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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 16:37:22 UTC
[22/49] incubator-taverna-server git commit: taverna-* module names
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-execution-delegate/src/test/java/SerializationTest.java
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diff --git a/taverna-server-execution-delegate/src/test/java/SerializationTest.java b/taverna-server-execution-delegate/src/test/java/SerializationTest.java
new file mode 100644
index 0000000..c4bf0b9
--- /dev/null
+++ b/taverna-server-execution-delegate/src/test/java/SerializationTest.java
@@ -0,0 +1,54 @@
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.io.StringWriter;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.SchemaOutputResolver;
+import javax.xml.transform.Result;
+import javax.xml.transform.stream.StreamResult;
+
+import org.junit.Before;
+import org.junit.Test;
+import org.taverna.server.execution_delegate.RemoteExecution.WorkflowReportDocument;
+
+public class SerializationTest {
+ private static final boolean PRINT = true;
+ SchemaOutputResolver sink;
+ StringWriter schema;
+
+ String schema() {
+ return schema.toString();
+ }
+
+ @Before
+ public void init() {
+ schema = new StringWriter();
+ sink = new SchemaOutputResolver() {
+ @Override
+ public Result createOutput(String namespaceUri,
+ String suggestedFileName) throws IOException {
+ StreamResult sr = new StreamResult(schema);
+ sr.setSystemId("/dev/null");
+ return sr;
+ }
+ };
+ assertEquals("", schema());
+ }
+
+ @Test
+ public void testSchemaGeneration() throws JAXBException, IOException {
+ JAXBContext.newInstance(WorkflowReportDocument.class).generateSchema(
+ sink);
+ assertFalse("generated schema must be non-empty", schema().isEmpty());
+ assertTrue(
+ "generated schema must define workflowReport element",
+ schema().contains(
+ "<xs:element name=\"workflowReport\" type=\"WorkflowReport\"/>\n"));
+ if (PRINT)
+ System.out.print(schema());
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/.gitignore
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diff --git a/taverna-server-port-description/.gitignore b/taverna-server-port-description/.gitignore
new file mode 100644
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+++ b/taverna-server-port-description/.gitignore
@@ -0,0 +1 @@
+/target
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/pom.xml
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diff --git a/taverna-server-port-description/pom.xml b/taverna-server-port-description/pom.xml
new file mode 100644
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--- /dev/null
+++ b/taverna-server-port-description/pom.xml
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+<?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
+
+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.server</groupId>
+ <artifactId>taverna-server</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-server-port-description</artifactId>
+ <name>Apache Taverna Server Workflow Port Descriptor Types</name>
+ <description>The structural types used to describe ports on workflows, as exported by Taverna Server.</description>
+
+ <properties>
+ <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+ </properties>
+ <build>
+ <pluginManagement>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-eclipse-plugin</artifactId>
+ <configuration>
+ <projectNameTemplate>[artifactId]-[version]</projectNameTemplate>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbsentValue.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbsentValue.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbsentValue.java
new file mode 100644
index 0000000..2ea392f
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbsentValue.java
@@ -0,0 +1,13 @@
+/*
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(name = "AbsentValue")
+public class AbsentValue extends AbstractValue {
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPort.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPort.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPort.java
new file mode 100644
index 0000000..e57c4f9
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPort.java
@@ -0,0 +1,26 @@
+/*
+ * Copyright (C) 2011-2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+
+import org.taverna.server.port_description.utils.IntAdapter;
+
+@XmlType(name = "Port")
+public class AbstractPort {
+ @XmlID
+ @XmlAttribute(required = true)
+ public String name;
+
+ @XmlAttribute
+ @XmlSchemaType(name = "int")
+ @XmlJavaTypeAdapter(IntAdapter.class)
+ public Integer depth;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPortDescription.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPortDescription.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPortDescription.java
new file mode 100644
index 0000000..7c3fe9a
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractPortDescription.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import java.net.URI;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(name = "PortDescription")
+public abstract class AbstractPortDescription {
+ @XmlAttribute
+ public String workflowId;
+ @XmlAttribute
+ @XmlSchemaType(name = "anyURI")
+ public URI workflowRun;
+ @XmlAttribute
+ public String workflowRunId;
+
+ public void fillInBaseData(String docId, String runId, URI runUrl) {
+ this.workflowId = docId;
+ this.workflowRun = runUrl;
+ this.workflowRunId = runId;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractValue.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractValue.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractValue.java
new file mode 100644
index 0000000..47232c2
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/AbstractValue.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import static org.taverna.server.port_description.Namespaces.XLINK;
+
+import java.net.URI;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(name = "Value")
+@XmlSeeAlso( { ErrorValue.class, LeafValue.class, ListValue.class, AbsentValue.class })
+public abstract class AbstractValue {
+ @XmlAttribute(namespace = XLINK)
+ @XmlSchemaType(name = "anyURI")
+ public URI href;
+
+ public void setAddress(URI uri, String localAddress) {
+ if (uri.getPath().endsWith("/")) {
+ href = URI.create(uri + "wd/out/" + localAddress);
+ } else {
+ href = URI.create(uri + "/wd/out/" + localAddress);
+ }
+ //about = "out/" + localAddress;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ErrorValue.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ErrorValue.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ErrorValue.java
new file mode 100644
index 0000000..0bb07b4
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ErrorValue.java
@@ -0,0 +1,25 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+
+import org.taverna.server.port_description.utils.IntAdapter;
+
+@XmlType(name = "ErrorValue")
+public class ErrorValue extends AbstractValue {
+ @XmlAttribute
+ @XmlSchemaType(name = "int")
+ @XmlJavaTypeAdapter(IntAdapter.class)
+ public Integer depth;
+ @XmlAttribute(name = "errorFile")
+ public String fileName;
+ @XmlAttribute(name = "errorByteLength")
+ public Long byteLength;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/InputDescription.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/InputDescription.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/InputDescription.java
new file mode 100644
index 0000000..60b9353
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/InputDescription.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import static org.taverna.server.port_description.Namespaces.XLINK;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+
+/**
+ * A description of the inputs of a workflow run, as they are currently known
+ * about.
+ *
+ * @author Donal Fellows.
+ */
+@XmlRootElement
+public class InputDescription extends AbstractPortDescription {
+ @XmlElement
+ public List<InputPort> input = new ArrayList<>();
+
+ @XmlType(name = "InputPort")
+ public static class InputPort extends AbstractPort {
+ @XmlAttribute(namespace = XLINK)
+ @XmlSchemaType(name = "anyURI")
+ public URI href;
+ }
+
+ /**
+ * Add an input port to the list of ports.
