Merge branch '2.5' into taverna-3
diff --git a/pom.xml b/pom.xml
index 1e38f26..fc7b0c9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -97,7 +97,7 @@
</roles>
</contributor>
<contributor>
- <name>Stian Soiland</name>
+ <name>Stian Soiland-Reyes</name>
<organization>The University of Manchester</organization>
<organizationUrl>http://www.manchester.ac.uk/</organizationUrl>
<timezone>0</timezone>
@@ -549,11 +549,12 @@
<module>server-webapp</module>
<module>server-runinterface</module>
<module>server-worker</module>
- <module>server-distribution</module>
<module>server-unix-forker</module>
<module>server-usagerecord</module>
<module>server-port-description</module>
<module>server-execution-delegate</module>
<module>server-rmidaemon</module>
+ <module>server-client</module>
+ <module>server-distribution</module>
</modules>
</project>
diff --git a/server-client/pom.xml b/server-client/pom.xml
new file mode 100644
index 0000000..e62978a
--- /dev/null
+++ b/server-client/pom.xml
@@ -0,0 +1,123 @@
+<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>uk.org.taverna.server</groupId>
+ <artifactId>server</artifactId>
+ <version>3.0-SNAPSHOT</version>
+ </parent>
+ <artifactId>server-client</artifactId>
+ <packaging>bundle</packaging>
+
+ <dependencies>
+ <dependency>
+ <groupId>org.jvnet.ws.wadl</groupId>
+ <artifactId>wadl-core</artifactId>
+ <version>1.1.6</version>
+ </dependency>
+ <dependency>
+ <groupId>com.sun.jersey</groupId>
+ <artifactId>jersey-client</artifactId>
+ <version>1.8</version>
+ </dependency>
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>2.4</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.tika</groupId>
+ <artifactId>tika-core</artifactId>
+ <version>1.5</version>
+ </dependency>
+ <dependency>
+ <groupId>uk.org.taverna.server</groupId>
+ <artifactId>server-usagerecord</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ </dependencies>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+ <Export-Package>uk.org.taverna.server.client</Export-Package>
+ <Private-Package>uk.org.taverna.server.client.*</Private-Package>
+ </instructions>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.7</source>
+ <target>1.7</target>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.jvnet.ws.wadl</groupId>
+ <artifactId>wadl-client-plugin</artifactId>
+ <version>1.1.6</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <packageName>org.taverna.server.client.wadl</packageName>
+ <includes>*.wadl</includes>
+ <customClassNames>
+ <property>
+ <name>http://example.com/taverna/rest</name>
+ <value>TavernaServer</value>
+ </property>
+ </customClassNames>
+ </configuration>
+ </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.jvnet.ws.wadl
+ </groupId>
+ <artifactId>
+ wadl-client-plugin
+ </artifactId>
+ <versionRange>
+ [1.1.6,)
+ </versionRange>
+ <goals>
+ <goal>generate</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute />
+ </action>
+ </pluginExecution>
+ </pluginExecutions>
+ </lifecycleMappingMetadata>
+ </configuration>
+ </plugin>
+ </plugins>
+ </pluginManagement>
+ </build>
+ <inceptionYear>2014</inceptionYear>
+ <name>Server Client OSGi Module</name>
+</project>
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Connected.java b/server-client/src/main/java/uk/org/taverna/server/client/Connected.java
new file mode 100644
index 0000000..263034c
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/Connected.java
@@ -0,0 +1,20 @@
+package uk.org.taverna.server.client;
+
+import uk.org.taverna.server.client.TavernaServer.ClientException;
+import uk.org.taverna.server.client.TavernaServer.ServerException;
+
+import com.sun.jersey.api.client.ClientResponse;
+
+abstract class Connected {
+ void checkError(ClientResponse response) throws ClientException,
+ ServerException {
+ ClientResponse.Status s = response.getClientResponseStatus();
+ if (s.getStatusCode() == 401)
+ throw new TavernaServer.AuthorizationException("not authorized",
