taverna 3 gis activity
authoredikaradumi <edikaradumi@gmail.com>
Mon, 11 Jul 2016 11:26:02 +0000 (12:26 +0100)
committerEdi Karadumi <edikaradumi@gmail.com>
Mon, 11 Jul 2016 11:36:06 +0000 (12:36 +0100)
27 files changed:
apache-taverna-activity-gis-activity-ui/pom.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png [new file with mode: 0644]
apache-taverna-activity-gis-activity/pom.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/resources/schema.json [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java [new file with mode: 0644]
apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java [new file with mode: 0644]
apache-taverna-activity-gis-plugin/pom.xml [new file with mode: 0644]
pom.xml
taverna-gis-client/pom.xml [new file with mode: 0644]

diff --git a/apache-taverna-activity-gis-activity-ui/pom.xml b/apache-taverna-activity-gis-activity-ui/pom.xml
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+<?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>org.apache.taverna.gis</groupId>
+               <artifactId>apache-taverna-activity-gis</artifactId>
+               <version>0.0.1-incubating.SNAPSHOT</version>
+       </parent>
+       <artifactId>apache-taverna-activity-gis-activity-ui</artifactId>
+       <packaging>bundle</packaging>
+       <name>Gis Taverna activity UI</name>
+
+       <dependencies>
+               <dependency>
+                       <groupId>${project.parent.groupId}</groupId>
+                       <artifactId>taverna-gis-client</artifactId>
+                       <version>${project.parent.version}</version>
+               </dependency>
+
+                                                               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-workflowmodel-api</artifactId>
+                       <version>${taverna.engine.version}</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-reference-api</artifactId>
+                       <version>${taverna.engine.version}</version>
+               </dependency>
+
+               <dependency>
+                       <groupId>com.fasterxml.jackson.core</groupId>
+                       <artifactId>jackson-databind</artifactId>
+                       <version>2.3.0</version>
+               </dependency>
+
+               <dependency>
+                       <groupId>junit</groupId>
+                       <artifactId>junit</artifactId>
+                       <version>4.4</version>
+                       <scope>test</scope>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-workflowmodel-impl</artifactId>
+                       <version>${taverna.engine.version}</version>
+                       <scope>test</scope>
+               </dependency>
+               
+
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-activity-palette-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-edits-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-selection-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-menu-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-activity-icons-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-helper-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>        
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-ui</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-configuration-ui-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-contextual-views-api</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.taverna.workbench</groupId>
+            <artifactId>taverna-activity-tools</artifactId>
+            <version>${taverna.workbench.version}</version>
+        </dependency>          
+
+       </dependencies>
+</project>
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigurationPanel.java
new file mode 100644 (file)
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+package org.apache.taverna.gis.ui.config;
+
+import java.awt.GridLayout;
+import java.net.URI;
+
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JTextField;
+
+import org.apache.taverna.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
+
+import org.apache.taverna.services.ServiceRegistry;
+import org.apache.taverna.scufl2.api.activity.Activity;
+
+@SuppressWarnings("serial")
+public class GisConfigurationPanel extends ActivityConfigurationPanel {
+
+       private final ServiceRegistry serviceRegistry;
+
+       private JTextField fieldString;
+       private JTextField fieldURI;
+
+       public GisConfigurationPanel(Activity activity, ServiceRegistry serviceRegistry) {
+               super(activity);
+               this.serviceRegistry = serviceRegistry;
+               initialise();
+       }
+
+       protected void initialise() {
+               // call super.initialise() to initialise the configuration
+               super.initialise();
+
+               removeAll();
+               setLayout(new GridLayout(0, 2));
+
+               // FIXME: Create GUI depending on activity configuration bean
+               JLabel labelString = new JLabel("Example string:");
+               add(labelString);
+               fieldString = new JTextField(20);
+               add(fieldString);
+               labelString.setLabelFor(fieldString);
+
+               JLabel labelURI = new JLabel("Example URI:");
+               add(labelURI);
+               fieldURI = new JTextField(25);
+               add(fieldURI);
+               labelURI.setLabelFor(fieldURI);
+
+               // Populate fields from activity configuration
+               fieldString.setText(getProperty("exampleString"));
+               fieldURI.setText(getProperty("exampleUri"));
+       }
+
+       /**
+        * Check that user values in UI are valid
+        */
+       @Override
+       public boolean checkValues() {
+               try {
+                       URI.create(fieldURI.getText());
+               } catch (IllegalArgumentException ex) {
+                       JOptionPane.showMessageDialog(this, ex.getCause().getMessage(),
+                                       "Invalid URI", JOptionPane.ERROR_MESSAGE);
+                       // Not valid, return false
+                       return false;
+               }
+               // All valid, return true
+               return true;
+       }
+
+       /**
+        * Set the configuration properties from the UI
+        */
+       @Override
+       public void noteConfiguration() {
+               // FIXME: Update bean fields from your UI elements
+               setProperty("exampleString", fieldString.getText());
+               setProperty("exampleUri", fieldURI.getText());
+
+               configureInputPorts(serviceRegistry);
+               configureOutputPorts(serviceRegistry);
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/config/GisConfigureAction.java
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+package org.apache.taverna.gis.ui.config;
+
+import java.awt.event.ActionEvent;
+
+import org.apache.taverna.services.ServiceRegistry;
+import org.apache.taverna.scufl2.api.activity.Activity;
+
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.actions.activity.ActivityConfigurationAction;
+import org.apache.taverna.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
+
+@SuppressWarnings("serial")
+public class GisConfigureAction extends ActivityConfigurationAction {
+
+       private final EditManager editManager;
+       private final FileManager fileManager;
+       private final ServiceRegistry serviceRegistry;
+
+       public GisConfigureAction(Activity activity,
+                       EditManager editManager, FileManager fileManager,
+                       ActivityIconManager activityIconManager,
+                       ServiceDescriptionRegistry serviceDescriptionRegistry,
+                       ServiceRegistry serviceRegistry) {
+               super(activity, activityIconManager, serviceDescriptionRegistry);
+               this.editManager = editManager;
+               this.fileManager = fileManager;
+               this.serviceRegistry = serviceRegistry;
+       }
+
+       public void actionPerformed(ActionEvent e) {
+               ActivityConfigurationDialog currentDialog = getDialog(getActivity());
+               if (currentDialog != null) {
+                       currentDialog.toFront();
+                       return;
+               }
+
+               GisConfigurationPanel panel = new GisConfigurationPanel(getActivity(), serviceRegistry);
+               ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(getActivity(), panel, editManager);
+
+               setDialog(getActivity(), dialog, fileManager);
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/menu/GisConfigureMenuAction.java
new file mode 100644 (file)
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+package org.apache.taverna.gis.ui.menu;
+
+import java.net.URI;
+
+import javax.swing.Action;
+
+import org.apache.taverna.services.ServiceRegistry;
+
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.ui.menu.ContextualMenuComponent;
+import org.apache.taverna.ui.menu.MenuComponent;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.activitytools.AbstractConfigureActivityMenuAction;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+
+import org.apache.taverna.gis.ui.config.GisConfigureAction;
+
+public class GisConfigureMenuAction extends AbstractConfigureActivityMenuAction implements
+               MenuComponent, ContextualMenuComponent {
+
+       private static final URI ACTIVITY_TYPE = URI
+                       .create("http://example.com/2013/activity/apache-taverna-activity-gis");
+
+       private EditManager editManager;
+       private FileManager fileManager;
+       private ActivityIconManager activityIconManager;
+       private ServiceDescriptionRegistry serviceDescriptionRegistry;
+       private ServiceRegistry serviceRegistry;
+
+       public GisConfigureMenuAction() {
+               super(ACTIVITY_TYPE);
+       }
+
+       @Override
+       protected Action createAction() {
+               Action result = new GisConfigureAction(findActivity(), editManager, fileManager,
+                               activityIconManager, serviceDescriptionRegistry, serviceRegistry);
+               result.putValue(Action.NAME, "Configure example service");
+               addMenuDots(result);
+               return result;
+       }
+
+       public void setEditManager(EditManager editManager) {
+               this.editManager = editManager;
+       }
+
+       public void setFileManager(FileManager fileManager) {
+               this.fileManager = fileManager;
+       }
+
+       public void setActivityIconManager(ActivityIconManager activityIconManager) {
+               this.activityIconManager = activityIconManager;
+       }
+
+       public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+               this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+       }
+
+       public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+               this.serviceRegistry = serviceRegistry;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceDesc.java
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+package org.apache.taverna.gis.ui.serviceprovider;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import org.apache.taverna.scufl2.api.configurations.Configuration;
+import org.apache.taverna.servicedescriptions.ServiceDescription;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+public class GisServiceDesc extends ServiceDescription {
+       public static final URI ACTIVITY_TYPE = URI
+                       .create("http://ns.taverna.org.uk/2016/activity/gis");
+
+       
+       /**
+        * The type of Activity which should be instantiated when adding a service
+        * for this description
+        */
+       @Override
+       public URI getActivityType() {
+               return ACTIVITY_TYPE;
+       }
+
+       @Override
+       public Configuration getActivityConfiguration() {
+               Configuration configuration = new Configuration();
+               configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
+               ObjectNode json = configuration.getJsonAsObjectNode();
+               json.put("ogcServiceUri", ogcServiceUri.toASCIIString());
+               json.put("processIdentifier", processIdentifier);
+               return configuration;
+       }
+       
+       /**
+        * An icon to represent this service description in the service palette.