+ *
+ * @param name
+ * The name of the port to add.
+ * @return The port (so that its details may be set);
+ */
+ public InputPort addPort(String name) {
+ InputPort p = new InputPort();
+ p.name = name;
+ input.add(p);
+ return p;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/LeafValue.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/LeafValue.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/LeafValue.java
new file mode 100644
index 0000000..052c0ef
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/LeafValue.java
@@ -0,0 +1,19 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+@XmlType(name = "LeafValue")
+public class LeafValue extends AbstractValue {
+ @XmlAttribute(name = "contentFile")
+ public String fileName;
+ @XmlAttribute(name = "contentType")
+ public String contentType;
+ @XmlAttribute(name = "contentByteLength")
+ public Long byteLength;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ListValue.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ListValue.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ListValue.java
new file mode 100644
index 0000000..b14cdf1
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+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/ListValue.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+
+import org.taverna.server.port_description.utils.IntAdapter;
+
+@XmlType(name = "ListValue")
+public class ListValue extends AbstractValue {
+ @XmlAttribute
+ @XmlSchemaType(name = "int")
+ @XmlJavaTypeAdapter(IntAdapter.class)
+ public Integer length;
+ @XmlElements({
+ @XmlElement(name = "value", type = LeafValue.class, nillable = false),
+ @XmlElement(name = "list", type = ListValue.class, nillable = false),
+ @XmlElement(name = "error", type = ErrorValue.class, nillable = false),
+ @XmlElement(name = "absent", type = AbsentValue.class, nillable = false) })
+ public List<AbstractValue> contents = new ArrayList<>();
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/Namespaces.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/Namespaces.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/Namespaces.java
new file mode 100644
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--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/Namespaces.java
@@ -0,0 +1,12 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+public interface Namespaces {
+ static final String DATA = "http://ns.taverna.org.uk/2010/port/";
+ static final String RUN = "http://ns.taverna.org.uk/2010/run/";
+ static final String XLINK = "http://www.w3.org/1999/xlink";
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/OutputDescription.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/OutputDescription.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/OutputDescription.java
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--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/OutputDescription.java
@@ -0,0 +1,52 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlElements;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+/**
+ * A description of the outputs of a workflow run, as they are currently known
+ * about.
+ *
+ * @author Donal Fellows
+ */
+@XmlRootElement(name = "workflowOutputs")
+public class OutputDescription extends AbstractPortDescription {
+ private static final AbsentValue ABSENT_VALUE = new AbsentValue();
+ @XmlElement(name = "output")
+ public List<OutputPort> ports = new ArrayList<>();
+
+ @XmlType(name = "OutputPort")
+ public static class OutputPort extends AbstractPort {
+ @XmlElements({
+ @XmlElement(name = "value", type = LeafValue.class, nillable = false, required = true),
+ @XmlElement(name = "list", type = ListValue.class, nillable = false, required = true),
+ @XmlElement(name = "error", type = ErrorValue.class, nillable = false, required = true),
+ @XmlElement(name = "absent", type = AbsentValue.class, nillable = false, required = true) })
+ public AbstractValue output;
+ }
+
+ /**
+ * Add an output port to the list of ports.
+ *
+ * @param name
+ * The name of the port to add.
+ * @return The port (so that its value may be set);
+ */
+ public OutputPort addPort(String name) {
+ OutputPort p = new OutputPort();
+ p.name = name;
+ p.output = ABSENT_VALUE;
+ ports.add(p);
+ return p;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/package-info.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/package-info.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/package-info.java
new file mode 100644
index 0000000..b1ac2c6
--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/package-info.java
@@ -0,0 +1,19 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+@XmlSchema(namespace = DATA, elementFormDefault = QUALIFIED, attributeFormDefault = QUALIFIED, xmlns = {
+ @XmlNs(prefix = "port", namespaceURI = DATA),
+ @XmlNs(prefix = "xlink", namespaceURI = XLINK),
+ @XmlNs(prefix = "run", namespaceURI = RUN) })
+package org.taverna.server.port_description;
+
+import static javax.xml.bind.annotation.XmlNsForm.QUALIFIED;
+import static org.taverna.server.port_description.Namespaces.DATA;
+import static org.taverna.server.port_description.Namespaces.RUN;
+import static org.taverna.server.port_description.Namespaces.XLINK;
+
+import javax.xml.bind.annotation.XmlNs;
+import javax.xml.bind.annotation.XmlSchema;
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/main/java/org/taverna/server/port_description/utils/IntAdapter.java
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diff --git a/taverna-server-port-description/src/main/java/org/taverna/server/port_description/utils/IntAdapter.java b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/utils/IntAdapter.java
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--- /dev/null
+++ b/taverna-server-port-description/src/main/java/org/taverna/server/port_description/utils/IntAdapter.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright (C) 2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.port_description.utils;
+
+import static javax.xml.bind.DatatypeConverter.parseInt;
+import static javax.xml.bind.DatatypeConverter.printInt;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+
+/**
+ * A type conversion utility for use with JAXB.
+ *
+ * @author Donal Fellows
+ */
+public class IntAdapter extends XmlAdapter<String, Integer> {
+ @Override
+ public String marshal(Integer value) throws Exception {
+ if (value == null)
+ return null;
+ return printInt(value);
+ }
+
+ @Override
+ public Integer unmarshal(String value) throws Exception {
+ if (value == null)
+ return null;
+ return parseInt(value);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-port-description/src/test/java/org/taverna/server/port_description/JaxbSanityTest.java
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diff --git a/taverna-server-port-description/src/test/java/org/taverna/server/port_description/JaxbSanityTest.java b/taverna-server-port-description/src/test/java/org/taverna/server/port_description/JaxbSanityTest.java
new file mode 100644
index 0000000..c952ec2
--- /dev/null
+++ b/taverna-server-port-description/src/test/java/org/taverna/server/port_description/JaxbSanityTest.java
@@ -0,0 +1,98 @@
+package org.taverna.server.port_description;
+
+import java.io.IOException;
+import java.io.StringWriter;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.SchemaOutputResolver;
+import javax.xml.transform.Result;
+import javax.xml.transform.stream.StreamResult;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+/**
+ * This test file ensures that the JAXB bindings will work once deployed instead
+ * of mysteriously failing in service.
