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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:43:53 UTC
[49/51] [partial] incubator-taverna-engine git commit: temporarily
empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-activity-test-utils/src/main/resources/inMemoryActivityTestsContext.xml
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diff --git a/taverna-activity-test-utils/src/main/resources/inMemoryActivityTestsContext.xml b/taverna-activity-test-utils/src/main/resources/inMemoryActivityTestsContext.xml
deleted file mode 100644
index 5268c9d..0000000
--- a/taverna-activity-test-utils/src/main/resources/inMemoryActivityTestsContext.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<!-- Context providing a full ReferenceService -->
-<beans xmlns="http://www.springframework.org/schema/beans"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:raven="http://taverna.sf.net/schema/artifact-support"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
- http://taverna.sf.net/schema/artifact-support
- http://taverna.sf.net/schema/artifact-support/artifact-support.xsd">
-
- <import resource="context-parts/raven_local.xml" />
- <!--
- <import resource="context-parts/hibernateprops_derby.xml" />
- <import resource="context-parts/dao_hibernate.xml" />
- -->
- <import resource="context-parts/dao_inmemory.xml" />
- <import resource="context-parts/componentservices.xml" />
- <import resource="context-parts/referenceservice.xml" />
-
- <!-- Load core extensions, needed for String to reference support -->
- <bean
- raven:artifact="net.sf.taverna.t2.core:reference-core-extensions:2.0.1-SNAPSHOT"
- raven:repository="raven.repository"
- class="net.sf.taverna.t2.reference.impl.core.LoadCoreExtensions">
- </bean>
-
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/pom.xml
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diff --git a/taverna-capability-api/pom.xml b/taverna-capability-api/pom.xml
deleted file mode 100644
index c0bfae5..0000000
--- a/taverna-capability-api/pom.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<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.engine</groupId>
- <artifactId>taverna-engine</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-capability-api</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna Platform Capability API</name>
- <dependencies>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-workflowmodel-api</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-api</artifactId>
- <version>${taverna.language.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson.version}</version>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityConfigurationException.java
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diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityConfigurationException.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityConfigurationException.java
deleted file mode 100644
index c9833e9..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityConfigurationException.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-/**
- * Thrown when an activity's configuration is incorrect.
- *
- * @author David Withers
- */
-public class ActivityConfigurationException extends ConfigurationException {
- private static final long serialVersionUID = 3132495676192826758L;
-
- public ActivityConfigurationException() {
- super();
- }
-
- public ActivityConfigurationException(String message) {
- super(message);
- }
-
- public ActivityConfigurationException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public ActivityConfigurationException(Throwable cause) {
- super(cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityNotFoundException.java
----------------------------------------------------------------------
diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityNotFoundException.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityNotFoundException.java
deleted file mode 100644
index 82a6e71..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityNotFoundException.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-/**
- * Thrown when an activity is not found.
- *
- * @author David Withers
- */
-public class ActivityNotFoundException extends Exception {
- private static final long serialVersionUID = 1232220199558615801L;
-
- public ActivityNotFoundException() {
- super();
- }
-
- public ActivityNotFoundException(String message) {
- super(message);
- }
-
- public ActivityNotFoundException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public ActivityNotFoundException(Throwable cause) {
- super(cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityService.java
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diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityService.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityService.java
deleted file mode 100644
index 8fd1619..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ActivityService.java
+++ /dev/null
@@ -1,126 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-import java.net.URI;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import uk.org.taverna.scufl2.api.port.InputActivityPort;
-import uk.org.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * Service for discovering available activities and the properties required to
- * configure the activities.
- *
- * @author David Withers
- */
-public interface ActivityService {
- /**
- * Returns the available activity types.
- *
- * @return the available activity types
- */
- Set<URI> getActivityTypes();
-
- /**
- * Returns true if and only if the activity type exists.
- *
- * @param uri
- * the activity type to check
- * @return whether the activity type exists
- */
- boolean activityExists(URI activityType);
-
- /**
- * Returns the JSON Schema for the configuration required by an activity.
- *
- * @param activityType
- * the activity type
- * @return the JSON Schema for the configuration required by an activity
- * @throws ActivityNotFoundException
- * if an activity cannot be found for the specified URI
- * @throws ActivityConfigurationException
- * if the JSON Schema cannot be created
- */
- JsonNode getActivityConfigurationSchema(URI activityType)
- throws ActivityNotFoundException, ActivityConfigurationException;
-
- /**
- * Returns the input ports that the activity type requires to be present in
- * order to execute with the specified configuration.