+        */
+       @Override
+       public Icon getIcon() {
+               return GisServiceIcon.getIcon();
+       }
+
+       /**
+        * The display name that will be shown in service palette and will
+        * be used as a template for processor name when added to workflow.
+        */
+       @Override
+       public String getName() {
+               return processIdentifier;
+       }
+
+       /**
+        * The path to this service description in the service palette. Folders
+        * will be created for each element of the returned path.
+        */
+       @Override
+       public List<String> getPath() {
+               // For deeper paths you may return several strings
+               return Arrays.asList("GIS", "WPS " + getOgcServiceUri());
+       }
+
+       /**
+        * Return a list of data values uniquely identifying this service
+        * description (to avoid duplicates). Include only primary key like fields,
+        * ie. ignore descriptions, icons, etc.
+        */
+       @Override
+       protected List<? extends Object> getIdentifyingData() {
+               // FIXME: Use your fields instead of example fields
+               return Arrays.<Object>asList(ogcServiceUri, processIdentifier);
+       }
+
+       
+       // All fields are searchable in the Service palette,
+       // for instance try a search for exampleString:3
+       private URI ogcServiceUri;
+       private String processIdentifier;
+       
+       public URI getOgcServiceUri() {
+               return ogcServiceUri;
+       }
+       public void setOgcServiceUri(URI ogcServiceUri) {
+               this.ogcServiceUri = ogcServiceUri;
+       }
+       public String getProcessIdentifier() {
+               return processIdentifier;
+       }
+       public void setProcessIdentifier(String processIdentifier) {
+               this.processIdentifier = processIdentifier;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceIcon.java
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+package org.apache.taverna.gis.ui.serviceprovider;
+
+import java.net.URI;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import org.apache.taverna.workbench.activityicons.ActivityIconSPI;
+
+public class GisServiceIcon implements ActivityIconSPI {
+
+       private static final URI ACTIVITY_TYPE = URI
+                       .create("http://example.com/2013/activity/apache-taverna-activity-gis");
+
+       private static Icon icon;
+
+       @Override
+       public int canProvideIconScore(URI activityType) {
+               if (ACTIVITY_TYPE.equals(activityType)) {
+                       return DEFAULT_ICON + 1;
+               }
+               return NO_ICON;
+       }
+
+       @Override
+       public Icon getIcon(URI activityType) {
+               return getIcon();
+       }
+
+       public static Icon getIcon() {
+               if (icon == null) {
+                       icon = new ImageIcon(GisServiceIcon.class.getResource("/exampleIcon.png"));
+               }
+               return icon;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/serviceprovider/GisServiceProvider.java
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--- /dev/null
@@ -0,0 +1,184 @@
+package org.apache.taverna.gis.ui.serviceprovider;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import javax.swing.Icon;
+
+import org.apache.taverna.scufl2.api.common.Visitor;
+import org.apache.taverna.scufl2.api.common.WorkflowBean;
+import org.apache.taverna.scufl2.api.configurations.Configuration;
+import org.apache.taverna.servicedescriptions.AbstractConfigurableServiceProvider;
+import org.apache.taverna.servicedescriptions.ConfigurableServiceProvider;
+import org.apache.taverna.servicedescriptions.ServiceDescription;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider;
+import org.apache.taverna.servicedescriptions.ServiceDescriptionProvider.FindServiceDescriptionsCallBack;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+import org.n52.wps.client.WPSClientSession;
+
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import net.opengis.wps.x100.InputDescriptionType;
+import net.opengis.wps.x100.OutputDescriptionType;
+import net.opengis.wps.x100.ProcessDescriptionType;
+
+public class GisServiceProvider extends AbstractConfigurableServiceProvider
+               implements ConfigurableServiceProvider {
+
+
+       public GisServiceProvider() {
+               super(defaultConfig());
+               
+       }
+
+       private static Configuration defaultConfig() {
+               Configuration c = new Configuration();
+               ObjectNode conf = c.getJsonAsObjectNode();
+               conf.put("osgiServiceUri", "http://localhost:8080/geoserver/ows");
+               conf.put("processIdentifier", "gs:StringConcatWPS");
+               return c;
+       }
+
+       private static final URI providerId = GisServiceDesc.ACTIVITY_TYPE.resolve("#provider");
+
+       /**
+        * Do the actual search for services. Return using the callBack parameter.
+        */
+       @SuppressWarnings("unchecked")
+       public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
+               // Use callback.status() for long-running searches
+               callBack.status("Resolving GIS services");
+
+               List<ServiceDescription> results = new ArrayList<ServiceDescription>();
+
+               // FIXME: Implement the actual service search/lookup instead
+               // of dummy for-loop
+
+               GisServiceDesc service = new GisServiceDesc();
+               // Populate the service description bean
+               ObjectNode conf = getConfiguration().getJsonAsObjectNode();
+               String serviceUri = conf.get("osgiServiceUri").asText();
+               service.setOgcServiceUri(URI.create(serviceUri));
+               String processIdentifier = conf.get("processIdentifier").asText();
+               service.setProcessIdentifier(processIdentifier);
+
+               // TODO: Optional: set description (Set a better description
+               service.setDescription(processIdentifier);
+
+               // TODO: Exctract in a separate method 
+               // Get input ports
+               
+               WPSClientSession wpsClient = WPSClientSession.getInstance();
+
+        ProcessDescriptionType processDescription;
+               try {
+                       processDescription = wpsClient
+                               .getProcessDescription(serviceUri, processIdentifier);
+               
+                       InputDescriptionType[] inputList = processDescription.getDataInputs()
+                       .getInputArray();
+
+               List<ActivityInputPortDefinitionBean> inputPortDefinitions = new ArrayList<ActivityInputPortDefinitionBean>();
+
+               for (InputDescriptionType input : inputList) {
+                       ActivityInputPortDefinitionBean newInputPort = new ActivityInputPortDefinitionBean();
+                       newInputPort.setName(input.getIdentifier().getStringValue());
+                       newInputPort.setDepth(0);
+                       newInputPort.setAllowsLiteralValues(true);
+                       newInputPort.setHandledReferenceSchemes(null);
+                       newInputPort.setTranslatedElementType(String.class);
+                       
+                       inputPortDefinitions.add(newInputPort);
+                       
+               }
+               
+              // service.setInputPortDefinitions(inputPortDefinitions);
+                       
+               
+               // Get output ports
+               
+               OutputDescriptionType[] outputList = processDescription.getProcessOutputs().getOutputArray();
+               List<ActivityOutputPortDefinitionBean> outputPortDefinitions = new ArrayList<ActivityOutputPortDefinitionBean>();
+               
+               for( OutputDescriptionType output : outputList )
+               {
+                       ActivityOutputPortDefinitionBean newOutputPort = new ActivityOutputPortDefinitionBean();
+                       newOutputPort.setName(output.getIdentifier().getStringValue());
+                       newOutputPort.setDepth(0);
+                       
+                       outputPortDefinitions.add(newOutputPort);
+                       
+               }
+               
+               //service.setOutputPortDefinitions(outputPortDefinitions);
+               
+               } catch (IOException e) {
+                       // TODO Auto-generated catch block
+                       e.printStackTrace();
+               }
+        
+               results.add(service);
+
+               // partialResults() can also be called several times from inside
+               // for-loop if the full search takes a long time
+               callBack.partialResults(results);
+
+               // No more results will be coming
+               callBack.finished();
+       }
+       
+       /**
+        * Icon for service provider
+        */
+       public Icon getIcon() {
+               return GisServiceIcon.getIcon();
+       }
+
+       /**
+        * Name of service provider, appears in right click for 'Remove service
+        * provider'
+        */
+       public String getName() {
+               return "Geospatial Web Services";
+       }
+
+       @Override
+       public String toString() {
+               return "Geospatial Web Services " + getConfiguration().getJson().get("osgiServiceUri");
+       }
+
+       public String getId() {
+               return providerId.toASCIIString();
+       }
+
+       @Override
+       protected List<? extends Object> getIdentifyingData() {
+               return Arrays.asList(getConfiguration().getJson().get("osgiServiceUri"), 
+                               getConfiguration().getJson().get("processIdentifier"));
+       }
+
+       @Override
+       public ServiceDescriptionProvider newInstance() {
+               return new GisServiceProvider();
+       }
+
+       @Override
+       public URI getType() {
+               return providerId;
+       }
+
+       @Override
+       public void setType(URI type) {
+       }
+
+       @Override
+       public boolean accept(Visitor visitor) {
+               return false;
+       }
+
+       
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisActivityContextViewFactory.java
new file mode 100644 (file)
index 0000000..1a0dc13
--- /dev/null
@@ -0,0 +1,59 @@
+package org.apache.taverna.gis.ui.view;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.taverna.services.ServiceRegistry;
+import org.apache.taverna.scufl2.api.activity.Activity;
+
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.views.contextualviews.ContextualView;
+import org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
+
+public class GisActivityContextViewFactory implements ContextualViewFactory<Activity> {
+
+       private static final URI ACTIVITY_TYPE = URI
+                       .create("http://example.com/2013/activity/apache-taverna-activity-gis");
+
+       private EditManager editManager;
+       private FileManager fileManager;
+       private ActivityIconManager activityIconManager;
+       private ServiceDescriptionRegistry serviceDescriptionRegistry;
+       private ServiceRegistry serviceRegistry;
+
+       @Override
+       public boolean canHandle(Object object) {
+               return object instanceof Activity && ((Activity) object).getType().equals(ACTIVITY_TYPE);
+       }
+
+       @Override