+ *
+ * @author Donal Fellows
+ */
+public class JaxbSanityTest {
+ SchemaOutputResolver sink;
+ StringWriter schema;
+
+ String schema() {
+ return schema.toString();
+ }
+
+ private String schemaTest(Class<?>... classes) throws IOException, JAXBException {
+ Assert.assertTrue(schema().isEmpty());
+ JAXBContext.newInstance(classes).generateSchema(sink);
+ Assert.assertFalse(schema().isEmpty());
+ return schema();
+ }
+
+ @Before
+ public void init() {
+ schema = new StringWriter();
+ sink = new SchemaOutputResolver() {
+ @Override
+ public Result createOutput(String namespaceUri,
+ String suggestedFileName) throws IOException {
+ StreamResult sr = new StreamResult(schema);
+ sr.setSystemId("/dev/null");
+ return sr;
+ }
+ };
+ }
+
+ @Test
+ public void testJAXBForInput() throws Exception {
+ schemaTest(InputDescription.InputPort.class);
+ }
+
+ @Test
+ public void testJAXBForInputDescription() throws Exception {
+ schemaTest(InputDescription.class);
+ }
+
+ @Test
+ public void testJAXBForAbsentValue() throws Exception {
+ schemaTest(AbstractValue.class);
+ }
+
+ @Test
+ public void testJAXBForAbstractValue() throws Exception {
+ schemaTest(AbstractValue.class);
+ }
+
+ @Test
+ public void testJAXBForErrorValue() throws Exception {
+ schemaTest(ErrorValue.class);
+ }
+
+ @Test
+ public void testJAXBForLeafValue() throws Exception {
+ schemaTest(LeafValue.class);
+ }
+
+ @Test
+ public void testJAXBForListValue() throws Exception {
+ schemaTest(ListValue.class);
+ }
+
+ @Test
+ public void testJAXBForOutputDescription() throws Exception {
+ schemaTest(OutputDescription.class);
+ }
+
+ @Test
+ public void testJAXBForEverythingAtOnce() throws Exception {
+ schemaTest(AbsentValue.class, AbstractValue.class, ListValue.class,
+ LeafValue.class, ErrorValue.class, OutputDescription.class,
+ InputDescription.InputPort.class, InputDescription.class);
+ // System.out.println(schema());
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-rmidaemon/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-server-rmidaemon/pom.xml b/taverna-server-rmidaemon/pom.xml
new file mode 100644
index 0000000..0e2a565
--- /dev/null
+++ b/taverna-server-rmidaemon/pom.xml
@@ -0,0 +1,61 @@
+<?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
+
+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.server</groupId>
+ <artifactId>taverna-server</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>taverna-server-rmidaemon</artifactId>
+ <name>Apache Taverna Server RMI registry daemon</name>
+ <description>Customised RMI registry that supports restricting to localhost.</description>
+
+ <properties>
+ <project.build.sourceEncoding>US-ASCII</project.build.sourceEncoding>
+ <mainClass>org.taverna.server.rmidaemon.Registry</mainClass>
+ </properties>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <archive>
+ <manifest>
+ <mainClass>${mainClass}</mainClass>
+ </manifest>
+ </archive>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/Registry.java
----------------------------------------------------------------------
diff --git a/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/Registry.java b/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/Registry.java
new file mode 100644
index 0000000..4be7579
--- /dev/null
+++ b/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/Registry.java
@@ -0,0 +1,72 @@
+package org.taverna.server.rmidaemon;
+
+import static java.lang.System.setProperty;
+import static java.net.InetAddress.getLocalHost;
+import static java.rmi.registry.LocateRegistry.createRegistry;
+import static java.rmi.registry.Registry.REGISTRY_PORT;
+import static java.rmi.server.RMISocketFactory.getDefaultSocketFactory;
+
+import java.io.IOException;
+import java.io.ObjectOutputStream;
+import java.net.ServerSocket;
+import java.rmi.MarshalledObject;
+import java.rmi.server.RMIServerSocketFactory;
+
+/**
+ * Special version of <tt>rmiregistry</tt>.
+ *
+ * @author Donal Fellows
+ */
+public class Registry {
+ /**
+ * Run a registry. The first optional argument is the port for the registry
+ * to listen on, and the second optional argument is whether the registry
+ * should restrict itself to connections from localhost only.
+ *
+ * @param args
+ * Arguments to the program.
+ */
+ public static void main(String... args) {
+ try {
+ if (args.length > 0)
+ port = Integer.parseInt(args[0]);
+ } catch (Exception e) {
+ System.err.println("failed to parse port: " + e.getMessage());
+ System.exit(2);
+ }
+ try {
+ if (args.length > 1)
+ localhostOnly = Boolean.parseBoolean(args[1]);
+ } catch (Exception e) {
+ System.err.println("failed to parse boolean localhost flag: "
+ + e.getMessage());
+ System.exit(2);
+ }
+ try {
+ Object registryHandle = makeRegistry();
+ try (ObjectOutputStream oos = new ObjectOutputStream(System.out)) {
+ oos.writeObject(registryHandle);
+ }
+ } catch (Exception e) {
+ System.err.println("problem creating registry: " + e.getMessage());
+ System.exit(1);
+ }
+ }
+
+ private static int port = REGISTRY_PORT;
+ private static boolean localhostOnly = false;
+
+ private static MarshalledObject<java.rmi.registry.Registry> makeRegistry() throws IOException {
+ if (!localhostOnly)
+ return new MarshalledObject<>(createRegistry(port));
+ setProperty("java.rmi.server.hostname", "127.0.0.1");
+ return new MarshalledObject<>(createRegistry(port,
+ getDefaultSocketFactory(), new RMIServerSocketFactory() {
+ @Override
+ public ServerSocket createServerSocket(int port)
+ throws IOException {
+ return new ServerSocket(port, 0, getLocalHost());
+ }
+ }));
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/package-info.java
----------------------------------------------------------------------
diff --git a/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/package-info.java b/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/package-info.java
new file mode 100644
index 0000000..32144b5
--- /dev/null
+++ b/taverna-server-rmidaemon/src/main/java/org/taverna/server/rmidaemon/package-info.java
@@ -0,0 +1,5 @@
+/**
+ * RMI daemon implementation. A variation of an RMI registry.