+ null);
+ if (s.getStatusCode() >= 500)
+ throw new TavernaServer.ServerException(s.getReasonPhrase(), null);
+ if (s.getStatusCode() >= 400)
+ throw new TavernaServer.ClientException(s.getReasonPhrase(), null);
+ }
+}
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java b/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java
new file mode 100644
index 0000000..267707d
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/DirEntry.java
@@ -0,0 +1,39 @@
+package uk.org.taverna.server.client;
+
+import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd.Path2;
+
+import uk.org.taverna.server.client.TavernaServer.ClientException;
+import uk.org.taverna.server.client.TavernaServer.ServerException;
+
+import com.sun.jersey.api.client.ClientResponse;
+
+public abstract class DirEntry extends Connected {
+ final Path2 handle;
+ final String path;
+ final Run run;
+
+ protected DirEntry(Run run, String path) {
+ this.run = run;
+ this.path = path.replaceFirst("/+$", "");
+ this.handle = run.run.wd().path2(this.path);
+ }
+
+ public void delete() throws ClientException, ServerException {
+ checkError(handle.deleteAsXml(ClientResponse.class));
+ }
+
+ String path(ClientResponse response) throws ClientException, ServerException {
+ checkError(response);
+ String[] bits = response.getLocation().getPath().split("/");
+ return concat(bits[bits.length - 1]);
+ }
+
+ String localName() {
+ String[] bits = path.split("/");
+ return bits[bits.length - 1];
+ }
+
+ String concat(String name) {
+ return path + "/" + name.split("/", 2)[0];
+ }
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Directory.java b/server-client/src/main/java/uk/org/taverna/server/client/Directory.java
new file mode 100644
index 0000000..38dc394
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/Directory.java
@@ -0,0 +1,94 @@
+package uk.org.taverna.server.client;
+
+import static java.io.File.createTempFile;
+import static javax.ws.rs.client.Entity.entity;
+import static javax.ws.rs.core.MediaType.APPLICATION_OCTET_STREAM_TYPE;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.zip.ZipFile;
+
+import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd;
+
+import uk.org.taverna.server.client.TavernaServer.ClientException;
+import uk.org.taverna.server.client.TavernaServer.ServerException;
+import uk.org.taverna.server.client.generic.DirectoryEntry;
+import uk.org.taverna.server.client.generic.DirectoryReference;
+import uk.org.taverna.server.client.generic.FileReference;
+import uk.org.taverna.server.client.rest.DirectoryContents;
+import uk.org.taverna.server.client.rest.MakeDirectory;
+import uk.org.taverna.server.client.rest.UploadFile;
+
+import com.sun.jersey.api.client.ClientResponse;
+
+public class Directory extends DirEntry {
+ private final Wd wd;
+
+ Directory(Run run) {
+ super(run, "");
+ this.wd = run.run.wd();
+ }
+
+ Directory(Run run, String path) {
+ super(run, path);
+ this.wd = run.run.wd();
+ }
+
+ public List<DirEntry> list() {
+ List<DirEntry> result = new ArrayList<>();
+ for (DirectoryEntry de : wd.path3(path)
+ .getAsXml(DirectoryContents.class).getDirOrFile())
+ if (de instanceof DirectoryReference)
+ result.add(new Directory(run, de.getValue()));
+ else if (de instanceof FileReference)
+ result.add(new File(run, de.getValue()));
+ return result;
+ }
+
+ public File createFile(String name, byte[] content) throws ClientException,
+ ServerException {
+ UploadFile uf = new UploadFile();
+ uf.setName(name);
+ uf.setValue(content);
+ return new File(run, path(wd.path(path).putAsXml(uf,
+ ClientResponse.class)));
+ }
+
+ public File createFile(String name, java.io.File content)
+ throws ClientException, ServerException {
+ return new File(run, path(wd.path(concat(name)).putOctetStreamAsXml(
+ entity(content, APPLICATION_OCTET_STREAM_TYPE),
+ ClientResponse.class)));
+ }
+
+ public File createFile(String name, URI source) throws ClientException,
+ ServerException {