- * <p>
- * If the activity does not require any input port for the configuration
- * then an empty set is returned.
- *
- * @param configuration
- * the activity configuration
- * @throws ActivityNotFoundException
- * if the activity cannot be found
- * @throws ActivityConfigurationException
- * if the activity configuration is incorrect
- * @return the input ports that the activity requires to be present in order
- * to execute
- */
- Set<InputActivityPort> getActivityInputPorts(URI activityType,
- JsonNode configuration) throws ActivityNotFoundException,
- ActivityConfigurationException;
-
- /**
- * Returns the output ports that the activity type requires to be present in
- * order to execute with the specified configuration.
- * <p>
- * If the activity type does not require any output ports for the
- * configuration then an empty set is returned.
- *
- * @param configuration
- * the activity configuration
- * @throws ActivityNotFoundException
- * if the activity cannot be found
- * @throws ActivityConfigurationException
- * if the activity configuration is incorrect
- * @return the output ports that the activity requires to be present in
- * order to execute
- */
- Set<OutputActivityPort> getActivityOutputPorts(URI activityType,
- JsonNode configuration) throws ActivityNotFoundException,
- ActivityConfigurationException;
-
- /**
- * Returns the activity for the specified activity type. If configuration is
- * not null the returned activity will be configured.
- *
- * @param activityType
- * the activity type
- * @param configuration
- * the configuration for the activity, can be <code>null</code>
- * @return the activity for the specified activityType
- * @throws ActivityNotFoundException
- * if an activity cannot be found for the specified activity
- * type
- * @throws ActivityConfigurationException
- * if the configuration is not valid
- */
- Activity<?> createActivity(URI activityType, JsonNode configuration)
- throws ActivityNotFoundException, ActivityConfigurationException;
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ConfigurationException.java
----------------------------------------------------------------------
diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ConfigurationException.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ConfigurationException.java
deleted file mode 100644
index be0e8a5..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/ConfigurationException.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-/**
- * Thrown when a {@link uk.org.taverna.scufl2.api.common.Configurable
- * Configurable} cannot be configured by a
- * {@link uk.org.taverna.scufl2.api.configurations.Configuration Configuration}.
- *
- * @author David Withers
- */
-public class ConfigurationException extends Exception {
- private static final long serialVersionUID = -6129960388197785712L;
-
- public ConfigurationException() {
- super();
- }
-
- public ConfigurationException(String message) {
- super(message);
- }
-
- public ConfigurationException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public ConfigurationException(Throwable cause) {
- super(cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerConfigurationException.java
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diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerConfigurationException.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerConfigurationException.java
deleted file mode 100644
index 824df29..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerConfigurationException.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-/**
- * Thrown when a dispatch layer's configuration is incorrect.
- *
- * @author David Withers
- */
-public class DispatchLayerConfigurationException extends ConfigurationException {
- private static final long serialVersionUID = -6180865500734235308L;
-
- public DispatchLayerConfigurationException() {
- super();
- }
-
- public DispatchLayerConfigurationException(String message) {
- super(message);
- }
-
- public DispatchLayerConfigurationException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public DispatchLayerConfigurationException(Throwable cause) {
- super(cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerNotFoundException.java
----------------------------------------------------------------------
diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerNotFoundException.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerNotFoundException.java
deleted file mode 100644
index 7492b61..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerNotFoundException.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-/**
- * Thrown when a dispatch layer is not found.
- *
- * @author David Withers
- */
-public class DispatchLayerNotFoundException extends Exception {
- private static final long serialVersionUID = -7227237239711803139L;
-
- public DispatchLayerNotFoundException() {
- super();
- }
-
- public DispatchLayerNotFoundException(String message) {
- super(message);
- }
-
- public DispatchLayerNotFoundException(String message, Throwable cause) {
- super(message, cause);
- }
-
- public DispatchLayerNotFoundException(Throwable cause) {
- super(cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerService.java
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diff --git a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerService.java b/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerService.java
deleted file mode 100644
index 978b1b5..0000000
--- a/taverna-capability-api/src/main/java/uk/org/taverna/platform/capability/api/DispatchLayerService.java
+++ /dev/null
@@ -1,90 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.api;
-
-import java.net.URI;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayer;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * Service for discovering available dispatch layers and the properties required
- * to configure the layers.
