPane instances within the plugin - public static final int DEFAULT_TOOLTIP_DURATION = 10000; // default duration of visibility of tooltips (in "ms") - public static final int DEFAULT_THREAD_STARTUP_TIME = 10; // this is the time (in "ms") that we think the system takes at most to start a new thread - - public static final int API_DEFAULT_REQUESTED_TAG_COUNT_PER_PAGE = 50; - public static final int API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE = 20; - public static final int API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE = 20; - public static final int API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE = 20; - public static final int API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE = 20; - public static final int API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE = 20; - - - public static final int SEARCH_HISTORY_LENGTH = 50; // maximum number of search history items to store (if exceeded, oldest will be removed) - public static final int FAVOURITE_SEARCHES_LENGTH = 30; // maximum number of favourite search settings to store (if exceeded, oldest will be removed) - public static final int FAVOURITE_FILTERS_LENGTH = 30; // maximum number of favourite service filters to store (if exceeded, oldest will be removed) - public static final int RESOURCE_PREVIEW_HISTORY_LENGTH = 50; - - public static final int RESOURCE_PREVIEW_BROWSER_PREFERRED_WIDTH = 750; - public static final int RESOURCE_PREVIEW_BROWSER_PREFERRED_HEIGHT = 600; - - public static final String ACTION_FILTER_FOUND_SERVICES = APP_PREFIX + "filterFoundServices:"; - public static final String ACTION_FILTER_BY_CATEGORY = APP_PREFIX + "filterByCategory:"; - public static final String ACTION_SHOW_IN_WEB_BROWSER = APP_PREFIX + "showInWebBrowser:"; - public static final String ACTION_SHOW_TAG_SELECTION_DIALOG = APP_PREFIX + "showTagSelectionDialgog"; - public static final String ACTION_PREVIEW_CURRENT_FILTER = APP_PREFIX + "previewCurrentFilter"; - public static final String ACTION_PREVIEW_RESOURCE = APP_PREFIX + "preview:"; - public static final String ACTION_PREVIEW_SOAP_OPERATION_AFTER_LOOKUP = APP_PREFIX + "previewSoapOperationAfterLookup:"; - public static final String ACTION_PREVIEWED_SERVICE_HEALTH_CHECK = APP_PREFIX + "previewedServiceHealthCheck"; - public static final String ACTION_TAG_SEARCH_PREFIX = APP_PREFIX + "tag:"; - - - - public static final String CONFIG_FILE_FOLDER_WHEN_RUNNING_STANDALONE = ".Taverna2-ServiceCatalogue Plugin"; - - - - // ---------------------------- CONTEXTUAL VIEWS -------------------------------- - - // this value currently makes contextual views generated by this - // plugin the to be the last in the list - public static final int CONTEXTUAL_VIEW_PREFERRED_POSITION = 600; - - - - // ------------------------------------------------------------------------------ - - /* - * Some of the settings are determined during the runtime - hence are non-final. - * - * These are set in MainComponent.initialiseEnvironment() - */ - - public static File CONFIG_FILE_FOLDER = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "conf"); - public static File LOG_FILE_FOLDER = new File(ApplicationRuntime.getInstance().getApplicationHomeDir(), "logs"); -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java deleted file mode 100644 index ecd4cf1..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/HTTPMethodInterpreter.java +++ /dev/null @@ -1,46 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -import org.apache.log4j.Logger; -import org.biocatalogue.x2009.xml.rest.HttpVerb; - -import net.sf.taverna.t2.activities.rest.RESTActivity.HTTP_METHOD; - -/** - * Very simple class for translating HTTP method values returned - * by the BioCatalogue API into the set of values that are used - * by the REST activity. - * - * @author Sergejs Aleksejevs - */ -public class HTTPMethodInterpreter -{ - // deny instantiation of this class - private HTTPMethodInterpreter() { } - - public static HTTP_METHOD