+       public List<ContextualView> getViews(Activity selection) {
+               return Arrays.<ContextualView>asList(new GisContextualView(selection, editManager,
+                               fileManager, activityIconManager, serviceDescriptionRegistry, serviceRegistry));
+       }
+
+       public void setEditManager(EditManager editManager) {
+               this.editManager = editManager;
+       }
+
+       public void setFileManager(FileManager fileManager) {
+               this.fileManager = fileManager;
+       }
+
+       public void setActivityIconManager(ActivityIconManager activityIconManager) {
+               this.activityIconManager = activityIconManager;
+       }
+
+       public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
+               this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+       }
+
+       public void setServiceRegistry(ServiceRegistry serviceRegistry) {
+               this.serviceRegistry = serviceRegistry;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java b/apache-taverna-activity-gis-activity-ui/src/main/java/org/apache/taverna/gis/ui/view/GisContextualView.java
new file mode 100644 (file)
index 0000000..08fff1f
--- /dev/null
@@ -0,0 +1,88 @@
+package org.apache.taverna.gis.ui.view;
+
+import java.awt.Frame;
+
+import javax.swing.Action;
+import javax.swing.JComponent;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+import org.apache.taverna.services.ServiceRegistry;
+
+import org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry;
+import org.apache.taverna.workbench.activityicons.ActivityIconManager;
+import org.apache.taverna.workbench.edits.EditManager;
+import org.apache.taverna.workbench.file.FileManager;
+import org.apache.taverna.workbench.ui.actions.activity.ActivityContextualView;
+
+import org.apache.taverna.scufl2.api.activity.Activity;
+
+import org.apache.taverna.gis.ui.config.GisConfigureAction;
+
+@SuppressWarnings("serial")
+public class GisContextualView extends ActivityContextualView {
+
+       private final EditManager editManager;
+       private final FileManager fileManager;
+       private final ActivityIconManager activityIconManager;
+       private final ServiceDescriptionRegistry serviceDescriptionRegistry;
+       private final ServiceRegistry serviceRegistry;
+
+       private JLabel description = new JLabel("ads");
+
+       public GisContextualView(Activity activity, EditManager editManager,
+                       FileManager fileManager, ActivityIconManager activityIconManager,
+                       ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
+               super(activity);
+               this.editManager = editManager;
+               this.fileManager = fileManager;
+               this.activityIconManager = activityIconManager;
+               this.serviceDescriptionRegistry = serviceDescriptionRegistry;
+               this.serviceRegistry = serviceRegistry;
+               initView();
+       }
+
+       @Override
+       public JComponent getMainFrame() {
+               JPanel jPanel = new JPanel();
+               jPanel.add(description);
+               refreshView();
+               return jPanel;
+       }
+
+       @Override
+       public String getViewTitle() {
+               JsonNode configuration = getConfigBean().getJson();
+               return "Gis service " + configuration.get("exampleString").asText();
+       }
+
+       /**
+        * Typically called when the activity configuration has changed.
+        */
+       @Override
+       public void refreshView() {
+               JsonNode configuration = getConfigBean().getJson();
+               description.setText("Gis service " + configuration.get("exampleUri").asText()
+                               + " - " + configuration.get("exampleString").asText());
+               // TODO: Might also show extra service information looked
+               // up dynamically from endpoint/registry
+       }
+
+       /**
+        * View position hint
+        */
+       @Override
+       public int getPreferredPosition() {
+               // We want to be on top
+               return 100;
+       }
+
+       @Override
+       public Action getConfigureAction(final Frame owner) {
+               return new GisConfigureAction(getActivity(), editManager, fileManager,
+                               activityIconManager, serviceDescriptionRegistry, serviceRegistry);
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context-osgi.xml
new file mode 100644 (file)
index 0000000..4987ea3
--- /dev/null
@@ -0,0 +1,26 @@
+<?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="GisServiceIcon" interface="org.apache.taverna.workbench.activityicons.ActivityIconSPI" />
+
+       <service ref="GisServiceProvider" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionProvider" />
+
+       <service ref="GisConfigureMenuAction" auto-export="interfaces" />
+
+       <service ref="GisActivityContextViewFactory" interface="org.apache.taverna.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
+
+       <reference id="editManager" interface="org.apache.taverna.workbench.edits.EditManager" />
+       <reference id="fileManager" interface="org.apache.taverna.workbench.file.FileManager" />
+       <reference id="menuManager" interface="org.apache.taverna.ui.menu.MenuManager" />
+       <reference id="selectionManager" interface="org.apache.taverna.workbench.selection.SelectionManager" />
+       <reference id="activityIconManager" interface="org.apache.taverna.workbench.activityicons.ActivityIconManager" />
+       <reference id="colourManager" interface="org.apache.taverna.workbench.configuration.colour.ColourManager" />
+       <reference id="serviceDescriptionRegistry" interface="org.apache.taverna.servicedescriptions.ServiceDescriptionRegistry" />
+       <reference id="serviceRegistry" interface="org.apache.taverna.services.ServiceRegistry" />
+
+</beans:beans>
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml b/apache-taverna-activity-gis-activity-ui/src/main/resources/META-INF/spring/context.xml
new file mode 100644 (file)
index 0000000..f0c1255
--- /dev/null
@@ -0,0 +1,31 @@
+<?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="GisServiceIcon"
+               class="org.apache.taverna.gis.ui.serviceprovider.GisServiceIcon" />
+
+       <bean id="GisServiceProvider"
+               class="org.apache.taverna.gis.ui.serviceprovider.GisServiceProvider" />
+
+       <bean id="GisConfigureMenuAction"
+               class="org.apache.taverna.gis.ui.menu.GisConfigureMenuAction">
+               <property name="editManager" ref="editManager" />
+               <property name="fileManager" ref="fileManager" />
+               <property name="activityIconManager" ref="activityIconManager" />
+               <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+               <property name="serviceRegistry" ref="serviceRegistry" />
+       </bean>
+
+       <bean id="GisActivityContextViewFactory"
+               class="org.apache.taverna.gis.ui.view.GisActivityContextViewFactory">
+               <property name="editManager" ref="editManager" />
+               <property name="fileManager" ref="fileManager" />
+               <property name="activityIconManager" ref="activityIconManager" />
+               <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
+               <property name="serviceRegistry" ref="serviceRegistry" />
+       </bean>
+
+</beans>
diff --git a/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png b/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png
new file mode 100644 (file)
index 0000000..8bb31c3
Binary files /dev/null and b/apache-taverna-activity-gis-activity-ui/src/main/resources/exampleIcon.png differ
diff --git a/apache-taverna-activity-gis-activity/pom.xml b/apache-taverna-activity-gis-activity/pom.xml
new file mode 100644 (file)
index 0000000..a118bb5
--- /dev/null
@@ -0,0 +1,57 @@
+<?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>org.apache.taverna.gis</groupId>
+               <artifactId>apache-taverna-activity-gis</artifactId>
+               <version>0.0.1-incubating.SNAPSHOT</version>
+       </parent>
+       <artifactId>apache-taverna-activity-gis-activity</artifactId>
+       <packaging>bundle</packaging>
+       <name>Gis Taverna activity</name>
+
+       <dependencies>
+                                                               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-workflowmodel-api</artifactId>
+                       <version>${taverna.engine.version}</version>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-reference-api</artifactId>
+                       <version>${taverna.engine.version}</version>
+               </dependency>
+
+               <dependency>
+                       <groupId>com.fasterxml.jackson.core</groupId>
+                       <artifactId>jackson-databind</artifactId>
+                       <version>2.3.0</version>
+               </dependency>
+
+               <dependency>
+                       <groupId>junit</groupId>
+                       <artifactId>junit</artifactId>
+                       <version>4.4</version>
+                       <scope>test</scope>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-workflowmodel-impl</artifactId>
+                       <version>${taverna.engine.version}</version>
+                       <scope>test</scope>
+               </dependency>
+               <dependency>
+                       <groupId>org.apache.taverna.engine</groupId>
+                       <artifactId>taverna-activity-test-utils</artifactId>
+                       <version>${taverna.engine.version}</version>
+                       <scope>test</scope>
+               </dependency>
+               
+               <dependency>
+                       <groupId>${project.parent.groupId}</groupId>
+                       <artifactId>taverna-gis-client</artifactId>
+                       <version>${project.parent.version}</version>
+               </dependency>
+       </dependencies>
+</project>
diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivity.java
new file mode 100644 (file)
index 0000000..aa5c952
--- /dev/null
@@ -0,0 +1,157 @@
+package org.apache.taverna.gis;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import org.geotools.ows.ServiceException;
+import org.n52.wps.client.ExecuteRequestBuilder;
+import org.n52.wps.client.ExecuteResponseAnalyser;
+import org.n52.wps.client.WPSClientException;
+import org.n52.wps.client.WPSClientSession;
+import org.n52.wps.io.data.IData;
+import org.n52.wps.io.data.binding.complex.GTVectorDataBinding;
+
+import net.opengis.wps.x100.DataType;
+import net.opengis.wps.x100.ExecuteDocument;
+import net.opengis.wps.x100.ExecuteResponseDocument;
+import net.opengis.wps.x100.OutputDataType;
+import net.opengis.wps.x100.ProcessDescriptionType;
+import org.apache.taverna.invocation.InvocationContext;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityInputPortDefinitionBean;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityOutputPortDefinitionBean;
+
+public class GisActivity extends AbstractAsynchronousActivity<GisActivityConfigurationBean>
+               implements AsynchronousActivity<GisActivityConfigurationBean> {
+       
+       private GisActivityConfigurationBean configBean;
+
+       @Override
+       public void configure(GisActivityConfigurationBean configBean) throws ActivityConfigurationException {
+
+               // TODO: Should I call HealthChecker here??