- *
- * @author David Withers
- */
-public interface DispatchLayerService {
- /**
- * Returns the available dispatch layer types.
- *
- * @return a the available dispatch layer types
- */
- Set<URI> getDispatchLayerTypes();
-
- /**
- * Returns true iff a dispatch layer exists for the specified URI.
- *
- * @param dispatchLayerType
- * the dispatch layer type to check
- * @return true if a dispatch layer exists for the specified URI
- */
- boolean dispatchLayerExists(URI dispatchLayerType);
-
- /**
- * Returns the JSON Schema for the configuration required by a dispatch
- * layer.
- *
- * @param activityType
- * the activity type
- * @return the JSON Schema for the configuration required by a dispatch
- * layer
- * @throws DispatchLayerNotFoundException
- * if a dispatch layer cannot be found for the specified URI
- * @throws DispatchLayerConfigurationException
- * if the JSON Schema cannot be created
- */
- JsonNode getDispatchLayerConfigurationSchema(URI dispatchLayerType)
- throws DispatchLayerNotFoundException,
- DispatchLayerConfigurationException;
-
- /**
- * Returns the dispatch layer for the specified URI.
- *
- * If configuration is not null the returned dispatch layer will be
- * configured.
- *
- * @param uri
- * a URI that identifies a dispatch layer
- * @param configuration
- * the configuration for the dispatch layer, can be
- * <code>null</code>
- * @return the dispatch layer for the specified URI
- * @throws DispatchLayerNotFoundException
- * if a dispatch layer cannot be found for the specified URI
- * @throws DispatchLayerConfigurationException
- * if the configuration is not valid
- */
- DispatchLayer<?> createDispatchLayer(URI uri, JsonNode configuration)
- throws DispatchLayerNotFoundException,
- DispatchLayerConfigurationException;
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/pom.xml b/taverna-capability-impl/pom.xml
deleted file mode 100644
index 14c6212..0000000
--- a/taverna-capability-impl/pom.xml
+++ /dev/null
@@ -1,59 +0,0 @@
-<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.engine</groupId>
- <artifactId>taverna-engine</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-capability-impl</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna Platform Capability Implementation</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <configuration>
- <instructions>
- <Import-Package>uk.org.taverna.platform.capability.api;provide:=true,*</Import-Package>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-capability-api</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-workflowmodel-api</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.language</groupId>
- <artifactId>taverna-scufl2-api</artifactId>
- <version>${taverna.language.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>${jdom.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/activity/impl/ActivityServiceImpl.java
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/activity/impl/ActivityServiceImpl.java b/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/activity/impl/ActivityServiceImpl.java
deleted file mode 100644
index 91f910c..0000000
--- a/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/activity/impl/ActivityServiceImpl.java
+++ /dev/null
@@ -1,140 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2010 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.activity.impl;
-
-import java.net.URI;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-import uk.org.taverna.platform.capability.api.ActivityConfigurationException;
-import uk.org.taverna.platform.capability.api.ActivityNotFoundException;
-import uk.org.taverna.platform.capability.api.ActivityService;
-import uk.org.taverna.scufl2.api.port.InputActivityPort;
-import uk.org.taverna.scufl2.api.port.OutputActivityPort;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class ActivityServiceImpl implements ActivityService {
- private List<ActivityFactory> activityFactories;
-
- @Override
- public Set<URI> getActivityTypes() {
- Set<URI> activityTypes = new HashSet<>();
- for (ActivityFactory activityFactory : activityFactories)
- activityTypes.add(activityFactory.getActivityType());
- return activityTypes;
- }
-
- @Override
- public boolean activityExists(URI uri) {
- for (ActivityFactory activityFactory : activityFactories)
- if (activityFactory.getActivityType().equals(uri))
- return true;
- return false;
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema(URI activityType)
- throws ActivityNotFoundException {
- ActivityFactory factory = getActivityFactory(activityType);
- return factory.getActivityConfigurationSchema();
- }
-
- @Override
- public Activity<?> createActivity(URI activityType, JsonNode configuration)
- throws ActivityNotFoundException, ActivityConfigurationException {
- ActivityFactory factory = getActivityFactory(activityType);
- @SuppressWarnings("unchecked")
- Activity<JsonNode> activity = (Activity<JsonNode>) factory
- .createActivity();
- try {
- if (configuration != null)
- activity.configure(configuration);
- } catch (net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException e) {
- throw new ActivityConfigurationException(e);
- }
- return activity;