getHTTPMethodForRESTActivity(HttpVerb.Enum httpVerb) - { - switch (httpVerb.intValue()) { - case HttpVerb.INT_GET: return HTTP_METHOD.GET; - case HttpVerb.INT_POST: return HTTP_METHOD.POST; - case HttpVerb.INT_PUT: return HTTP_METHOD.PUT; - case HttpVerb.INT_DELETE: return HTTP_METHOD.DELETE; - default: - String errorMsg = "Unable to translate " + httpVerb.toString() + " to correct representation for REST activity;\n" + - "this HTTP method wasn't supported at the time of implementation."; - Logger.getLogger(HTTPMethodInterpreter.class).error(errorMsg); - throw new UnsupportedHTTPMethodException(errorMsg); - } - } - - - public static class UnsupportedHTTPMethodException extends IllegalArgumentException - { - public UnsupportedHTTPMethodException() { - /* empty constructor */ - } - - public UnsupportedHTTPMethodException(String message) { - super(message); - } - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java deleted file mode 100644 index cbd3f2e..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingExpandedResource.java +++ /dev/null @@ -1,41 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -import org.biocatalogue.x2009.xml.rest.ResourceLink; -import org.biocatalogue.x2009.xml.rest.impl.ResourceLinkImpl; - -/** - * @author Sergejs Aleksejevs - */ -public class LoadingExpandedResource extends ResourceLinkImpl -{ - private boolean nowLoading; - private ResourceLink associatedObj; - - public LoadingExpandedResource(ResourceLink associatedObj) - { - super(ResourceLink.type); - - this.associatedObj = associatedObj; - this.nowLoading = true; - } - - public ResourceLink getAssociatedObj() { - return associatedObj; - } - - public boolean isLoading() { - return (nowLoading); - } - public void setLoading(boolean isLoading) { - this.nowLoading = isLoading; - } - - public String getHref() { - return (associatedObj.getHref()); - } - - public String getResourceName() { - return (associatedObj.getResourceName()); - } -} - http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java deleted file mode 100644 index a003075..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/LoadingResource.java +++ /dev/null @@ -1,39 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -import org.biocatalogue.x2009.xml.rest.ResourceLink; -import org.biocatalogue.x2009.xml.rest.impl.ResourceLinkImpl; - -/** - * @author Sergejs Aleksejevs - */ -public class LoadingResource extends ResourceLinkImpl -{ - private boolean nowLoading; - private ResourceLink associatedObj; - - public LoadingResource(String resourceURL, String resourceName) { - super(ResourceLink.type); - - associatedObj = ResourceLink.Factory.newInstance(); - associatedObj.setHref(resourceURL); - associatedObj.setResourceName(resourceName); - - this.nowLoading = false; - } - - public String getHref() { - return (associatedObj.getHref()); - } - - public String getResourceName() { - return (associatedObj.getResourceName()); - } - - public boolean isLoading() { - return (nowLoading); - } - public void setLoading(boolean isLoading) { - this.nowLoading = isLoading; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java deleted file mode 100644 index b694db8..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Pair.java +++ /dev/null @@ -1,30 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -/** - * Trivial class to represent a generic pair of objects. - * Any types of objects can be used. - * - * @author Sergejs Aleksejevs - * - * @param <T1> Type of the first object. - * @param <T2> Type of the second object. - */ -public class Pair<T1,T2> -{ - private final T1 firstObject; - private final T2 secondObject; - - public Pair(T1 firstObject, T2 secondObject) { - this.firstObject = firstObject; - this.secondObject = secondObject; - } - - public T1 getFirstObject() { - return firstObject; - } - - public T2 getSecondObject() { - return secondObject; - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench/blob/dc466d6d/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java ---------------------------------------------------------------------- diff --git a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java b/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java deleted file mode 100644 index 3095863..0000000 --- a/taverna-workbench-perspective-biocatalogue/src/main/java/net/sf/taverna/biocatalogue/model/Resource.java +++ /dev/null @@ -1,506 +0,0 @@ -package net.sf.taverna.biocatalogue.model; - -import java.util.HashMap; -import java.util.Map; - -import javax.swing.Icon; -import javax.swing.JOptionPane; -import javax.swing.ListCellRenderer; - -import net.sf.taverna.biocatalogue.model.connectivity.BeansForJSONLiteAPI; -import net.sf.taverna.biocatalogue.model.connectivity.BioCatalogueClient; -import net.sf.taverna.biocatalogue.ui.search_results.RESTMethodListCellRenderer; -import net.sf.taverna.biocatalogue.ui.search_results.SOAPOperationListCellRenderer; -import net.sf.taverna.biocatalogue.ui.search_results.ServiceListCellRenderer; -import net.sf.taverna.t2.workbench.MainWindow; - -import org.apache.log4j.Logger; -import org.biocatalogue.x2009.xml.rest.Registry; -import org.biocatalogue.x2009.xml.rest.ResourceLink; -import org.biocatalogue.x2009.xml.rest.RestMethod; -import org.biocatalogue.x2009.xml.rest.RestMethods; -import org.biocatalogue.x2009.xml.rest.Service; -import org.biocatalogue.x2009.xml.rest.ServiceProvider; -import org.biocatalogue.x2009.xml.rest.Services; -import org.biocatalogue.x2009.xml.rest.SoapOperation; -import org.biocatalogue.x2009.xml.rest.SoapOperations; -import org.biocatalogue.x2009.xml.rest.User; - -/** - * @author Sergejs Aleksejevs - */ -public class Resource -{ - /** - * A single point of definition of the types of resources that the BioCatalogue plugin - * "knows" about. This enum provides various details about resource types - - * display names for single items of that type, names of collections of items of that - * type, icons to represent the items of a particular type, etc. - * - * @author Sergejs Aleksejevs - */ - public static enum TYPE - { - // the order is important - all these types will appear in the user interface - // in the same order as listed here - @SuppressWarnings("serial") - SOAPOperation (SoapOperation.class, SoapOperations.class, BeansForJSONLiteAPI.SOAPOperationsIndex.class, "WSDL service", "WSDL services", - "WSDL services can be directly imported into the current workflow or Service Panel", - ResourceManager.getIconFromTaverna(ResourceManager.SOAP_OPERATION_ICON), true, true, true, false, true, true, true, true, - SOAPOperationListCellRenderer.class, BioCatalogueClient.API_SOAP_OPERATIONS_URL, - new HashMap<String,String>() {{ - }}, - new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_ANCESTORS) {{ - put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE); - }}, - BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SOAP_OPERATION_COUNT_PER_PAGE, - BioCatalogueClient.API_SOAP_OPERATION_FILTERS_URL), - - @SuppressWarnings("serial") - RESTMethod (RestMethod.class, RestMethods.class, BeansForJSONLiteAPI.RESTMethodsIndex.class, "REST service", "REST services", - "REST services can be directly imported into the current workflow or Service Panel", - ResourceManager.getIconFromTaverna(ResourceManager.REST_METHOD_ICON), true, true, true, false, true, false, true, true, - RESTMethodListCellRenderer.class, BioCatalogueClient.API_REST_METHODS_URL, - new HashMap<String,String>() {{ - }}, - new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_ANCESTORS) {{ - put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE); - }}, - BioCataloguePluginConstants.API_DEFAULT_REQUESTED_REST_METHOD_COUNT_PER_PAGE, - BioCatalogueClient.API_REST_METHOD_FILTERS_URL); //, - - // TODO - the following resource types have been disabled, as no actions for them can be done yet - // -- they are still to be implemented; if the following types are uncommented, they will be - // automatically searchable and visible in BioCatalogue Exploration tab; ListCellRenderers, however, - // would need to be added first. -// @SuppressWarnings("serial") -// Service (Service.class, Services.class, BeansForJSONLiteAPI.ServicesIndex.class, "Web service", "Web services", -// "<html>Web services represent collections of WSDL services or REST services.