+               // Any pre-config sanity checks
+               if (configBean.getOgcServiceUri().equals("")) {
+                       throw new ActivityConfigurationException("Geospatial web service URI can't be empty");
+               }
+               // Store for getConfiguration()
+               this.configBean = configBean;
+
+               // REQUIRED: (Re)create input/output ports depending on configuration
+               configurePorts();
+       }
+
+       protected void configurePorts() {
+               // In case we are being reconfigured - remove existing ports first
+               // to avoid duplicates
+               removeInputs();
+               removeOutputs();
+
+               // Add input ports
+               for(ActivityInputPortDefinitionBean inputPort : configBean.getInputPortDefinitions())
+               {
+                       addInput(inputPort.getName(),inputPort.getDepth(),inputPort.getAllowsLiteralValues(),inputPort.getHandledReferenceSchemes(), inputPort.getTranslatedElementType());
+               }
+               
+               // Add output ports
+               for(ActivityOutputPortDefinitionBean outputPort : configBean.getOutputPortDefinitions())
+               {
+                       addOutput(outputPort.getName(),outputPort.getDepth());
+               }
+               
+       }
+
+       @SuppressWarnings("unchecked")
+       @Override
+       public void executeAsynch(final Map<String, T2Reference> inputs, final AsynchronousActivityCallback callback) {
+               // Execute service asynchronously
+               callback.requestRun(new Runnable() {
+
+                       public void run() {
+                               InvocationContext context = callback.getContext();
+                               ReferenceService referenceService = context.getReferenceService();
+
+                               // Declare outputs variable
+                               Map<String, T2Reference> outputs = null;
+                               
+                               try {
+                                       
+                                       // prepare the execute object
+                                       WPSClientSession wpsClient = WPSClientSession.getInstance();
+
+                                       ProcessDescriptionType processDescription = wpsClient.getProcessDescription(configBean.getOgcServiceUri().toString(), configBean.getProcessIdentifier());
+                                       
+                                       ExecuteRequestBuilder executeBuilder = new ExecuteRequestBuilder(processDescription);
+
+                                       for (ActivityInputPortDefinitionBean activityInputPort : configBean.getInputPortDefinitions()) {
+                                               String portValue = (String) referenceService.renderIdentifier(inputs.get(activityInputPort.getName()), String.class, context);
+                                               executeBuilder.addLiteralData(activityInputPort.getName(), portValue);
+                                       }
+                               
+                                       ExecuteDocument execute = executeBuilder.getExecute();
+                       
+                                       execute.getExecute().setService("WPS");
+                                       
+                                       Object responseObject = null;
+                                       
+                                       try {
+                                               // execute service
+                                               responseObject = wpsClient.execute(configBean.getOgcServiceUri().toString(), execute);
+                                       } catch (WPSClientException e) {
+                                               // if the an error return from service
+                                               callback.fail(e.getServerException().xmlText());
+                                       }
+
+                                       // Register outputs
+                                       outputs = new HashMap<String, T2Reference>();
+                                       T2Reference simpleRef = null;
+                                       
+                                       if (responseObject instanceof ExecuteResponseDocument) {
+                                   ExecuteResponseDocument response = (ExecuteResponseDocument) responseObject;
+                                   
+                                   // analyser is used to get complex data
+                                   ExecuteResponseAnalyser analyser = new ExecuteResponseAnalyser(
+                                           execute, response, processDescription);
+                                   
+                                   for(OutputDataType output : response.getExecuteResponse().getProcessOutputs().getOutputArray())
+                                               {
+                                       DataType data = output.getData();
+                                       
+                                       if (data.isSetLiteralData())
+                                                       {
+                                               simpleRef = referenceService.register(data.getLiteralData().getStringValue(), 0, true, context);
+
+                                                               outputs.put(output.getIdentifier().getStringValue(), simpleRef);
+                                                       }
+                                       
+                                               }
+                                   
+                               }
+                                       
+                                       
+                               } catch (WPSClientException e) {
+                                       callback.fail(e.getMessage());
+                               } catch (IOException e) {
+                                       callback.fail(e.getMessage());
+                               }
+
+                               callback.receiveResult(outputs, new int[0]);
+                       }
+               });
+       }
+
+       @Override
+       public GisActivityConfigurationBean getConfiguration() {
+               return this.configBean;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityConfigurationBean.java
new file mode 100644 (file)
index 0000000..31d193b
--- /dev/null
@@ -0,0 +1,52 @@
+package org.apache.taverna.gis;
+
+import java.io.Serializable;
+import java.net.URI;
+import java.util.List;
+
+import net.opengis.wps.x100.InputDescriptionType;
+import net.opengis.wps.x100.OutputDescriptionType;
+import org.apache.taverna.workflowmodel.processor.activity.config.ActivityPortsDefinitionBean;
+
+/**
+ * Gis activity configuration bean.
+ * 
+ */
+public class GisActivityConfigurationBean extends ActivityPortsDefinitionBean implements Serializable {
+
+       /*
+        * TODO: Remove this comment. Should the jackson ojbect be managed in this class?
+        * 
+        * The configuration specifies the variable options and configurations for
+        * an activity that has been added to a workflow. For instance for a WSDL
+        * activity, the configuration contains the URL for the WSDL together with
+        * the method name. String constant configurations contain the string that
+        * is to be returned, while Beanshell script configurations contain both the
+        * scripts and the input/output ports (by subclassing
+        * ActivityPortsDefinitionBean).
+        * 
+        * Configuration beans are serialised as XML (currently by using XMLBeans)
+        * when Taverna is saving the workflow definitions. Therefore the
+        * configuration beans need to follow the JavaBeans style and only have
+        * fields of 'simple' types such as Strings, integers, etc. Other beans can
+        * be referenced as well, as long as they are part of the same plugin.
+        */
+       
+
+       private URI ogcServiceUri;
+       private String processIdentifier;
+       
+       public URI getOgcServiceUri() { 
+               return ogcServiceUri;
+       }
+       public void setOgcServiceUri(URI ogcServiceUri) {
+               this.ogcServiceUri = ogcServiceUri;
+       }
+       public String getProcessIdentifier() {
+               return processIdentifier;
+       }
+       public void setProcessIdentifier(String processIdentifier) {
+               this.processIdentifier = processIdentifier;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityExample.java
new file mode 100644 (file)
index 0000000..e533b43
--- /dev/null
@@ -0,0 +1,132 @@
+package org.apache.taverna.gis;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+import org.apache.taverna.invocation.InvocationContext;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.workflowmodel.processor.activity.AbstractAsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivity;
+import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityCallback;
+
+/**
+ * Gis <code>Activity<code>.
+ */
+public class GisActivityExample extends AbstractAsynchronousActivity<JsonNode>
+               implements AsynchronousActivity<JsonNode> {
+
+       public static final String ACTIVITY_TYPE = "http://example.com/2013/activity/apache-taverna-activity-gis";
+
+       /*
+        * Best practice: Keep port names as constants to avoid misspelling. This
+        * would not apply if port names are looked up dynamically from the service
+        * operation, like done for WSDL services.