+ return new File(run, path(wd.path(concat(name)).postTextUriListAsXml(
+ source.toString(), ClientResponse.class)));
+ }
+
+ public Directory createDirectory(String name) throws ClientException,
+ ServerException {
+ MakeDirectory mkdir = new MakeDirectory();
+ mkdir.setName(name);
+ return new Directory(run, path(wd.path(path).putAsXml(mkdir,
+ ClientResponse.class)));
+ }
+
+ public byte[] getZippedContents() {
+ return wd.path3(path).getAsZip(byte[].class);
+ }
+
+ public ZipFile getZip() throws IOException {
+ byte[] contents = getZippedContents();
+ java.io.File tmp = createTempFile(localName(), ".zip");
+ try (OutputStream os = new FileOutputStream(tmp)) {
+ os.write(contents);
+ }
+ return new ZipFile(tmp);
+ }
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/File.java b/server-client/src/main/java/uk/org/taverna/server/client/File.java
new file mode 100644
index 0000000..0287afb
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/File.java
@@ -0,0 +1,95 @@
+package uk.org.taverna.server.client;
+
+import static java.io.File.createTempFile;
+import static javax.ws.rs.client.Entity.entity;
+import static javax.ws.rs.core.MediaType.APPLICATION_OCTET_STREAM_TYPE;
+import static org.apache.commons.io.IOUtils.copy;
+import static org.apache.tika.mime.MimeTypes.getDefaultMimeTypes;
+
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.nio.charset.Charset;
+
+import org.apache.tika.mime.MimeTypeException;
+import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName.Wd;
+
+import uk.org.taverna.server.client.TavernaServer.ClientException;
+import uk.org.taverna.server.client.TavernaServer.ServerException;
+
+import com.sun.jersey.api.client.ClientHandlerException;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.UniformInterfaceException;
+
+public class File extends DirEntry {
+ private final Wd wd;
+
+ File(Run run, String path) {
+ super(run, path);
+ wd = run.run.wd();
+ }
+
+ public InputStream getAsStream() {
+ return wd.path3(path).getAsOctetStream(InputStream.class);
+ }
+
+ public byte[] get() {
+ return wd.path3(path).getAsOctetStream(byte[].class);
+ }
+
+ public String get(Charset encoding) {
+ return new String(wd.path3(path).getAsOctetStream(byte[].class),
+ encoding);
+ }
+
+ public java.io.File getAsFile() throws ClientHandlerException,
+ UniformInterfaceException, IOException, MimeTypeException,
+ ClientException, ServerException {
+ ClientResponse cr = wd.path3(path).getAsOctetStream(
+ ClientResponse.class);
+ checkError(cr);
+ String[] bits = localName().split("[.]");
+ String ext = getDefaultMimeTypes().forName(
+ cr.getHeaders().getFirst("Content-Type")).getExtension();
+ if (ext == null)
+ ext = bits[bits.length - 1];
+ java.io.File tmp = createTempFile(bits[0], ext);
+ try (OutputStream os = new FileOutputStream(tmp);
+ InputStream is = cr.getEntity(InputStream.class)) {
+ copy(is, os);
+ }
+ return tmp;
+ }
+
+ public void setContents(byte[] newContents) throws ClientException,
+ ServerException {
+ checkError(wd.path(path).putOctetStreamAsXml(newContents,
+ ClientResponse.class));
+ }
+
+ public void setContents(String newContents) throws ClientException,
+ ServerException {
+ checkError(wd.path(path).putOctetStreamAsXml(newContents,
+ ClientResponse.class));
+ }
+
+ public void setContents(String newContents, Charset encoding)
+ throws ClientException, ServerException {
+ checkError(wd.path(path).putOctetStreamAsXml(
+ newContents.getBytes(encoding), ClientResponse.class));
+ }
+
+ public void setContents(InputStream newContents) throws ClientException,
+ ServerException {
+ checkError(wd.path(path).putOctetStreamAsXml(newContents,
+ ClientResponse.class));
+ }
+
+ public void setContents(java.io.File newContents) throws IOException,
+ ClientException, ServerException {
+ checkError(wd.path(path).putOctetStreamAsXml(
+ entity(newContents, APPLICATION_OCTET_STREAM_TYPE),
+ ClientResponse.class));
+ }