<br>" + -// "They cannot be directly imported into the current workflow or Service Panel,<br>" + -// "but they may contain much more information about individual WSDL or REST<br>" + -// "services and also provide some context for their usage.</html>", -// ResourceManager.getImageIcon(ResourceManager.SERVICE_ICON), true, true, true, false, false, false, true, -// ServiceListCellRenderer.class, BioCatalogueClient.API_SERVICES_URL, -// new HashMap<String,String>(BioCatalogueClient.API_INCLUDE_SUMMARY) {{ -// }}, -// new HashMap<String,String>() {{ -// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE); -// }}, -// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_WEB_SERVICE_COUNT_PER_PAGE, -// BioCatalogueClient.API_SERVICE_FILTERS_URL), -// -// ServiceProvider (ServiceProvider.class, ServiceProviders.class, BeansForJSONLiteAPI.ServiceProvidersIndex.class, "Service Provider", "Service Providers", "", -// ResourceManager.getImageIcon(ResourceManager.SERVICE_PROVIDER_ICON), false, false, false, false, false, false, false, -// ServiceProviderListCellRenderer.class, BioCatalogueClient.API_SERVICE_PROVIDERS_URL, -// new HashMap<String,String>() {{ -// }}, -// new HashMap<String,String>() {{ -// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE); -// }}, -// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_SERVICE_PROVIDER_COUNT_PER_PAGE, -// null), -// -// User (User.class, Users.class, BeansForJSONLiteAPI.UsersIndex.class, "User", "Users", "", -// ResourceManager.getImageIcon(ResourceManager.USER_ICON), false, false, true, false, false, false, false, -// UserListCellRenderer.class, BioCatalogueClient.API_USERS_URL, -// new HashMap<String,String>() {{ -// }}, -// new HashMap<String,String>() {{ -// put(BioCatalogueClient.API_PER_PAGE_PARAMETER, ""+BioCataloguePluginConstants.API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE); -// }}, -// BioCataloguePluginConstants.API_DEFAULT_REQUESTED_USER_COUNT_PER_PAGE, -// BioCatalogueClient.API_USER_FILTERS_URL); - - - @SuppressWarnings("unchecked") - private Class xmlbeansGeneratedClass; - @SuppressWarnings("unchecked") - private Class xmlbeansGeneratedCollectionClass; - private Class<?> jsonLiteAPIBindingBeanClass; - private String resourceTypeName; - private String resourceCollectionName; - private String resourceTabTooltip; - private Icon icon; - private boolean defaultType; - private boolean suitableForTagSearch; - private boolean suitableForFiltering; - private boolean suitableForOpeningInPreviewBrowser; - private boolean suitableForAddingToServicePanel; - private boolean suitableForAddingToWorkflowDiagram; - private boolean suitableForHealthCheck; - private Class<? extends ListCellRenderer> resultListingCellRendererClass; - private String apiResourceCollectionIndex; - private Map<String,String> apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters; - private Map<String,String> apiResourceCollectionIndexAdditionalParameters; - private int apiResourceCountPerIndexPage; - private String apiResourceCollectionFilters; - private final boolean suitableForAddingAllToServicePanel; - - @SuppressWarnings("unchecked") - TYPE(Class xmlbeansGeneratedClass, Class xmlbeansGeneratedCollectionClass, Class<?