- }
-
- @Override
- public Set<InputActivityPort> getActivityInputPorts(URI activityType,
- JsonNode configuration) throws ActivityNotFoundException,
- ActivityConfigurationException {
- Set<InputActivityPort> inputPorts = new HashSet<>();
- try {
- for (ActivityInputPort port : getActivityFactory(activityType)
- .getInputPorts(configuration)) {
- InputActivityPort inputActivityPort = new InputActivityPort();
- inputActivityPort.setName(port.getName());
- inputActivityPort.setDepth(port.getDepth());
- inputPorts.add(inputActivityPort);
- }
- return inputPorts;
- } catch (net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException e) {
- throw new ActivityConfigurationException(e);
- }
- }
-
- @Override
- public Set<OutputActivityPort> getActivityOutputPorts(URI activityType,
- JsonNode configuration) throws ActivityNotFoundException,
- ActivityConfigurationException {
- Set<OutputActivityPort> outputPorts = new HashSet<>();
- try {
- for (ActivityOutputPort port : getActivityFactory(activityType)
- .getOutputPorts(configuration)) {
- OutputActivityPort outputActivityPort = new OutputActivityPort();
- outputActivityPort.setName(port.getName());
- outputActivityPort.setDepth(port.getDepth());
- outputActivityPort.setGranularDepth(port.getGranularDepth());
- outputPorts.add(outputActivityPort);
- }
- } catch (net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException e) {
- throw new ActivityConfigurationException(e);
- }
- return outputPorts;
- }
-
- /**
- * Sets the list of available <code>ActivityFactory</code>s. In a production
- * environment this should be set by Spring DM.
- *
- * @param activityFactories
- * the list of available <code>ActivityFactory</code>s
- */
- public void setActivityFactories(List<ActivityFactory> activityFactories) {
- this.activityFactories = activityFactories;
- }
-
- private ActivityFactory getActivityFactory(URI activityType)
- throws ActivityNotFoundException {
- for (ActivityFactory activityFactory : activityFactories)
- if (activityFactory.getActivityType().equals(activityType))
- return activityFactory;
- throw new ActivityNotFoundException("Could not find an activity for "
- + activityType);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/dispatch/impl/DispatchLayerServiceImpl.java
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/dispatch/impl/DispatchLayerServiceImpl.java b/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/dispatch/impl/DispatchLayerServiceImpl.java
deleted file mode 100644
index 0de59b1..0000000
--- a/taverna-capability-impl/src/main/java/uk/org/taverna/platform/capability/dispatch/impl/DispatchLayerServiceImpl.java
+++ /dev/null
@@ -1,112 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package uk.org.taverna.platform.capability.dispatch.impl;
-
-import java.net.URI;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.logging.Logger;
-
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayer;
-import net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayerFactory;
-import uk.org.taverna.platform.capability.api.DispatchLayerConfigurationException;
-import uk.org.taverna.platform.capability.api.DispatchLayerNotFoundException;
-import uk.org.taverna.platform.capability.api.DispatchLayerService;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * @author David Withers
- */
-public class DispatchLayerServiceImpl implements DispatchLayerService {
- @SuppressWarnings("unused")
- private static Logger logger = Logger
- .getLogger(DispatchLayerServiceImpl.class.getName());
-
- private List<DispatchLayerFactory> dispatchLayerFactories;
-
- @Override
- public Set<URI> getDispatchLayerTypes() {
- Set<URI> dispatchLayerTypes = new HashSet<>();
- for (DispatchLayerFactory dispatchLayerFactory : dispatchLayerFactories)
- dispatchLayerTypes.addAll(dispatchLayerFactory
- .getDispatchLayerTypes());
- return dispatchLayerTypes;
- }
-
- @Override
- public boolean dispatchLayerExists(URI dispatchLayerType) {
- for (DispatchLayerFactory dispatchLayerFactory : dispatchLayerFactories)
- if (dispatchLayerFactory.getDispatchLayerTypes().contains(
- dispatchLayerType))
- return true;
- return false;
- }
-
- @Override
- public JsonNode getDispatchLayerConfigurationSchema(URI dispatchLayerType)
- throws DispatchLayerNotFoundException {
- DispatchLayerFactory factory = getDispatchLayerFactory(dispatchLayerType);
- return factory.getDispatchLayerConfigurationSchema(dispatchLayerType);
- }
-
- @Override
- public DispatchLayer<?> createDispatchLayer(URI dispatchLayerType,
- JsonNode configuration) throws DispatchLayerNotFoundException,
- DispatchLayerConfigurationException {
- DispatchLayerFactory factory = getDispatchLayerFactory(dispatchLayerType);
- @SuppressWarnings("unchecked")
- DispatchLayer<JsonNode> dispatchLayer = (DispatchLayer<JsonNode>) factory
- .createDispatchLayer(dispatchLayerType);
-
- try {
- if (configuration != null)
- dispatchLayer.configure(configuration);
- } catch (net.sf.taverna.t2.workflowmodel.ConfigurationException e) {
- throw new DispatchLayerConfigurationException(e);
- }
- return dispatchLayer;
- }
-
- /**
- * Sets the list of available <code>DispatchLayerFactory</code>s.