+        */
+       public static final String IN_FIRST_INPUT = "firstInput";
+       public static final String IN_EXTRA_DATA = "extraData";
+       public static final String OUT_MORE_OUTPUTS = "moreOutputs";
+       public static final String OUT_SIMPLE_OUTPUT = "simpleOutput";
+       public static final String OUT_REPORT = "report";
+
+       private JsonNode configuration;
+
+       @Override
+       public void configure(JsonNode configuration) throws ActivityConfigurationException {
+
+               // Any pre-config sanity checks
+               if (configuration.get("exampleString").asText().equals("invalidExample")) {
+                       throw new ActivityConfigurationException(
+                                       "Example string can't be 'invalidExample'");
+               }
+               // Store for getConfiguration(), but you could also make
+               // getConfiguration() return a new bean from other sources
+               this.configuration = configuration;
+
+               // OPTIONAL:
+               // Do any server-side lookups and configuration, like resolving WSDLs
+
+               // myClient = new MyClient(configuration.get("exampleUri").asText());
+               // this.service = myClient.getService(configuration.get("exampleString").asText());
+
+       }
+
+       @Override
+       public JsonNode getConfiguration() {
+               return configuration;
+       }
+
+       @SuppressWarnings("unchecked")
+       @Override
+       public void executeAsynch(final Map<String, T2Reference> inputs,
+                       final AsynchronousActivityCallback callback) {
+               // Don't execute service directly now, request to be run ask to be run
+               // from thread pool and return asynchronously
+               callback.requestRun(new Runnable() {
+
+                       public void run() {
+                               InvocationContext context = callback
+                                               .getContext();
+                               ReferenceService referenceService = context
+                                               .getReferenceService();
+                               // Resolve inputs
+                               String firstInput = (String) referenceService.renderIdentifier(inputs.get(IN_FIRST_INPUT),
+                                               String.class, context);
+
+                               // Support our configuration-dependendent input
+                               boolean optionalPorts = configuration.get("exampleString").asText().equals("specialCase");
+
+                               List<byte[]> special = null;
+                               // We'll also allow IN_EXTRA_DATA to be optionally not provided
+                               if (optionalPorts && inputs.containsKey(IN_EXTRA_DATA)) {
+                                       // Resolve as a list of byte[]
+                                       special = (List<byte[]>) referenceService.renderIdentifier(
+                                                       inputs.get(IN_EXTRA_DATA), byte[].class, context);
+                               }
+
+
+                               // TODO: Do the actual service invocation
+//                             try {
+//                                     results = this.service.invoke(firstInput, special)
+//                             } catch (ServiceException ex) {
+//                                     callback.fail("Could not invoke Gis service " + configBean.getExampleUri(),
+//                                                     ex);
+//                                     // Make sure we don't call callback.receiveResult later
+//                                     return;
+//                             }
+
+                               // Register outputs
+                               Map<String, T2Reference> outputs = new HashMap<>();
+                               String simpleValue = "simple";
+                               T2Reference simpleRef = referenceService.register(simpleValue, 0, true, context);
+                               outputs.put(OUT_SIMPLE_OUTPUT, simpleRef);
+
+                               // For list outputs, only need to register the top level list
+                               List<String> moreValues = new ArrayList<>();
+                               moreValues.add("Value 1");
+                               moreValues.add("Value 2");
+                               T2Reference moreRef = referenceService.register(moreValues, 1, true, context);
+                               outputs.put(OUT_MORE_OUTPUTS, moreRef);
+
+                               if (optionalPorts) {
+                                       // Populate our optional output port
+                                       // NOTE: Need to return output values for all defined output ports
+                                       String report = "Everything OK";
+                                       outputs.put(OUT_REPORT, referenceService.register(report,
+                                                       0, true, context));
+                               }
+
+                               // return map of output data, with empty index array as this is
+                               // the only and final result (this index parameter is used if
+                               // pipelining output)
+                               callback.receiveResult(outputs, new int[0]);
+                       }
+               });
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityFactory.java
new file mode 100644 (file)
index 0000000..540dd3d
--- /dev/null
@@ -0,0 +1,94 @@
+package org.apache.taverna.gis;
+
+import static org.apache.taverna.gis.GisActivity.*;
+
+import java.io.IOException;
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import org.apache.taverna.workflowmodel.Edits;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityFactory;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+/**
+ * Gis <code>ActivityFactory<code>.
+ */
+public class GisActivityFactory implements ActivityFactory {
+
+       private Edits edits;
+
+       @Override
+       public GisActivity createActivity() {
+               return new GisActivity();
+       }
+
+       @Override
+       public URI getActivityType() {
+               return URI.create(GisActivity.ACTIVITY_TYPE);
+       }
+
+       @Override
+       public JsonNode getActivityConfigurationSchema() {
+               ObjectMapper objectMapper = new ObjectMapper();
+               try {
+                       return objectMapper.readTree(getClass().getResource("/schema.json"));
+               } catch (IOException e) {
+                       return objectMapper.createObjectNode();
+               }
+       }
+
+       @Override
+       public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
+               Set<ActivityInputPort> inputPorts = new HashSet<>();
+
+               // FIXME: Replace with your input port definitions
+
+               // Hard coded input port, expecting a single String
+               inputPorts.add(edits.createActivityInputPort(IN_FIRST_INPUT, 0, true, null, String.class));
+
+               // Optional ports depending on configuration
+               if (configuration.get("exampleString").asText().equals("specialCase")) {
+                       // depth 1, ie. list of binary byte[] arrays
+                       inputPorts.add(edits.createActivityInputPort(IN_EXTRA_DATA, 1, true, null, byte[].class));
+               }
+
+               return inputPorts;
+       }
+
+       @Override
+       public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
+               Set<ActivityOutputPort> outputPorts = new HashSet<>();
+
+               // FIXME: Replace with your output port definitions
+
+               // Optional ports depending on configuration
+               if (configuration.get("exampleString").asText().equals("specialCase")) {
+                       outputPorts.add(edits.createActivityOutputPort(OUT_REPORT, 0, 0));
+               }
+
+               // Single value output port (depth 0)
+               outputPorts.add(edits.createActivityOutputPort(OUT_SIMPLE_OUTPUT, 0, 0));
+               // Output port with list of values (depth 1)
+               outputPorts.add(edits.createActivityOutputPort(OUT_MORE_OUTPUTS, 1, 1));
+
+               return outputPorts;
+       }
+
+       /**
+        * Sets the edits property.
+        * <p>
+        * This method is used by Spring. The property name must match the property specified
+        * in the Spring context file.
+        *
+        * @param edits the <code>Edits</code> used to create input/output ports
+        */
+       public void setEdits(Edits edits) {
+               this.edits = edits;
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java b/apache-taverna-activity-gis-activity/src/main/java/org/apache/taverna/gis/GisActivityHealthChecker.java
new file mode 100644 (file)
index 0000000..9e143b5
--- /dev/null
@@ -0,0 +1,63 @@
+package org.apache.taverna.gis;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.databind.JsonNode;
+
+import org.apache.taverna.visit.VisitReport;
+import org.apache.taverna.visit.VisitReport.Status;
+import org.apache.taverna.workflowmodel.health.HealthCheck;
+import org.apache.taverna.workflowmodel.health.HealthChecker;
+
+/**
+ * Gis <code>HealthChecker</code>.
+ */
+public class GisActivityHealthChecker implements
+               HealthChecker<GisActivity> {
+
+       public boolean canVisit(Object o) {
+               // Return True if we can visit the object. We could do
+               // deeper (but not time consuming) checks here, for instance
+               // if the health checker only deals with GisActivity where
+               // a certain configuration option is enabled.
+               return o instanceof GisActivity;
+       }
+
+       public boolean isTimeConsuming() {
+               // Return true if the health checker does a network lookup
+               // or similar time consuming checks, in which case
+               // it would only be performed when using File->Validate workflow
+               // or File->Run.