+ * @author Donal Fellows
+ */
+package org.taverna.server.rmidaemon;
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/.gitignore b/taverna-server-runinterface/.gitignore
new file mode 100644
index 0000000..ea8c4bf
--- /dev/null
+++ b/taverna-server-runinterface/.gitignore
@@ -0,0 +1 @@
+/target
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/pom.xml b/taverna-server-runinterface/pom.xml
new file mode 100644
index 0000000..efd3763
--- /dev/null
+++ b/taverna-server-runinterface/pom.xml
@@ -0,0 +1,30 @@
+<?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
+
+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.server</groupId>
+ <artifactId>taverna-server</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+
+ <artifactId>taverna-server-runinterface</artifactId>
+ <name>Apache Taverna Server RMI Interface: Webapp <-> Worker</name>
+ <description>This is the implementation of the RMI interface between the workflow run factory and the web-app service front-end.</description>
+
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/META-INF/MANIFEST.MF
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/META-INF/MANIFEST.MF b/taverna-server-runinterface/src/main/java/META-INF/MANIFEST.MF
new file mode 100644
index 0000000..5e94951
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/META-INF/MANIFEST.MF
@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+Class-Path:
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/IllegalStateTransitionException.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/IllegalStateTransitionException.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/IllegalStateTransitionException.java
new file mode 100644
index 0000000..9f4bf50
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/IllegalStateTransitionException.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import javax.xml.ws.WebFault;
+
+/**
+ * Exception that indicates where a change of a workflow run's status is
+ * illegal.
+ *
+ * @author Donal Fellows
+ * @see RemoteSingleRun#setStatus(RemoteStatus)
+ */
+@WebFault(name = "IllegalStateTransitionFault", targetNamespace = "http://ns.taverna.org.uk/2010/xml/server/worker/")
+public class IllegalStateTransitionException extends Exception {
+ private static final long serialVersionUID = 159673249162345L;
+
+ public IllegalStateTransitionException() {
+ this("illegal state transition");
+ }
+
+ public IllegalStateTransitionException(String message) {
+ super(message);
+ }
+
+ public IllegalStateTransitionException(Throwable cause) {
+ this("illegal state transition", cause);
+ }
+
+ public IllegalStateTransitionException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/ImplementationException.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/ImplementationException.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/ImplementationException.java
new file mode 100644
index 0000000..a47d112
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/ImplementationException.java
@@ -0,0 +1,26 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import javax.xml.ws.WebFault;
+
+/**
+ * Exception that indicates that the implementation has gone wrong in some
+ * unexpected way.
+ *
+ * @author Donal Fellows
+ */
+@WebFault(name = "ImplementationFault", targetNamespace = "http://ns.taverna.org.uk/2010/xml/server/worker/")
+@SuppressWarnings("serial")
+public class ImplementationException extends Exception {
+ public ImplementationException(String message) {
+ super(message);
+ }
+
+ public ImplementationException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectory.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectory.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectory.java
new file mode 100644
index 0000000..395842a
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectory.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.io.IOException;
+import java.rmi.RemoteException;
+import java.util.Collection;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Represents a directory that is the working directory of a workflow run, or a
+ * sub-directory of it.
+ *
+ * @author Donal Fellows
+ * @see RemoteFile
+ */
+public interface RemoteDirectory extends RemoteDirectoryEntry {
+ /**
+ * @return A list of the contents of the directory.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If anything goes wrong with listing the directory.
+ */
+ @Nonnull
+ public Collection<RemoteDirectoryEntry> getContents()
+ throws RemoteException, IOException;
+
+ /**
+ * Creates a sub-directory of this directory.
+ *
+ * @param name
+ * The name of the sub-directory.
+ * @return A handle to the newly-created directory.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong with creating the subdirectory.
+ */
+ @Nonnull
+ public RemoteDirectory makeSubdirectory(@Nonnull String name)
+ throws RemoteException, IOException;
+
+ /**
+ * Creates an empty file in this directory.
+ *
+ * @param name
+ * The name of the file to create.
+ * @return A handle to the newly-created file.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If anything goes wrong with creating the file.
+ */
+ @Nonnull
+ public RemoteFile makeEmptyFile(@Nonnull String name)
+ throws RemoteException, IOException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectoryEntry.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectoryEntry.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectoryEntry.java
new file mode 100644
index 0000000..1e04b44
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteDirectoryEntry.java
@@ -0,0 +1,62 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.io.IOException;
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+import java.util.Date;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+/**
+ * An entry in a {@link RemoteDirectory} representing a file or sub-directory.
+ *
+ * @author Donal Fellows
+ * @see RemoteDirectory
+ * @see RemoteFile
+ */
+public interface RemoteDirectoryEntry extends Remote {
+ /**
+ * @return The "local" name of the entry. This will never be "<tt>..</tt>"
+ * or contain the character "<tt>/</tt>".
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String getName() throws RemoteException;
+
+ /**
+ * @return The time when the entry was last modified.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public Date getModificationDate() throws RemoteException;
+
+ /**
+ * Gets the directory containing this directory entry.
+ *
+ * @return A directory handle, or <tt>null</tt> if called on the workflow
+ * run's working directory.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ public RemoteDirectory getContainingDirectory() throws RemoteException;
+
+ /**
+ * Destroy this directory entry, deleting the file or sub-directory. The
+ * workflow run's working directory can never be manually destroyed.
+ *
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong when deleting the directory entry.
+ */
+ public void destroy() throws RemoteException, IOException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteFile.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteFile.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteFile.java
new file mode 100644
index 0000000..e09466d
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteFile.java
@@ -0,0 +1,98 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.io.IOException;
+import java.rmi.RemoteException;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Represents a file in the working directory of a workflow instance run, or in
+ * some sub-directory of it.
+ *
+ * @author Donal Fellows
+ * @see RemoteDirectory
+ */
+public interface RemoteFile extends RemoteDirectoryEntry {
+ /**
+ * Read from the file.
+ *
+ * @param offset
+ * Where in the file to read the bytes from.
+ * @param length
+ * How much of the file to read; -1 for "to the end".
+ * @return The literal byte contents of the given section of the file.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong reading the file.
+ */
+ @Nonnull
+ byte[] getContents(int offset, int length) throws RemoteException,
+ IOException;
+
+ /**
+ * Write the data to the file, totally replacing what was there before.
+ *
+ * @param data
+ * The literal bytes that will form the new contents of the file.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong writing the contents.