> jsonLiteAPIBindingBeanClass, - String resourceTypeName, String resourceCollectionName, String resourceTabTooltip, Icon icon, - boolean defaultType, boolean suitableForTagSearch, boolean suitableForFiltering, boolean suitableForOpeningInPreviewBrowser, - boolean suitableForAddingToServicePanel, boolean suitableForAddingAllToServicePanel, boolean suitableForAddingToWorkflowDiagram, - boolean suitableForHealthCheck, Class<? extends ListCellRenderer> resultListingCellRendererClass, - String apiResourceCollectionIndex, Map<String,String> apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters, - Map<String,String> apiResourceCollectionIndexAdditionalParameters, int apiResourceCountPerIndexListingPage, - String apiResourceCollectionFilters) - { - this.xmlbeansGeneratedClass = xmlbeansGeneratedClass; - this.xmlbeansGeneratedCollectionClass = xmlbeansGeneratedCollectionClass; - this.jsonLiteAPIBindingBeanClass = jsonLiteAPIBindingBeanClass; - this.resourceTypeName = resourceTypeName; - this.resourceCollectionName = resourceCollectionName; - this.resourceTabTooltip = resourceTabTooltip; - this.icon = icon; - this.defaultType = defaultType; - this.suitableForTagSearch = suitableForTagSearch; - this.suitableForFiltering = suitableForFiltering; - this.suitableForOpeningInPreviewBrowser = suitableForOpeningInPreviewBrowser; - this.suitableForAddingToServicePanel = suitableForAddingToServicePanel; - this.suitableForAddingAllToServicePanel = suitableForAddingAllToServicePanel; - this.suitableForAddingToWorkflowDiagram = suitableForAddingToWorkflowDiagram; - this.suitableForHealthCheck = suitableForHealthCheck; - this.resultListingCellRendererClass = resultListingCellRendererClass; - this.apiResourceCollectionIndex = apiResourceCollectionIndex; - this.apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters = apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters; - this.apiResourceCollectionIndexAdditionalParameters = apiResourceCollectionIndexAdditionalParameters; - this.apiResourceCountPerIndexPage = apiResourceCountPerIndexListingPage; - this.apiResourceCollectionFilters = apiResourceCollectionFilters; - } - - - - @SuppressWarnings("unchecked") - public Class getXmlBeansGeneratedClass() { - return this.xmlbeansGeneratedClass; - } - - /** - * @return Class that represents collection of resources of this type, - * as represented by XmlBeans. - */ - @SuppressWarnings("unchecked") - public Class getXmlBeansGeneratedCollectionClass() { - return this.xmlbeansGeneratedCollectionClass; - } - - - /** - * @return Class of the bean to be used when de-serialising JSON - * data received from the 'Lite' BioCatalogue JSON API's index - * of resources of this type. - */ - public Class<?> getJsonLiteAPIBindingBeanClass() { - return this.jsonLiteAPIBindingBeanClass; - } - - - /** - * @return Display name of a type of a single item belonging to that type. - * (E.g. 'User' or 'Service') - */ - public String getTypeName() { - return this.resourceTypeName; - } - - /** - * @return Display name of a collection of items of this type. - * (E.g. 'Users' or 'Services'). - */ - public String getCollectionName() { - return this.resourceCollectionName; - } - - /** - * @return HTML-formatted string that can be used as a tooltip - * for tabs in BioCatalogue Exploration tab of BioCatalogue - * perspective. - */ - public String getCollectionTabTooltip() { - return this.resourceTabTooltip; - } - - /** - * @return Small icon that represents this resource type. - */ - public Icon getIcon() { - return this.icon; - } - - /** - * @return <code>true</code> - if used for search by default;<br/> - * <code>false</code> - otherwise. - */ - public boolean isDefaultSearchType() { - return this.defaultType; - } - - /** - * Resources not of all resource types can be searched for by tags (although every resource type - * can be searched for by a free-text query). - * - * @return <code>true</code> if resources of this type can be searched for by tags,<br/> - * <code>false</code> otherwise. - */ - public boolean isSuitableForTagSearch() { - return this.suitableForTagSearch; - } - - /** - * Not all resource types are suitable for filtering - for example, there are no - * filters available for service providers in BioCatalogue. - * - * @return <code>true</code> indicates that tab dedicated to displaying search - * results of this resource type can have a filter tree. - */ - public boolean