+               return false;
+       }
+
+       public VisitReport visit(GisActivity activity, List<Object> ancestry) {
+               JsonNode config = activity.getConfiguration();
+
+               // We'll build a list of subreports
+               List<VisitReport> subReports = new ArrayList<>();
+
+               if (!URI.create(config.get("exampleUri").asText()).isAbsolute()) {
+                       // Report Severe problems we know won't work
+                       VisitReport report = new VisitReport(HealthCheck.getInstance(),
+                                       activity, "Example URI must be absolute", HealthCheck.INVALID_URL,
+                                       Status.SEVERE);
+                       subReports.add(report);
+               }
+
+               if (config.get("exampleString").asText().equals("")) {
+                       // Warning on possible problems
+                       subReports.add(new VisitReport(HealthCheck.getInstance(), activity,
+                                       "Example string empty", HealthCheck.NO_CONFIGURATION,
+                                       Status.WARNING));
+               }
+
+               // The default explanation here will be used if the subreports list is
+               // empty
+               return new VisitReport(HealthCheck.getInstance(), activity,
+                               "Gis service OK", HealthCheck.NO_PROBLEM, subReports);
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/resources/schema.json b/apache-taverna-activity-gis-activity/src/main/resources/schema.json
new file mode 100644 (file)
index 0000000..1e396b3
--- /dev/null
@@ -0,0 +1,25 @@
+{
+    "$schema": "http://json-schema.org/draft-03/schema#",
+    "id": "http://example.com/2013/activity/apache-taverna-activity-gis.schema.json",
+    "title": "Gis activity configuration",
+    "type": "object",
+    "properties": {
+        "@context": {
+            "description": "JSON-LD context for interpreting the configuration as RDF",
+            "required": true,
+            "enum": ["http://example.com/2013/activity/apache-taverna-activity-gis.context.json"]
+        },
+        "exampleString": {
+            "title": "Example String",
+            "description": "An example string property",
+            "type": "string",
+            "required": true
+        },
+        "exampleUri": {
+            "title": "Example URI",
+            "description": "An example uri property",
+            "type": "string",
+            "required": true
+        }
+    }
+}
diff --git a/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml b/apache-taverna-activity-gis-activity/src/main/resources/spring/context-osgi.xml
new file mode 100644 (file)
index 0000000..1b2a8c3
--- /dev/null
@@ -0,0 +1,17 @@
+<?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">
+
+       <!-- Services to be registered with the OSGi service register -->
+       <service ref="GisActivityHealthChecker" interface="org.apache.taverna.workflowmodel.health.HealthChecker" />
+
+       <service ref="GisActivityFactory" interface="org.apache.taverna.workflowmodel.processor.activity.ActivityFactory" />
+
+       <!-- References to services required from the OSGi service register -->
+       <reference id="edits" interface="org.apache.taverna.workflowmodel.Edits" />
+
+</beans:beans>
diff --git a/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml b/apache-taverna-activity-gis-activity/src/main/resources/spring/context.xml
new file mode 100644 (file)
index 0000000..e2b290e
--- /dev/null
@@ -0,0 +1,12 @@
+<?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="GisActivityHealthChecker" class="org.apache.taverna.gis.GisActivityHealthChecker" />
+
+       <bean id="GisActivityFactory" class="org.apache.taverna.gis.GisActivityFactory">
+               <property name="edits" ref="edits" />
+       </bean>
+
+</beans>
diff --git a/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml b/apache-taverna-activity-gis-activity/src/main/resources/wps_config.xml
new file mode 100644 (file)
index 0000000..cd73904
--- /dev/null
@@ -0,0 +1,212 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<WPSConfiguration xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://n52.org/wps https://raw.githubusercontent.com/52North/wps-config/52n-wps-config-1.2.1/src/main/xsd/schema_v2.xsd" xmlns="http://n52.org/wps">
+       <Datahandlers>
+               <ParserList>
+                       <Parser name="WCPSQueryParser"
+                               className="org.n52.wps.io.datahandler.parser.WCPSQueryParser"
+                               active="true">
+                               <Format mimetype="text/plain"
+                                       schema="http://schemas.opengis.net/wcps/1.0/wcpsAll.xsd" />
+                       </Parser>
+                       <Parser name="WKTParser"
+                               className="org.n52.wps.io.datahandler.parser.WKTParser"
+                               active="true">
+                               <Format mimetype="application/wkt"/>
+                       </Parser>
+                       <Parser name="GenericXMLDataParser"
+                               className="org.n52.wps.io.datahandler.parser.GenericXMLDataParser"
+                               active="true">
+                               <Format mimetype="text/xml" />
+                               <Format mimetype="text/xml; subtype=gml/2.1.2"
+                                       schema="http://schemas.opengis.net/gml/2.1.2/feature.xsd" />
+                       </Parser>
+                       <Parser name="GenericFileParser"
+                               className="org.n52.wps.io.datahandler.parser.GenericFileParser"
+                               active="true">
+                               <Format mimetype="application/x-zipped-shp" />
+                               <Format mimetype="application/img" />
+                               <Format mimetype="image/tiff" />
+                               <Format mimetype="image/geotiff" />
+                               <Format mimetype="application/geotiff" />
+                               <Format mimetype="application/dbase" />
+                               <Format mimetype="application/remap" />
+                               <Format mimetype="application/x-erdas-hfa" />
+                               <Format mimetype="application/x-netcdf" />
+                               <Format mimetype="application/dgn" />
+                               <Format mimetype="image/jpeg" />
+                               <Format mimetype="image/png" />
+                               <Format mimetype="application/x-geotiff" />
+                               <Format mimetype="application/hdf4-eos" />
+                               <Format mimetype="text/plain" />
+                               <Format mimetype="application/rData" />
+                               <Format mimetype="application/rData+Spatial" />
+                               <Format mimetype="application/rData+SpatialPoints" />
+                               <Format mimetype="application/rData+SpatialPolygons" />
+                               <Format mimetype="text/html" />
+
+                               <Format mimetype="application/rData" encoding="base64" />
+                               <Format mimetype="application/rData+Spatial" encoding="base64" />
+                               <Format mimetype="application/rData+SpatialPoints" encoding="base64" />
+                               <Format mimetype="application/rData+SpatialPolygons" encoding="base64" />
+                               <Format mimetype="application/x-zipped-shp" encoding="base64" />
+                               <Format mimetype="application/img" encoding="base64" />
+                               <Format mimetype="image/tiff" encoding="base64" />
+                               <Format mimetype="application/geotiff" encoding="base64" />
+                               <Format mimetype="application/dbase" encoding="base64" />
+                               <Format mimetype="application/remap" encoding="base64" />
+                               <Format mimetype="application/x-erdas-hfa" encoding="base64" />
+                               <Format mimetype="application/x-netcdf" encoding="base64" />
+                               <Format mimetype="application/dgn" encoding="base64" />
+                               <Format mimetype="image/jpeg" encoding="base64" />
+                               <Format mimetype="image/png" encoding="base64" />
+                               <Format mimetype="application/x-geotiff" encoding="base64" />
+                               <Format mimetype="application/hdf4-eos" encoding="base64" />
+                               <Format mimetype="text/plain" encoding="base64" />
+                       </Parser>
+               </ParserList>
+               <GeneratorList>                 
+                       <Generator name="WKTGenerator"
+                               className="org.n52.wps.io.datahandler.generator.WKTGenerator"
+                               active="true">
+                               <Format mimetype="application/wkt"/>
+                       </Generator>
+                       <Generator name="GenericXMLDataGenerator"
+                               className="org.n52.wps.io.datahandler.generator.GenericXMLDataGenerator"
+                               active="true">
+                               <Format mimetype="text/xml" />
+                               <Format mimetype="text/xml; subtype=gml/2.1.2"
+                                       schema="http://schemas.opengis.net/gml/2.1.2/feature.xsd" />
+                       </Generator>
+                       <Generator name="GenericFileGenerator"
+                               className="org.n52.wps.io.datahandler.generator.GenericFileGenerator"
+                               active="true">
+                               <Format mimetype="application/x-zipped-shp" encoding="base64" />
+                               <Format mimetype="application/shp" encoding="base64" />
+                               <Format mimetype="application/img" encoding="base64" />
+                               <Format mimetype="image/tiff" encoding="base64" />
+                               <Format mimetype="image/geotiff" encoding="base64" />
+                               <Format mimetype="application/geotiff" encoding="base64" />
+                               <Format mimetype="application/dbase" encoding="base64" />
+                               <Format mimetype="application/remap" encoding="base64" />
+                               <Format mimetype="application/x-erdas-hfa" encoding="base64" />
+                               <Format mimetype="application/x-netcdf" encoding="base64" />
+                               <Format mimetype="application/netcdf" encoding="base64" />
+                               <Format mimetype="application/dgn" encoding="base64" />
+                               <Format mimetype="image/jpeg" encoding="base64" />
+                               <Format mimetype="image/png" encoding="base64" />