- *
- * In a production environment this should be set by Spring DM.
- *
- * @param dispatchLayerFactories
- * the list of available <code>DispatchLayerFactory</code>s
- */
- public void setDispatchLayerFactories(
- List<DispatchLayerFactory> dispatchLayerFactories) {
- this.dispatchLayerFactories = dispatchLayerFactories;
- }
-
- private DispatchLayerFactory getDispatchLayerFactory(URI dispatchLayerType)
- throws DispatchLayerNotFoundException {
- for (DispatchLayerFactory dispatchLayerFactory : dispatchLayerFactories)
- if (dispatchLayerFactory.getDispatchLayerTypes().contains(
- dispatchLayerType))
- return dispatchLayerFactory;
- throw new DispatchLayerNotFoundException(
- "Could not find a dispatch layer for " + dispatchLayerType);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context-osgi.xml b/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context-osgi.xml
deleted file mode 100644
index 8aa5619..0000000
--- a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context-osgi.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="activityService" interface="uk.org.taverna.platform.capability.api.ActivityService" />
-
- <list id="activityFactories" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" cardinality="0..N" />
-
- <service ref="dispatchLayerService" interface="uk.org.taverna.platform.capability.api.DispatchLayerService" />
-
- <list id="dispatchLayerFactories" interface="net.sf.taverna.t2.workflowmodel.processor.dispatch.DispatchLayerFactory" cardinality="0..N" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
----------------------------------------------------------------------
diff --git a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml b/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
deleted file mode 100644
index fad027e..0000000
--- a/taverna-capability-impl/src/main/resources/META-INF/spring/taverna-capability-context.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="activityService" class="uk.org.taverna.platform.capability.activity.impl.ActivityServiceImpl">
- <property name="activityFactories" ref="activityFactories" />
- </bean>
-
- <bean id="dispatchLayerService" class="uk.org.taverna.platform.capability.dispatch.impl.DispatchLayerServiceImpl">
- <property name="dispatchLayerFactories" ref="dispatchLayerFactories" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-credential-manager-impl/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-credential-manager-impl/pom.xml b/taverna-credential-manager-impl/pom.xml
deleted file mode 100644
index ab1536c..0000000
--- a/taverna-credential-manager-impl/pom.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-<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.engine</groupId>
- <artifactId>taverna-engine</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
- </parent>
- <artifactId>taverna-credential-manager-impl</artifactId>
- <packaging>bundle</packaging>
- <name>Apache Taverna Credential Manager Implementation</name>
-
- <profiles>
- <profile>
- <id>strongEncryption</id>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-failsafe-plugin</artifactId>
- <version>2.9</version>
- <configuration>
- <forkMode>always</forkMode>
- </configuration>
- <executions>
- <execution>
- <id>integration-test</id>
- <goals>
- <goal>integration-test</goal>
- </goals>
- </execution>
- <execution>
- <id>verify</id>
- <goals>
- <goal>verify</goal>
- </goals>
- </execution>
- </executions>
- </plugin>
- </plugins>
- </build>
- </profile>
- </profiles>
-
- <dependencies>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-credential-manager</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.taverna.osgi</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.osgi.version}</version>
- </dependency>
- <dependency>
- <groupId>${project.parent.groupId}</groupId>
- <artifactId>taverna-observer</artifactId>
- <version>${project.parent.version}</version>
- </dependency>
- <dependency>
- <groupId>org.bouncycastle</groupId>
- <artifactId>bcprov-jdk16</artifactId>
- <version>${bcprov.jdk16.version}</version>
- </dependency>
- <dependency>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
- <dependency>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- <version>${commons.io.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.mortbay.jetty</groupId>