+ */
+ void setContents(@Nonnull byte[] data) throws RemoteException, IOException;
+
+ /**
+ * Append the data to the file.
+ *
+ * @param data
+ * The literal bytes that will be appended.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong writing the contents.
+ */
+ void appendContents(@Nonnull byte[] data) throws RemoteException,
+ IOException;
+
+ /**
+ * @return The length of the file, in bytes.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ long getSize() throws RemoteException;
+
+ /**
+ * Copy from another file to this one.
+ *
+ * @param sourceFile
+ * The other file to copy from.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws IOException
+ * If things go wrong during the copy.
+ */
+ void copy(@Nonnull RemoteFile sourceFile) throws RemoteException,
+ IOException;
+
+ /**
+ * @return The full native OS name for the file.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ String getNativeName() throws RemoteException;
+
+ /**
+ * @return The host holding the file.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ String getNativeHost() throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteInput.java
----------------------------------------------------------------------
diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteInput.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteInput.java
new file mode 100644
index 0000000..7a7510c
--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteInput.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+/**
+ * This represents the assignment of inputs to input ports of the workflow. Note
+ * that the <tt>file</tt> and <tt>value</tt> properties are never set at the
+ * same time.
+ *
+ * @author Donal Fellows
+ */
+public interface RemoteInput extends Remote {
+ /**
+ * @return The file currently assigned to this input port, or <tt>null</tt>
+ * if no file is assigned.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ String getFile() throws RemoteException;
+
+ /**
+ * @return The name of this input port. This may not be changed.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ String getName() throws RemoteException;
+
+ /**
+ * @return The value currently assigned to this input port, or <tt>null</tt>
+ * if no value is assigned.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ String getValue() throws RemoteException;
+
+ /**
+ * @return The delimiter currently used to split this input port's value
+ * into a list, or <tt>null</tt> if no delimiter is to be used
+ * (i.e., the value is a singleton).
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ String getDelimiter() throws RemoteException;
+
+ /**
+ * Sets the file to use for this input. This overrides the use of the
+ * previous file and any set value.
+ *
+ * @param file
+ * The filename to use. Must not start with a <tt>/</tt> or
+ * contain any <tt>..</tt> segments. Will be interpreted relative
+ * to the run's working directory.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setFile(@Nonnull String file) throws RemoteException;
+
+ /**
+ * Sets the value to use for this input. This overrides the use of the
+ * previous value and any set file.
+ *
+ * @param value
+ * The value to use.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setValue(@Nonnull String value) throws RemoteException;
+
+ /**
+ * Sets the delimiter used to split this input port's value into a list.
+ *
+ * @param delimiter
+ * The delimiter character, or <tt>null</tt> if no delimiter is
+ * to be used (i.e., the value is a singleton).
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setDelimiter(@Nullable String delimiter) throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteListener.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteListener.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteListener.java
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--- /dev/null
+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteListener.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+
+import javax.annotation.Nonnull;
+
+/**
+ * An event listener that is attached to a {@link RemoteSingleRun}.
+ *
+ * @author Donal Fellows
+ */
+public interface RemoteListener extends Remote {
+ /**
+ * @return The name of the listener.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String getName() throws RemoteException;
+
+ /**
+ * @return The type of the listener.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String getType() throws RemoteException;
+
+ /**
+ * @return The configuration document for the listener.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String getConfiguration() throws RemoteException;
+
+ /**
+ * @return The supported properties of the listener.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String[] listProperties() throws RemoteException;
+
+ /**
+ * Get the value of a particular property, which should be listed in the
+ * {@link #listProperties()} method.
+ *
+ * @param propName
+ * The name of the property to read.
+ * @return The value of the property.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public String getProperty(@Nonnull String propName) throws RemoteException;
+
+ /**
+ * Set the value of a particular property, which should be listed in the
+ * {@link #listProperties()} method.
+ *
+ * @param propName
+ * The name of the property to write.
+ * @param value
+ * The value to set the property to.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ public void setProperty(@Nonnull String propName, @Nonnull String value)
+ throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteRunFactory.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteRunFactory.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteRunFactory.java
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@@ -0,0 +1,84 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+import java.util.UUID;
+
+import org.taverna.server.localworker.server.UsageRecordReceiver;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+/**
+ * The main RMI-enabled interface for creating runs.
+ *
+ * @author Donal Fellows
+ */
+public interface RemoteRunFactory extends Remote {
+ /**
+ * Makes a workflow run that will process a particular workflow document.
+ *
+ * @param workflow
+ * The (serialised) workflow to instantiate as a run.
+ * @param creator
+ * Who is this run created for?
+ * @param usageRecordReceiver
+ * Where to write any usage records. May be <tt>null</tt> to
+ * cause them to not be written.
+ * @param masterID
+ * The UUID of the run to use, or <tt>null</tt> if the execution
+ * engine is to manufacture a new one for itself.
+ * @return A remote handle for the run.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ RemoteSingleRun make(@Nonnull byte[] workflow, @Nonnull String creator,
+ @Nullable UsageRecordReceiver usageRecordReceiver,
+ @Nullable UUID masterID) throws RemoteException;
+
+ /**
+ * Asks this factory to unregister itself from the registry and cease
+ * operation.
+ *
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void shutdown() throws RemoteException;
+
+ /**
+ * Configures the details to use when setting up the workflow run's
+ * connnection to the interaction feed.
+ *
+ * @param host
+ * The host where the feed is located.
+ * @param port
+ * The port where the feed is located.
+ * @param webdavPath
+ * The path used for pushing web pages into the feed.
+ * @param feedPath
+ * The path used for reading and writing notifications on the
+ * feed.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setInteractionServiceDetails(@Nonnull String host,
+ @Nonnull String port, @Nonnull String webdavPath,
+ @Nonnull String feedPath) throws RemoteException;
+
+ /**
+ * Gets a count of the number of {@linkplain RemoteSingleRun workflow runs}
+ * that this factor knows about that are in the
+ * {@link RemoteStatus#Operating Operating} state.
+ *
+ * @return A count of "running" workflow runs.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ int countOperatingRuns() throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSecurityContext.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSecurityContext.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSecurityContext.java
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@@ -0,0 +1,34 @@
+/*
+ * Copyright (C) 2010-2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.net.URI;
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+import java.util.Map;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Outline of the security context for a workflow run.