+                               <Format mimetype="application/x-geotiff" encoding="base64" />
+                               <Format mimetype="text/plain" encoding="base64" />
+                               <Format mimetype="application/x-zipped-shp" encoding="base64" />
+                               <Format mimetype="application/rData" encoding="base64" />
+                               <Format mimetype="application/rData+Spatial" encoding="base64" />
+                               <Format mimetype="application/rData+SpatialPoints" encoding="base64" />
+                               <Format mimetype="application/rData+SpatialPolygons" encoding="base64" />
+                               
+                               <Format mimetype="application/rData" />
+                               <Format mimetype="application/rData+Spatial" />
+                               <Format mimetype="application/rData+SpatialPoints" />
+                               <Format mimetype="application/rData+SpatialPolygons" />
+                               <Format mimetype="application/x-zipped-shp" />
+                               <Format mimetype="application/shp" />
+                               <Format mimetype="application/img" />
+                               <Format mimetype="image/tiff" />
+                               <Format mimetype="image/geotiff" />
+                               <Format mimetype="application/geotiff" />
+                               <Format mimetype="application/dbase" />
+                               <Format mimetype="application/remap" />
+                               <Format mimetype="application/x-erdas-hfa" />
+                               <Format mimetype="application/x-netcdf" />
+                               <Format mimetype="application/netcdf" />
+                               <Format mimetype="application/dgn" />
+                               <Format mimetype="image/jpeg" />
+                               <Format mimetype="image/png" />
+                               <Format mimetype="application/x-geotiff" />
+                               <Format mimetype="text/plain" />
+                               <Format mimetype="application/pdf" />
+                               <Format mimetype="application/zip" />
+                               <Format mimetype="text/html" />
+                       </Generator>
+               </GeneratorList>
+       </Datahandlers>
+       <AlgorithmRepositoryList>
+               <Repository name="LocalAlgorithmRepository"
+                       className="org.n52.wps.server.LocalAlgorithmRepository" active="true">
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.JTSConvexHullAlgorithm</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.DummyTestClass</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.LongRunningDummyTestClass</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultipleComplexInAndOutputsDummyTestClass</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultiReferenceInputAlgorithm</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.MultiReferenceBinaryInputAlgorithm</Property>
+                       <Property name="Algorithm" active="true">org.n52.wps.server.algorithm.test.EchoProcess</Property>
+               </Repository>
+               <Repository name="UploadedAlgorithmRepository"
+                       className="org.n52.wps.server.UploadedAlgorithmRepository" active="false">
+               </Repository>
+               <Repository name="ServiceLoaderAlgorithmRepository"
+                       className="org.n52.wps.server.ServiceLoaderAlgorithmRepository" active="true">
+               </Repository>
+               <!--
+               <Repository name="MCProcessRepository" className="org.n52.wps.mc.MCProcessRepository" active="true">
+                       <Property name="REMOTE_REPOSITORY" active="false">http://141.30.100.178/gpfeed2/gpfeed.xml</Property>
+                       <Property name="LOCAL_REPOSITORY" active="true">D:\MCpackages</Property>
+               </Repository>
+               -->
+  </AlgorithmRepositoryList>
+       <RemoteRepositoryList />
+
+       <Server protocol="http" hostname="localhost" hostport="8080"
+               includeDataInputsInResponse="false" computationTimeoutMilliSeconds="5"
+               cacheCapabilites="false" webappPath="wps" repoReloadInterval="0" maxPoolSize="20" keepAliveSeconds="1000" maxQueuedTasks="100" minPoolSize="10" >
+               <!-- Setting to 'true' will enable filtering of responses documents.  Any server URL in
+             the response document will be replaced with the server URL used in the HTTP request. -->
+        <Property name="responseURLFilterEnabled" active="true">false</Property>
+               <Database>
+                       <!-- NOTE: database wipe is only implemented for the FlatFileDatabase (the default) -->
+                       <!-- enable database wiping base on values below -->
+                       <Property name="wipe.enabled" active="true">true</Property>
+                       <!-- scans database every 1 hour -->
+                       <Property name="wipe.period" active="true">PT1H</Property>
+                       <!-- deletes files older than 7 days -->
+                       <Property name="wipe.threshold" active="true">P7D</Property>
+               </Database>
+
+        <!--
+            POSTGRES Connector
+            ==================
+            Ensure that the postgres driver is available to the server during
+            launch. The server will fail to start if Postgres is active but the
+            driver is missing. However, if the driver exists and the database
+            cannot be connected to (unavailable, username/pass issue, etc), the
+            framework will fail-over to the Flatfile Database
+            jndiName or username/password: If jndiName exists, username
+            and password are not used.
+            saveResultsToDb: Setting to false will save results output to file
+            and put the URI link to the file in the database. Setting to true
+            stores the actual result output in the database (You probably don't
+            want this if you have large results).
+            JNDI Configuration:
+            <Database>
+                <Property active="true" name="databaseClass">org.n52.wps.server.database.PostgresDatabase</Property>
+                <Property active="true" name="jndiName">jndiname</Property>
+                <Property active="true" name="saveResultsToDb">false</Property>
+                <Property name="wipe.enabled" active="true">true</Property>
+                <Property name="wipe.period" active="true">PT1H</Property>
+                <Property name="wipe.threshold" active="true">P7D</Property>
+            </Database>
+            Direct connection configuration:
+            <Database>
+                Alternative connection method
+                <Property active="true" name="databaseName">postgres</Property>
+                <Property active="true" name="databasePath">//localhost:5432</Property>
+                <Property active="true" name="username">username</Property>
+                <Property active="true" name="password">password</Property>
+                <Property active="true" name="saveResultsToDb">false</Property>
+                <Property name="wipe.enabled" active="true">true</Property>
+                <Property name="wipe.period" active="true">PT1H</Property>
+                <Property name="wipe.threshold" active="true">P7D</Property>
+            </Database>
+-->
+
+       </Server>
+</WPSConfiguration>
\ No newline at end of file
diff --git a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityFactoryTest.java
new file mode 100644 (file)
index 0000000..4b137c6
--- /dev/null
@@ -0,0 +1,100 @@
+package org.apache.taverna.gis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNotSame;
+import static org.junit.Assert.assertTrue;
+
+import java.net.URI;
+import java.util.HashSet;
+import java.util.Set;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import org.apache.taverna.workflowmodel.impl.EditsImpl;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class GisActivityFactoryTest {
+
+       private ObjectNode configuration;
+
+       private GisActivityFactory activityFactory;
+
+       @Before
+       public void setUp() throws Exception {
+               configuration = JsonNodeFactory.instance.objectNode();
+               configuration.put("exampleString", "something");
+               configuration.put("exampleUri", "http://localhost:8080/myEndPoint");
+
+               activityFactory = new GisActivityFactory();
+               activityFactory.setEdits(new EditsImpl());
+       }
+
+       @Test
+       public void testCreateActivity() {
+               GisActivity activity = activityFactory.createActivity();
+               assertNotNull(activity);
+               assertNotSame(activity, activityFactory.createActivity());
+       }
+
+       @Test
+       public void testGetActivityURI() {
+               assertEquals(URI.create(GisActivity.ACTIVITY_TYPE), activityFactory.getActivityType());
+       }
+
+       @Test
+       public void testGetActivityConfigurationSchema() {
+               JsonNode configurationSchema = activityFactory.getActivityConfigurationSchema();
+               assertNotNull(configurationSchema);
+               assertTrue(configurationSchema.has("properties"));
+               JsonNode propertiesNode = configurationSchema.get("properties");
+               assertTrue(propertiesNode.has("exampleString"));
+               assertTrue(propertiesNode.has("exampleUri"));
+       }
+
+       @Test
+       public void testGetInputPorts() {
+               Set<String> expectedInputs = new HashSet<String>();
+               expectedInputs.add("firstInput");
+
+               Set<ActivityInputPort> inputPorts = activityFactory.getInputPorts(configuration);
+               assertEquals("Unexpected inputs", expectedInputs.size(), inputPorts.size());
+               for (ActivityInputPort inputPort : inputPorts) {
+                       assertTrue("Wrong input : " + inputPort.getName(), expectedInputs
+                                       .remove(inputPort.getName()));
+               }
+
+               ObjectNode specialConfiguration = JsonNodeFactory.instance.objectNode();
+               specialConfiguration.put("exampleString", "specialCase");
+               specialConfiguration.put("exampleUri", "http://localhost:8080/myEndPoint");
+
+               assertEquals("Unexpected inputs", 2, activityFactory.getInputPorts(specialConfiguration).size());
+       }
+
+       @Test
+       public void testGetOutputPorts() {
+               Set<String> expectedOutputs = new HashSet<String>();
+               expectedOutputs.add("simpleOutput");
+               expectedOutputs.add("moreOutputs");
+
+               Set<ActivityOutputPort> outputPorts = activityFactory.getOutputPorts(configuration);
+               assertEquals("Unexpected outputs", expectedOutputs.size(), outputPorts.size());
+               for (ActivityOutputPort outputPort : outputPorts) {