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Property.java b/server-client/src/main/java/uk/org/taverna/server/client/Property.java
new file mode 100644
index 0000000..0e6542f
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/Property.java
@@ -0,0 +1,18 @@
+package uk.org.taverna.server.client;
+
+public enum Property {
+ STDOUT("stdout"), STDERR("stderr"), EXIT_CODE("exitcode"), READY_TO_NOTIFY(
+ "readyToNotify"), EMAIL("notificationAddress"), USAGE(
+ "usageRecord");
+
+ private String s;
+
+ private Property(String s) {
+ this.s = s;
+ }
+
+ @Override
+ public String toString() {
+ return s;
+ }
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Run.java b/server-client/src/main/java/uk/org/taverna/server/client/Run.java
new file mode 100644
index 0000000..5c6875e
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/Run.java
@@ -0,0 +1,215 @@
+package uk.org.taverna.server.client;
+
+import static org.joda.time.format.ISODateTimeFormat.dateTime;
+import static org.joda.time.format.ISODateTimeFormat.dateTimeParser;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.util.Date;
+import java.util.List;
+
+import javax.xml.bind.JAXBException;
+
+import org.apache.commons.io.IOUtils;
+import org.joda.time.DateTime;
+import org.ogf.usage.JobUsageRecord;
+import org.taverna.server.client.wadl.TavernaServer.Root.RunsRunName;
+import org.w3c.dom.Element;
+
+import uk.org.taverna.server.client.TavernaServer.ClientException;
+import uk.org.taverna.server.client.TavernaServer.ServerException;
+import uk.org.taverna.server.client.generic.KeyPairCredential;
+import uk.org.taverna.server.client.generic.PasswordCredential;
+import uk.org.taverna.server.client.generic.port.InputPort;
+import uk.org.taverna.server.client.generic.port.OutputPort;
+import uk.org.taverna.server.client.rest.InputDescription;
+import uk.org.taverna.server.client.rest.InputDescription.Value;
+
+import com.sun.jersey.api.client.ClientResponse;
+
+public class Run extends Connected {
+ RunsRunName run;
+
+ Run(TavernaServer server, String value) {
+ run = server.root.runsRunName(value);
+ }
+
+ public String getName() {
+ return run.name().getAsTextPlain(ClientResponse.class)
+ .getEntity(String.class);
+ }
+
+ public void setName(String name) {
+ run.name().putTextPlain(name, String.class);
+ }
+
+ public Date getExpiry() {
+ return dateTimeParser().parseDateTime(
+ run.expiry().getAsTextPlain(String.class)).toDate();
+ }
+
+ public void setExpiry(Date expiryTimestamp) {
+ run.expiry().putTextPlain(
+ dateTime().print(new DateTime(expiryTimestamp)), String.class);
+ }
+
+ public Date getCreate() {
+ String timestamp = run.createTime().getAsTextPlain(String.class);
+ if (timestamp == null || timestamp.trim().isEmpty())
+ return null;
+ return dateTimeParser().parseDateTime(timestamp).toDate();
+ }
+
+ public Date getStart() {
+ String timestamp = run.startTime().getAsTextPlain(String.class);
+ if (timestamp == null || timestamp.trim().isEmpty())
+ return null;
+ return dateTimeParser().parseDateTime(timestamp).toDate();
+ }
+
+ public Date getFinish() {
+ String timestamp = run.finishTime().getAsTextPlain(String.class);
+ if (timestamp == null || timestamp.trim().isEmpty())
+ return null;
+ return dateTimeParser().parseDateTime(timestamp).toDate();
+ }
+
+ public Status getStatus() {
+ return Status.valueOf(run.status().getAsTextPlain(String.class));
+ }
+
+ public void setStatus(Status status) {
+ run.status().putTextPlain(status, String.class);
+ }
+
+ public void start() {
+ setStatus(Status.Operating);
+ }
+
+ public void kill() {
+ setStatus(Status.Finished);
+ }
+
+ public boolean isRunning() {
+ return getStatus() == Status.Operating;
+ }
+
+ public String getStandardOutput() {
+ return run.stdout().getAsTextPlain(String.class);
+ }
+
+ public String getStandardError() {
+ return run.stderr().getAsTextPlain(String.class);
+ }
+
+ public String getLog() {
+ return run.log().getAsTextPlain(String.class);
+ }
+