- <artifactId>jetty</artifactId>
- <version>${jetty.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-engine/blob/3ecb1291/taverna-credential-manager-impl/src/main/java/net/sf/taverna/t2/security/credentialmanager/impl/CredentialManagerAuthenticator.java
----------------------------------------------------------------------
diff --git a/taverna-credential-manager-impl/src/main/java/net/sf/taverna/t2/security/credentialmanager/impl/CredentialManagerAuthenticator.java b/taverna-credential-manager-impl/src/main/java/net/sf/taverna/t2/security/credentialmanager/impl/CredentialManagerAuthenticator.java
deleted file mode 100644
index 3a0193e..0000000
--- a/taverna-credential-manager-impl/src/main/java/net/sf/taverna/t2/security/credentialmanager/impl/CredentialManagerAuthenticator.java
+++ /dev/null
@@ -1,112 +0,0 @@
-package net.sf.taverna.t2.security.credentialmanager.impl;
-
-import static java.net.Authenticator.RequestorType.PROXY;
-
-import java.net.Authenticator;
-import java.net.PasswordAuthentication;
-import java.net.URI;
-import java.net.URISyntaxException;
-import net.sf.taverna.t2.security.credentialmanager.CMException;
-import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
-import net.sf.taverna.t2.security.credentialmanager.UsernamePassword;
-
-import org.apache.log4j.Logger;
-
-/**
- * Credential Manager backed {@link Authenticator}.
- * <p>
- * Initialize by using: <code>
- * Authenticator.setDefault(new CredentialManagerAuthenticator());
- * </code>
- * <p>
- * Special case included for proxy authentication.
- *
- * @author Stian Soiland-Reyes
- *
- */
-public class CredentialManagerAuthenticator extends Authenticator {
- private Logger logger;
- private CredentialManager credManager;
-
- public CredentialManagerAuthenticator(CredentialManager credManager) {
- logger = Logger.getLogger(CredentialManagerAuthenticator.class);
- setCredentialManager(credManager);
- }
-
- public void setCredentialManager(CredentialManager credManager) {
- this.credManager = credManager;
- }
-
- @Override
- protected PasswordAuthentication getPasswordAuthentication() {
- if (getRequestorType().equals(PROXY)) {
- String password = System.getProperty("http.proxyPassword");
- String username = System.getProperty("http.proxyUser");
- if (username == null || password == null)
- // No proxy authentication set
- return null;
-
- return new PasswordAuthentication(username, password.toCharArray());
- }
-
- URI uri;
- if (getRequestingURL() != null) {
- try {
- uri = getRequestingURL().toURI();
- } catch (URISyntaxException e) {
- logger.warn("Unsupported request (invalid URL) for "
- + getRequestingURL());
- return null;
- }
- } else {
- // Construct an URI of socket://hostname:port
- String host = getRequestingHost();
- if (host == null)
- // Use IP address
- host = getRequestingSite().getHostAddress();
- int port = getRequestingPort();
- if (host == null || port < 0) {
- logger.warn("Unsupported request for " + getRequestingScheme()
- + " " + getRequestingSite());
- return null;
- }
- uri = URI.create("socket://" + host + ":" + port);
- }
-
- if (credManager == null) {
- logger.warn("No Credential Manager");
- return null;
- }
- boolean usePathRecursion = false;
- String realm = getRequestingPrompt();
- if (getRequestingScheme().equals("basic")
- || getRequestingScheme().equals("digest")) {
- usePathRecursion = true;
- if (realm != null && realm.length() > 0)
- try {
- uri = DistinguishedNameParserImpl.resolveUriFragment(uri, realm);
- } catch (URISyntaxException e) {
- logger.warn("Could not URI-encode fragment for realm: "
- + realm);
- }
- }
-
- UsernamePassword usernameAndPassword;
- try {
- usernameAndPassword = credManager.getUsernameAndPasswordForService(uri,
- usePathRecursion, realm);
- } catch (CMException e) {
- logger.warn("Could not get username and password for " + uri, e);
- return null;
- }
- if (usernameAndPassword == null) {
- logger.warn("No username/password found for " + uri);
- return null;
- }
- PasswordAuthentication pwAuth = new PasswordAuthentication(
- usernameAndPassword.getUsername(), usernameAndPassword
- .getPassword());
- usernameAndPassword.resetPassword();
- return pwAuth;
- }
-}