+                       assertTrue("Wrong output : " + outputPort.getName(),
+                                       expectedOutputs.remove(outputPort.getName()));
+               }
+
+               ObjectNode specialConfiguration = JsonNodeFactory.instance.objectNode();
+               specialConfiguration.put("exampleString", "specialCase");
+               specialConfiguration.put("exampleUri", "http://localhost:8080/myEndPoint");
+
+               assertEquals("Unexpected outputs", 3, activityFactory.getOutputPorts(specialConfiguration).size());
+       }
+
+}
diff --git a/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java b/apache-taverna-activity-gis-activity/src/test/java/org/apache/taverna/gis/GisActivityTest.java
new file mode 100644 (file)
index 0000000..1134774
--- /dev/null
@@ -0,0 +1,73 @@
+package org.apache.taverna.gis;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.net.URI;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.node.JsonNodeFactory;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
+import org.apache.taverna.activities.testutils.ActivityInvoker;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityConfigurationException;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityInputPort;
+import org.apache.taverna.workflowmodel.processor.activity.ActivityOutputPort;
+
+import org.junit.Before;
+import org.junit.Test;
+
+public class GisActivityTest {
+
+       private ObjectNode configuration;
+
+       private GisActivity activity = new GisActivity();
+
+       @Before
+       public void makeConfiguration() throws Exception {
+               configuration = JsonNodeFactory.instance.objectNode();
+               configuration.put("exampleString", "something");
+               configuration.put("exampleUri", "http://localhost:8080/myEndPoint");
+       }
+
+       @Test
+       public void configureActivity() throws Exception {
+               activity.configure(configuration);
+               assertTrue(configuration.equals(activity.getConfiguration()));
+       }
+
+       @Test(expected = ActivityConfigurationException.class)
+       public void invalidConfiguration() throws ActivityConfigurationException {
+               ObjectNode invalidBean = JsonNodeFactory.instance.objectNode();
+               invalidBean.put("exampleString", "invalidExample");
+               // Should throw ActivityConfigurationException
+               activity.configure(invalidBean);
+       }
+
+       @Test
+       public void executeAsynch() throws Exception {
+               activity.configure(configuration);
+
+               Map<String, Object> inputs = new HashMap<String, Object>();
+               inputs.put("firstInput", "hello");
+
+               Map<String, Class<?>> expectedOutputTypes = new HashMap<String, Class<?>>();
+               expectedOutputTypes.put("simpleOutput", String.class);
+               expectedOutputTypes.put("moreOutputs", String.class);
+
+               Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
+                               activity, inputs, expectedOutputTypes);
+
+               assertEquals("Unexpected outputs", 2, outputs.size());
+               assertEquals("simple", outputs.get("simpleOutput"));
+               assertEquals(Arrays.asList("Value 1", "Value 2"), outputs
+                               .get("moreOutputs"));
+
+       }
+
+}
diff --git a/apache-taverna-activity-gis-plugin/pom.xml b/apache-taverna-activity-gis-plugin/pom.xml
new file mode 100644 (file)
index 0000000..ebc2cd5
--- /dev/null
@@ -0,0 +1,28 @@
+<?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>org.apache.taverna.gis</groupId>
+               <artifactId>apache-taverna-activity-gis</artifactId>
+               <version>0.0.1-incubating.SNAPSHOT</version>
+       </parent>
+       <artifactId>apache-taverna-activity-gis-plugin</artifactId>
+       <packaging>taverna-plugin</packaging>
+       <name>Gis Taverna plugin</name>
+       <description>Description of Example Taverna plugin</description>
+       <dependencies>
+               <dependency>
+                       <groupId>${project.groupId}</groupId>
+                       <artifactId>apache-taverna-activity-gis-activity</artifactId>
+                       <version>0.0.1-incubating.SNAPSHOT</version>
+               </dependency>
+               <!-- Enable for Workbench integration
+               <dependency>
+                       <groupId>${project.groupId}</groupId>
+                       <artifactId>apache-taverna-activity-gis-activity-ui</artifactId>
+                       <version>0.0.1-incubating.SNAPSHOT</version>
+               </dependency>
+               -->
+       </dependencies>
+</project>
diff --git a/pom.xml b/pom.xml
index 14b5ca5..9c2ab12 100644 (file)
--- a/pom.xml
+++ b/pom.xml
@@ -1,63 +1,74 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
-   Licensed to the Apache Software Foundation (ASF) under one or more
-   contributor license agreements.  See the NOTICE file distributed with
-   this work for additional information regarding copyright ownership.
-   The ASF licenses this file to You under the Apache License, Version 2.0
-   (the "License"); you may not use this file except in compliance with
-   the License.  You may obtain a copy of the License at
+<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+       license agreements. See the NOTICE file distributed with this work for additional 
+       information regarding copyright ownership. The ASF licenses this file to 
+       You under the Apache License, Version 2.0 (the "License"); you may not use 
+       this file except in compliance with the License. You may obtain a copy of 
+       the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+       by applicable law or agreed to in writing, software distributed under the 
+       License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+       OF ANY KIND, either express or implied. See the License for the specific 
+       language governing permissions and limitations under the License. -->
+<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>org.apache.taverna</groupId>
+               <artifactId>apache-taverna-parent</artifactId>
+               <version>2-incubating</version>
+       </parent>
+       <groupId>org.apache.taverna.gis</groupId>
+       <artifactId>apache-taverna-plugin-gis</artifactId>
+       <version>0.0.1-incubating-SNAPSHOT</version>
+       <packaging>pom</packaging>
 
-       http://www.apache.org/licenses/LICENSE-2.0
-
-   Unless required by applicable law or agreed to in writing, software
-   distributed under the License is distributed on an "AS IS" BASIS,
-   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-   See the License for the specific language governing permissions and
-   limitations under the License.
--->
-<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>org.apache.taverna</groupId>
-    <artifactId>apache-taverna-parent</artifactId>
-    <version>2-incubating</version>
-  </parent>
-  <groupId>org.apache.taverna.gis</groupId>
-  <artifactId>apache-taverna-plugin-gis</artifactId>
-  <version>0.0.1-incubating-SNAPSHOT</version>
-  <packaging>pom</packaging>
-
-  <name>Apache Taverna Plugin GIS</name>
-  <description>
+       <name>Apache Taverna Plugin GIS</name>
+       <description>
        Taverna support for Geographical Information Systems, in particular
        the OGC activity.
   </description>
-  <properties>
-    <taverna.language.version>0.15.0-incubating</taverna.language.version>
-    <taverna.osgi.version>0.2.1-incubating</taverna.osgi.version>
-    <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
-  </properties>
+       <properties>
+               <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+               <taverna.language.version>0.15.1-incubating</taverna.language.version>
+               <taverna.osgi.version>0.2.1-incubating</taverna.osgi.version>
+               <taverna.engine.version>3.1.0-incubating</taverna.engine.version>
+               <taverna.workbench.version>3.1.0-incubating-SNAPSHOT</taverna.workbench.version>
+       </properties>
+
+       <scm>
+               <connection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis.git</connection>
+               <developerConnection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis.git</developerConnection>
+               <url>https://github.com/apache/incubator-taverna-plugin-gis</url>
+               <tag>HEAD</tag>
+       </scm>
 
-  <scm>
-    <connection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis.git</connection>
-    <developerConnection>scm:git:https://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-gis.git</developerConnection>
-    <url>https://github.com/apache/incubator-taverna-plugin-gis</url>
-    <tag>HEAD</tag>
-  </scm>
+       <repositories>
+               <repository>
+                       <id>apache.snapshots</id>
+                       <name>Apache Snapshot Repository</name>
+                       <url>http://repository.apache.org/snapshots</url>
+                       <releases>
+                               <enabled>false</enabled>
+                       </releases>
+               </repository>
+               <repository>
+                       <id>n52-releases</id>
+                       <name>52n Releases</name>
+                       <url>http://52north.org/maven/repo/releases</url>
+                       <releases>
+                               <enabled>true</enabled>
+                       </releases>
+                       <snapshots>
+                               <enabled>true</enabled>
+                       </snapshots>
+               </repository>
+       </repositories>
 
-  <repositories>
-    <repository>
-      <id>apache.snapshots</id>
-      <name>Apache Snapshot Repository</name>
-      <url>http://repository.apache.org/snapshots</url>
-      <releases>
-        <enabled>false</enabled>
-      </releases>
-    </repository>
-  </repositories>
+       <modules>
+               <module>apache-taverna-activity-gis-plugin</module>
+               <module>apache-taverna-activity-gis-activity</module>
+               <module>apache-taverna-activity-gis-activity-ui</module>
+               <module>taverna-gis-client</module>
+       </modules>
 
-  <modules>
-    <module>taverna-ogc-activity</module>
-    <module>taverna-ogc-activity-ui</module>
-  </modules>
 </project>
diff --git a/taverna-gis-client/pom.xml b/taverna-gis-client/pom.xml
new file mode 100644 (file)
index 0000000..909a17e
--- /dev/null
@@ -0,0 +1,17 @@
+<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/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+  <parent>
+    <groupId>org.apache.taverna.gis</groupId>
+    <artifactId>apache-taverna-activity-gis</artifactId>
+    <version>0.0.1-incubating.SNAPSHOT</version>
+  </parent>
+  <artifactId>taverna-gis-client</artifactId>
+  
+  <dependencies>
+               <dependency>
+                       <groupId>org.n52.wps</groupId>
+                       <artifactId>52n-wps-client-lib</artifactId>
+                       <version>3.3.1</version>
+               </dependency>
+  </dependencies>
+</project>
\ No newline at end of file