+ public Integer getExitCode() {
+ String code = run.listeners().name("io")
+ .propertiesPropertyName("exitCode")
+ .getAsTextPlain(String.class);
+ if (code == null || code.trim().isEmpty())
+ return null;
+ return Integer.parseInt(code);
+ }
+
+ public String getProperty(Property prop) {
+ return run.listeners().name("io")
+ .propertiesPropertyName(prop.toString())
+ .getAsTextPlain(String.class);
+ }
+
+ public void setGenerateRunBundle(boolean generateRunBundle) {
+ run.generateProvenance().putTextPlain(generateRunBundle, String.class);
+ }
+
+ public byte[] getRunBundle() {
+ return run.runBundle().getAsVndWf4everRobundleZip(byte[].class);
+ }
+
+ public List<InputPort> getInputs() {
+ return run.input().expected().getAsInputDescriptionXml().getInput();
+ }
+
+ public List<OutputPort> getOutputs() {
+ return run.output().getAsOutputDescriptionXml().getOutput();
+ }
+
+ public void setInput(String name, String value) {
+ Value v = new Value();
+ v.setValue(value);
+ InputDescription idesc = new InputDescription();
+ idesc.setValue(v);
+ run.input().inputName(name).putXmlAsInputDescription(idesc);
+ }
+
+ public void setInput(String name, String value, char listSeparator) {
+ Value v = new Value();
+ v.setValue(value);
+ InputDescription idesc = new InputDescription();
+ idesc.setValue(v);
+ idesc.setListDelimiter(new String(new char[] { listSeparator }));
+ run.input().inputName(name).putXmlAsInputDescription(idesc);
+ }
+
+ public byte[] getWorkflow() {
+ return run.workflow().getAsVndTavernaT2flowXml(byte[].class);
+ }
+
+ // TODO Consider better ways to do this
+ public Element getInteractionFeed() {
+ return run.interaction().getAsAtomXml(Element.class);
+ }
+
+ public Element getInteractionEntry(String id) {
+ return run.interaction().id(id).getAsAtomXml(Element.class);
+ }
+
+ public JobUsageRecord getUsageRecord() throws JAXBException {
+ return JobUsageRecord.unmarshal(run.usage().getAsXml(Element.class));
+ }
+
+ public Directory getWorkingDirectory() {
+ return new Directory(this);
+ }
+
+ public String getOwner() {
+ return run.security().owner().getAsTextPlain(String.class);
+ }
+
+ // TODO permissions
+
+ public void grantPasswordCredential(URI contextService, String username,
+ String password) throws ClientException, ServerException {
+ PasswordCredential pc = new PasswordCredential();
+ pc.setServiceURI(contextService.toString());
+ pc.setUsername(username);
+ pc.setPassword(password);
+ checkError(run.security().credentials()
+ .postXmlAsOctetStream(pc, ClientResponse.class));
+ }
+
+ public void grantKeyCredential(URI contextService, java.io.File source,
+ String unlockPassword, String aliasEntry) throws IOException,
+ ClientException, ServerException {
+ KeyPairCredential kpc = new KeyPairCredential();
+ kpc.setServiceURI(contextService.toString());
+ try (InputStream in = new FileInputStream(source)) {
+ byte[] buffer = new byte[(int) source.length()];
+ IOUtils.read(in, buffer);
+ kpc.setCredentialBytes(buffer);
+ }
+ if (source.getName().endsWith(".p12"))
+ kpc.setFileType("PKCS12");
+ else
+ kpc.setFileType("JKS");
+ kpc.setCredentialName(aliasEntry);
+ kpc.setUnlockPassword(unlockPassword);
+ checkError(run.security().credentials()
+ .postXmlAsOctetStream(kpc, ClientResponse.class));
+ }
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/Status.java b/server-client/src/main/java/uk/org/taverna/server/client/Status.java
new file mode 100644
index 0000000..9c375ad
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/Status.java
@@ -0,0 +1,36 @@
+package uk.org.taverna.server.client;
+
+/**
+ * States of a workflow run. They are {@link #Initialized Initialized},
+ * {@link #Operating Operating}, {@link #Stopped Stopped}, and
+ * {@link #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 Status {
+ /**
+ * The workflow run has been created, but is not yet running. The run
+ * will need to be manually moved to {@link #Operating Operating} when
+ * ready.