+ *
+ * @author Donal Fellows
+ */
+public interface RemoteSecurityContext extends Remote {
+ void setKeystore(@Nonnull byte[] keystore) throws RemoteException,
+ ImplementationException;
+
+ void setPassword(@Nonnull char[] password) throws RemoteException,
+ ImplementationException;
+
+ void setTruststore(@Nonnull byte[] truststore) throws RemoteException,
+ ImplementationException;
+
+ void setUriToAliasMap(@Nonnull Map<URI, String> uriToAliasMap)
+ throws RemoteException;
+
+ void setHelioToken(@Nonnull String helioToken) throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
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+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
@@ -0,0 +1,254 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+import java.net.URL;
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+import java.util.Date;
+import java.util.List;
+
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
+
+public interface RemoteSingleRun extends Remote {
+ /**
+ * @return The name of the Baclava file to use for all inputs, or
+ * <tt>null</tt> if no Baclava file is set.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ public String getInputBaclavaFile() throws RemoteException;
+
+ /**
+ * Sets the Baclava file to use for all inputs. This overrides the use of
+ * individual inputs.
+ *
+ * @param filename
+ * The filename to use. Must not start with a <tt>/</tt> or
+ * contain any <tt>..</tt> segments. Will be interpreted relative
+ * to the run's working directory.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ public void setInputBaclavaFile(@Nonnull String filename)
+ throws RemoteException;
+
+ /**
+ * @return The list of input assignments.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public List<RemoteInput> getInputs() throws RemoteException;
+
+ /**
+ * Create an input assignment.
+ *
+ * @param name
+ * The name of the port that this will be an input for.
+ * @return The assignment reference.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public RemoteInput makeInput(@Nonnull String name) throws RemoteException;
+
+ /**
+ * @return The file (relative to the working directory) to write the outputs
+ * of the run to as a Baclava document, or <tt>null</tt> if they are
+ * to be written to non-Baclava files in a directory called
+ * <tt>out</tt>.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ public String getOutputBaclavaFile() throws RemoteException;
+
+ /**
+ * Sets where the output of the run is to be written to. This will cause the
+ * output to be generated as a Baclava document, rather than a collection of
+ * individual non-Baclava files in the subdirectory of the working directory
+ * called <tt>out</tt>.
+ *
+ * @param filename
+ * Where to write the Baclava file (or <tt>null</tt> to cause the
+ * output to be written to individual files); overwrites any
+ * previous setting of this value.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ public void setOutputBaclavaFile(@Nullable String filename)
+ throws RemoteException;
+
+ /**
+ * @return The current status of the run.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public RemoteStatus getStatus() throws RemoteException;
+
+ /**
+ * Set the status of the run, which should cause it to move into the given
+ * state. This may cause some significant changes.
+ *
+ * @param s
+ * The state to try to change to.
+ * @throws IllegalStateTransitionException
+ * If the requested state change is impossible. (Note that it is
+ * always legal to set the status to the current status.)
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws ImplementationException
+ * If something goes horribly wrong on the back end.
+ * @throws StillWorkingOnItException
+ * If the startup time of the workflow implementation exceeds a
+ * built-in threshold.
+ */
+ public void setStatus(@Nonnull RemoteStatus s)
+ throws IllegalStateTransitionException, RemoteException,
+ ImplementationException, StillWorkingOnItException;
+
+ /**
+ * @return When this workflow run was found to have finished, or
+ * <tt>null</tt> if it has never finished (either still running or
+ * never started).
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ public Date getFinishTimestamp() throws RemoteException;
+
+ /**
+ * @return When this workflow run was started, or <tt>null</tt> if it has
+ * never been started.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nullable
+ public Date getStartTimestamp() throws RemoteException;
+
+ /**
+ * @return Handle to the main working directory of the run.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public RemoteDirectory getWorkingDirectory() throws RemoteException;
+
+ /**
+ * @return The list of listener instances attached to the run.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public List<RemoteListener> getListeners() throws RemoteException;
+
+ /**
+ * Add a listener to the run.
+ *
+ * @param listener
+ * The listener to add.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws ImplementationException
+ * If something goes wrong when adding the listener.
+ */
+ public void addListener(@Nonnull RemoteListener listener)
+ throws RemoteException, ImplementationException;
+
+ /**
+ * @return The security context structure for this run.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws ImplementationException
+ * If something goes wrong when getting the context.
+ */
+ @Nonnull
+ public RemoteSecurityContext getSecurityContext() throws RemoteException,
+ ImplementationException;
+
+ /**
+ * Kill off this run, removing all resources which it consumes.
+ *
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ * @throws ImplementationException
+ * If something goes horribly wrong when destroying the run.
+ */
+ public void destroy() throws RemoteException, ImplementationException;
+
+ /**
+ * Get the types of listener supported by this run.
+ *
+ * @return A list of listener type names.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public List<String> getListenerTypes() throws RemoteException;
+
+ /**
+ * Create a listener that can be attached to this run.
+ *
+ * @param type
+ * The type name of the listener to create; it must be one of the
+ * names returned by the {@link #getListenerTypes()} operation.
+ * @param configuration
+ * The configuration document for this listener. The nature of
+ * the contents of this are determined by the type.
+ * @return A handle for the listener.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ @Nonnull
+ public RemoteListener makeListener(@Nonnull String type,
+ @Nonnull String configuration) throws RemoteException;
+
+ /**
+ * Configures the details to use when setting up the workflow run's
+ * connnection to the interaction feed.
+ *
+ * @param interactionFeed
+ * The location of the interaction feed. If <tt>null</tt>,
+ * defaults from the factory will be used instead.
+ * @param webdavPath
+ * The location used for pushing web pages to support the feed.
+ * If <tt>null</tt>, a default from the factory will be used
+ * instead.
+ * @param publishUrlBase
+ * Where to <i>actually</i> publish to, if this needs to be
+ * different from the location presented in the published HTML
+ * and Feed entries. Necessary in complex network scenarios.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setInteractionServiceDetails(@Nonnull URL interactionFeed,
+ @Nonnull URL webdavPath, @Nullable URL publishUrlBase) throws RemoteException;
+
+ /**
+ * A do-nothing method, used to check the general reachability of the
+ * workflow run.
+ *
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void ping() throws RemoteException;
+
+ /**
+ * Sets whether we should generate provenance information from a run.
+ *
+ * @param generateProvenance
+ * Boolean flag, true for do the generation. Must be set before
+ * starting the run for this to have an effect.