isSuitableForFiltering() { - return this.suitableForFiltering; - } - - /** - * @return <code>true</code> indicates that "Preview" option can be made - * available for items of this type, as preview factory would be implemented - * for such resources. - */ - public boolean isSuitableForOpeningInPreviewBrowser() { - return this.suitableForOpeningInPreviewBrowser; - } - - public boolean isSuitableForAddingToServicePanel() { - return this.suitableForAddingToServicePanel; - } - - public boolean isSuitableForAddingToWorkflowDiagram() { - return this.suitableForAddingToWorkflowDiagram; - } - - /** - * @return <code>true</code> indicates that monitoring data can be obtained - * from BioCatalougue for this type of resource. - */ - public boolean isSuitableForHealthCheck() { - return this.suitableForHealthCheck; - } - - - /** - * This method helps to defer instantiation of ListCellRenderers - * until they are first accessed - it is because construction of - * the renderers requires knowledge of all available resource types, - * therefore they cannot be instantiated until after Resource class - * has been fully loaded. - * - * @return {@link ListCellRenderer} for this type of resources or - * <code>null</code> if an error has occurred during - * instantiation of required renderer. - */ - public ListCellRenderer getResultListingCellRenderer() { - try { - return this.resultListingCellRendererClass.newInstance(); - } - catch (Exception e) { - Logger.getLogger(Resource.class).error("Unable to instantiate search results ListCellRenderer for " + - this.getCollectionName(), e); - JOptionPane.showMessageDialog(MainWindow.getMainWindow(), - "Taverna was unable to instantiate ListCellRenderer for " + this.getCollectionName() + ".\n\n" + - "This may make Taverna unstable.", "Service Catalogue Plugin", JOptionPane.ERROR_MESSAGE); - return null; - } - } - - /** - * @return URL in the BioCatalogue API that provides an index of the collection of - * all resources of this type. - */ - public String getAPIResourceCollectionIndex() { - return apiResourceCollectionIndex; - } - - /** - * @return Keys and values for any additional URL parameters that need to be included into the - * BioCatalogue API requests that are made in order to fetch all necessary additional - * details for a *single* expanded entry in the search results listing. - */ - public Map<String,String> getResourceCollectionIndexSingleExpandedResourceAdditionalParameters() { - return apiResourceCollectionIndexSingleExpandedResourceAdditionalParameters; - } - - /** - * @return Keys and values for any additional URL parameters that need to be included into the - * requests sent to filtered indexes of collections of this type in the BioCatalogue API. - */ - public Map<String,String> getAPIResourceCollectionIndexAdditionalParameters() { - return apiResourceCollectionIndexAdditionalParameters; - } - - /** - * @return Number of resources of this type that one page of search results from - * the API will contain. - */ - public int getApiResourceCountPerIndexPage() { - return apiResourceCountPerIndexPage; - } - - /** - * @return BioCatalogue API URL that provides a collection of filters for the - * resource of this type. - */ - public String getAPIResourceCollectionFiltersURL() { - return apiResourceCollectionFilters; - } - - - /** - * This method is useful for adding / removing tabs into the results view - provides - * and index for the tabbed view to place a tab, relevant to a particular resource type. - * This helps to preserve the order of tabs after adding / removing them. - * - * @return Zero-based index of this resource type in the <code>RESOURCE_TYPE</code> enum or - * <code>-1</code> if not found (which is impossible under normal conditions). - */ - public int index() - { - TYPE[] values = TYPE.values(); - for (int i = 0; i < values.length; i++) { - if (this == values[i]) { - return (i); - } - } - return (-1); - } - - - - /** - * @return the suitableForAddingAllToServicePanel - */ - public boolean isSuitableForAddingAllToServicePanel() { - return suitableForAddingAllToServicePanel; - } - - }; - - - - // ----------------------------- RESOURCE CLASS ------------------------------- - - - // current resource data - private final TYPE resourceType; - private final String resourceURL; - private final String resourceTitle; - - - public Resource(String resourceURL, String resourceTitle) - { - this.resourceURL = extractPureResourceURLFromPreviewActionCommand(resourceURL); - this.resourceTitle = resourceTitle; - this.resourceType = getResourceTypeFromResourceURL(resourceURL); - } - - public TYPE getType() { - return resourceType; - } - - public String getURL() { - return resourceURL; - } - - public String getTitle() { - return resourceTitle; - } - - - - public boolean equals(Object other) - { - if (other instanceof Resource) - { - // compare by all components - Resource otherRes = (Resource)other; - return (this.resourceType == otherRes.resourceType && - this.resourceTitle.equals(otherRes.resourceTitle) && - this.resourceURL.equals(otherRes.resourceURL)); - } - else { - // other object is of different type - return (false); - } - } - - - /** - * @param url Either URL of the resource in BioCatalogue or preview action command - * ({@link BioCataloguePluginConstants#ACTION_PREVIEW_RESOURCE}). - * @return Type of this resource according to the BioCatalogue URL that points to this - * resource or <code>null</code> if the type of the resource couldn't be determined. - */ - public static TYPE getResourceTypeFromResourceURL(String url) - { - String pureURL = extractPureResourceURLFromPreviewActionCommand(url); - -// if (pureURL.startsWith(BioCatalogueClient.API_SERVICES_URL)) return(TYPE.Service); -// else - if (pureURL.startsWith(BioCatalogueClient.API_SOAP_OPERATIONS_URL)) { - return(TYPE.SOAPOperation); - } - if (pureURL.startsWith(BioCatalogueClient.API_REST_METHODS_URL)) { - return(TYPE.RESTMethod); - } -// else if (pureURL.startsWith(BioCatalogueClient.API_SERVICE_PROVIDERS_URL)) return(TYPE.ServiceProvider); // TODO - re-enable these lines as soon as ServiceProvider and User type are started to be used -// else if (pureURL.startsWith(BioCatalogueClient.API_USERS_URL)) return(TYPE.User); - return (null); - } - - - /** - * @param previewActionCommand Either resource preview action command or a 'pure' resource URL already. - * @return A "pure" resource URL in BioCatalogue with the action prefix - * ({@link BioCataloguePluginConstants#ACTION_PREVIEW_RESOURCE}) removed. - */ - public static String extractPureResourceURLFromPreviewActionCommand(String previewActionCommand) - { - return (previewActionCommand.startsWith(BioCataloguePluginConstants.ACTION_PREVIEW_RESOURCE) ? - previewActionCommand.substring(BioCataloguePluginConstants.ACTION_PREVIEW_RESOURCE.length()) : - previewActionCommand); - } - - - /** - * @param resource - * @return Display name for listings of items. - */ - public static String getDisplayNameForResource(ResourceLink resource) - { - if (resource instanceof SoapOperation) { - return ((SoapOperation)resource).getName(); - } - else if (resource instanceof RestMethod) - { - RestMethod restMethod = (RestMethod)resource; - return (restMethod.getName() == null || restMethod.getName().length() == 0 ? - restMethod.getEndpointLabel() : - restMethod.getName()); - } - else if (resource instanceof Service) { - return ((Service)resource).getName(); - } - else if (resource instanceof ServiceProvider) { - return ((ServiceProvider)resource).getName(); - } - else if (resource instanceof User) { - return ((User)resource).getName(); - } - else if (resource instanceof Registry) { - return ((Registry)resource).getName(); - } - else if (resource instanceof LoadingResource) { - return (resource.getResourceName()); - } - else { - return ("ERROR: ITEM NOT RECOGNISED - Item is of known generic type from the Service Catalogue Plugin, but not specifically recognised" + resource.toString()); - } - } - -}