+ * @throws RemoteException
+ * If anything goes wrong with the communication.
+ */
+ void setGenerateProvenance(boolean generateProvenance)
+ throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteStatus.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteStatus.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteStatus.java
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@@ -0,0 +1,40 @@
+/*
+ * Copyright (C) 2010 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+/**
+ * States of a workflow run. They are {@link RemoteStatus#Initialized
+ * Initialized}, {@link RemoteStatus#Operating Operating},
+ * {@link RemoteStatus#Stopped Stopped}, and {@link RemoteStatus#Finished
+ * Finished}. Conceptually, there is also a <tt>Destroyed</tt> state, but the
+ * workflow run does not exist (and hence can't have its state queried or set)
+ * in that case.
+ *
+ * @author Donal Fellows
+ */
+public enum RemoteStatus {
+ /**
+ * The workflow run has been created, but is not yet running. The run will
+ * need to be manually moved to {@link #Operating} when ready.
+ */
+ Initialized,
+ /**
+ * The workflow run is going, reading input, generating output, etc. Will
+ * eventually either move automatically to {@link #Finished} or can be moved
+ * manually to {@link #Stopped} (where supported).
+ */
+ Operating,
+ /**
+ * The workflow run is paused, and will need to be moved back to
+ * {@link #Operating} manually.
+ */
+ Stopped,
+ /**
+ * The workflow run has ceased; data files will continue to exist until the
+ * run is destroyed (which may be manual or automatic).
+ */
+ Finished
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/StillWorkingOnItException.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/StillWorkingOnItException.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/StillWorkingOnItException.java
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+++ b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/StillWorkingOnItException.java
@@ -0,0 +1,20 @@
+/*
+ * Copyright (C) 2013 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.remote;
+
+/**
+ * Exception that indicates that the implementation is still working on
+ * processing the operation. Note that though this is an exception, it is <i>not
+ * a failure</i>.
+ *
+ * @author Donal Fellows
+ */
+@SuppressWarnings("serial")
+public class StillWorkingOnItException extends Exception {
+ public StillWorkingOnItException(String string) {
+ super(string);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/package-info.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/package-info.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/remote/package-info.java
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+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+/**
+ * Interfaces exported by worker classes to the server.
+ */
+package org.taverna.server.localworker.remote;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/UsageRecordReceiver.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/UsageRecordReceiver.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/UsageRecordReceiver.java
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@@ -0,0 +1,29 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.localworker.server;
+
+import java.rmi.Remote;
+import java.rmi.RemoteException;
+
+/**
+ * Interface exported by (part of) the webapp to allow processes it creates to
+ * push in usage records.
+ *
+ * @author Donal Fellows
+ */
+public interface UsageRecordReceiver extends Remote {
+ /**
+ * Called to push in a usage record. Note that it is assumed that the usage
+ * record already contains all the information required to locate and
+ * process the job; there is no separate handle.
+ *
+ * @param usageRecord
+ * The serialised XML of the usage record.
+ * @throws RemoteException
+ * if anything goes wrong.
+ */
+ void acceptUsageRecord(String usageRecord) throws RemoteException;
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/package-info.java
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diff --git a/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/package-info.java b/taverna-server-runinterface/src/main/java/org/taverna/server/localworker/server/package-info.java
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@@ -0,0 +1,9 @@
+/*
+ * Copyright (C) 2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+/**
+ * Interfaces exported by the server to worker classes.
+ */
+package org.taverna.server.localworker.server;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-unix-forker/pom.xml
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diff --git a/taverna-server-unix-forker/pom.xml b/taverna-server-unix-forker/pom.xml
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@@ -0,0 +1,61 @@
+<?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
+
+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.server</groupId>
+ <artifactId>taverna-server</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-server-unix-forker</artifactId>
+ <name>Apache Taverna Server Impersonation Module (Unix)</name>
+ <description>Manages the starting of the worker processes as different users. Unix-specific.</description>
+
+ <properties>
+ <project.build.sourceEncoding>US-ASCII</project.build.sourceEncoding>
+ <forkerMainClass>org.taverna.server.unixforker.Forker</forkerMainClass>
+ </properties>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-assembly-plugin</artifactId>
+ <configuration>
+ <descriptorRefs>
+ <descriptorRef>jar-with-dependencies</descriptorRef>
+ </descriptorRefs>
+ <archive>
+ <manifest>
+ <mainClass>${forkerMainClass}</mainClass>
+ </manifest>
+ </archive>
+ </configuration>
+ <executions>
+ <execution>
+ <id>make-assembly</id>
+ <phase>package</phase>
+ <goals>
+ <goal>single</goal>
+ </goals>
+ </execution>
+ </executions>
+ </plugin>
+ </plugins>
+ </build>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-unix-forker/src/main/java/org/taverna/server/unixforker/Forker.java
----------------------------------------------------------------------
diff --git a/taverna-server-unix-forker/src/main/java/org/taverna/server/unixforker/Forker.java b/taverna-server-unix-forker/src/main/java/org/taverna/server/unixforker/Forker.java
new file mode 100644
index 0000000..f9dc632
--- /dev/null
+++ b/taverna-server-unix-forker/src/main/java/org/taverna/server/unixforker/Forker.java
@@ -0,0 +1,208 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.unixforker;
+
+import static java.lang.System.err;
+import static java.lang.System.getProperty;
+import static java.lang.System.in;
+import static java.lang.System.out;
+import static java.util.Arrays.asList;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.util.List;
+
+import javax.annotation.Nonnull;
+
+/**
+ * A simple class that forks off processes when asked to over its standard
+ * input. The one complication is that it forks them off as other users, through
+ * the use of the <tt>sudo</tt> utility. It is Unix-specific.
+ *
+ * @author Donal Fellows
+ */
+public class Forker extends Thread {
+ private static String password;
+ private static BufferedReader br;
+
+ /**
+ * Helper to make reading a password from a file clearer. The password must
+ * be the first line of the file.
+ *
+ * @param passwordFile
+ * The file to load from.
+ * @throws IOException
+ * If anything goes wrong.
+ */
+ private static void loadPassword(@Nonnull File passwordFile)
+ throws IOException {
+ try {
+ err.println("attempting to load password from " + passwordFile);
+ try (FileReader fr = new FileReader(passwordFile)) {
+ password = new BufferedReader(fr).readLine();
+ }
+ } catch (IOException e) {
+ err.println("failed to read password from file " + passwordFile
+ + "described in password.file property");
+ throw e;
+ }
+ }
+
+ /**
+ * Initialization code, which runs before the main loop starts processing.
+ *
+ * @param args
+ * The arguments to the program.
+ * @throws Exception
+ * If anything goes wrong.
+ */
+ public static void init(String[] args) throws Exception {
+ if (args.length < 1)
+ throw new IllegalArgumentException(
+ "wrong # args: must be \"program ?argument ...?\"");
+ if (getProperty("password.file") != null)
+ loadPassword(new File(getProperty("password.file")));
+ if (password == null)
+ err.println("no password.file property or empty file; "
+ + "assuming password-less sudo is configured");
+ else
+ err.println("password is of length " + password.length());
+ br = new BufferedReader(new InputStreamReader(in));
+ }
+
+ /**
+ * The body of the main loop of this program.
+ *
+ * @param args
+ * The arguments to use when running the other program.
+ * @return Whether to repeat the loop.
+ * @throws Exception
+ * If anything goes wrong. Note that the loop is repeated if an
+ * exception occurs in it.
+ */
+ public static boolean mainLoopBody(String[] args) throws Exception {
+ String line = br.readLine();
+ if (line == null)
+ return false;
+ List<String> vals = asList(line.split("[ \t]+"));
+ if (vals.size() != 2) {
+ out.println("wrong # values: must be \"username UUID\"");
+ return true;
+ }
+ ProcessBuilder pb = new ProcessBuilder();
+ pb.command()
+ .addAll(asList("sudo", "-u", vals.get(0), "-S", "-H", "--"));
+ pb.command().addAll(asList(args));
+ pb.command().add(vals.get(1));
+ Forker f = new Forker(pb);
+ f.setDaemon(true);
+ f.start();
+ return true;
+ }
+
+ /**
+ * The main code for this class, which turns this into an executable
+ * program. Runs the initialisation and then the main loop, in both cases
+ * with appropriate error handling.
+ *
+ * @param args
+ * Arguments to this program.
+ */
+ public static void main(String... args) {
+ try {
+ init(args);
+ while (true) {
+ try {
+ if (!mainLoopBody(args))
+ break;
+ } catch (Exception e) {
+ e.printStackTrace(err);
+ out.println(e.getClass().getName() + ": " + e.getMessage());
+ }
+ }
+ System.exit(0);
+ } catch (Exception e) {
+ e.printStackTrace(err);
+ System.exit(1);
+ }
+ }
+
+ // -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
+
+ public Forker(ProcessBuilder pb) throws IOException {
+ out.println("Starting subprocess: " + pb.command());
+ final Process p = pb.start();
+ abstract class ProcessAttachedDaemon extends Thread {
+ public ProcessAttachedDaemon() {
+ setDaemon(true);
+ start();
+ }
+
+ abstract void act() throws Exception;
+
+ @Override
+ public final void run() {
+ try {
+ act();
+ p.waitFor();
+ } catch (InterruptedException e) {
+ // Just drop
+ } catch (Exception e) {
+ p.destroy();
+ e.printStackTrace(err);
+ }
+ }
+ }
+ new ProcessAttachedDaemon() {
+ @Override
+ void act() throws Exception {
+ copyFromSudo("Subprocess(out):", p.getInputStream());
+ }
+ };
+ new ProcessAttachedDaemon() {
+ @Override
+ void act() throws Exception {
+ copyFromSudo("Subprocess(err):", p.getErrorStream());
+ }
+ };
+ new ProcessAttachedDaemon() {
+ @Override
+ void act() throws Exception {
+ interactWithSudo(p.getOutputStream());
+ }
+ };
+ }
+
+ protected void interactWithSudo(OutputStream os) throws Exception {
+ if (password != null) {
+ OutputStreamWriter osw = new OutputStreamWriter(os);
+ osw.write(password + "\n");
+ osw.flush();
+ }
+ os.close();
+ }
+
+ protected void copyFromSudo(String header, InputStream sudoStream)
+ throws Exception {
+ int b = '\n';
+ while (true) {
+ if (b == '\n')
+ out.print(header);
+ b = sudoStream.read();
+ if (b == -1)
+ break;
+ out.write(b);
+ out.flush();
+ }
+ sudoStream.close();
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-usagerecord/.gitignore
----------------------------------------------------------------------
diff --git a/taverna-server-usagerecord/.gitignore b/taverna-server-usagerecord/.gitignore
new file mode 100644
index 0000000..ea8c4bf
--- /dev/null
+++ b/taverna-server-usagerecord/.gitignore
@@ -0,0 +1 @@
+/target
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-usagerecord/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-server-usagerecord/pom.xml b/taverna-server-usagerecord/pom.xml
new file mode 100644
index 0000000..47ab732
--- /dev/null
+++ b/taverna-server-usagerecord/pom.xml
@@ -0,0 +1,79 @@
+<?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
+
+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.server</groupId>
+ <artifactId>taverna-server</artifactId>
+ <version>3.1.0-incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-server-usagerecord</artifactId>
+ <name>Apache Taverna Server Usage Record Support</name>
+ <description>Basic Java bindings for the OGF Usage Record Format, version 1.0, plus a simple wrapper to make working with it easier.</description>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>jaxb2-maven-plugin</artifactId>
+ <version>1.3.1</version>
+ <executions>
+ <execution>
+ <id>xsd2java</id>
+ <goals>
+ <goal>xjc</goal>
+ </goals>
+ <configuration>
+ <outputDirectory>${project.build.directory}/generated-sources/xjc</outputDirectory>
+ <schemaDirectory>${basedir}/src/main/xsd</schemaDirectory>
+ </configuration>
+ </execution>
+ </executions>
+ </plugin>
+
+ </plugins>
+ <pluginManagement>
+ <plugins>
+ <!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
+ <plugin>
+ <groupId>org.eclipse.m2e</groupId>
+ <artifactId>lifecycle-mapping</artifactId>
+ <version>1.0.0</version>
+ <configuration>
+ <lifecycleMappingMetadata>
+ <pluginExecutions>
+ <pluginExecution>
+ <pluginExecutionFilter>
+ <groupId>org.codehaus.mojo</groupId>
+ <artifactId>jaxb2-maven-plugin</artifactId>
+ <versionRange>[1.3.1,)</versionRange>
+ <goals>
+ <goal>xjc</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute />
+ </action>
+ </pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+</project>