+ */
+ Initialized,
+ /**
+ * The workflow run is going, reading input, generating output, etc.
+ * Will eventually either move automatically to {@link #Finished
+ * Finished} or can be moved manually to {@link #Stopped Stopped} (where
+ * supported).
+ */
+ Operating,
+ /**
+ * The workflow run is paused, and will need to be moved back to
+ * {@link #Operating 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
+}
\ No newline at end of file
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java
new file mode 100644
index 0000000..7c0dcdd
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServer.java
@@ -0,0 +1,128 @@
+package uk.org.taverna.server.client;
+
+import static java.nio.file.Files.readAllBytes;
+import static org.taverna.server.client.wadl.TavernaServer.createClient;
+import static org.taverna.server.client.wadl.TavernaServer.root;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.taverna.server.client.wadl.TavernaServer.Root;
+
+import uk.org.taverna.server.client.generic.Capability;
+import uk.org.taverna.server.client.generic.TavernaRun;
+import uk.org.taverna.server.client.generic.VersionedElement;
+
+import com.sun.jersey.api.client.Client;
+import com.sun.jersey.api.client.ClientResponse;
+import com.sun.jersey.api.client.filter.HTTPBasicAuthFilter;
+
+public class TavernaServer extends Connected {
+ final Root root;
+ private final URI location;
+ private final boolean authenticated;
+
+ TavernaServer(URI serviceRoot) {
+ root = root(createClient(), location = serviceRoot);
+ authenticated = false;
+ }
+
+ TavernaServer(URI serviceRoot, String username, String password) {
+ Client client = createClient();
+ client.addFilter(new HTTPBasicAuthFilter(username, password));
+ authenticated = true;
+ root = root(client, location = serviceRoot);
+ }
+
+ TavernaServer(TavernaServer service, String username, String password) {
+ Client client = createClient();
+ client.addFilter(new HTTPBasicAuthFilter(username, password));
+ authenticated = true;
+ root = root(client, location = service.location);
+ getServerVersionInfo();
+ }
+
+ public TavernaServer upgradeToAuth(String username, String password) {
+ if (authenticated)
+ throw new IllegalStateException("may only upgrade an unauthenticated connection");
+ return new TavernaServer(this, username, password);
+ }
+
+ public List<Capability> getCapabilities() {
+ return root.policy().capabilities().getAsCapabilitiesXml()
+ .getCapability();
+ }
+
+ public int getRunLimit() {
+ return root.policy().runLimit().getAsTextPlain(Integer.class);
+ }
+
+ public int getOperatingLimit() {
+ return root.policy().operatingLimit().getAsTextPlain(Integer.class);
+ }
+
+ public List<String> getPermittedWorkflows() {
+ return root.policy().permittedWorkflows().getAsPermittedWorkflowsXml()
+ .getWorkflow();
+ }
+
+ public List<Run> getExistingRuns() {
+ List<Run> runs = new ArrayList<>();
+ for (TavernaRun run : root.runs().getAsRunListXml().getRun())
+ runs.add(new Run(this, run.getValue()));
+ return runs;
+ }
+
+ public VersionedElement getServerVersionInfo() {
+ return root.getAsServerDescriptionXml();
+ }
+
+ private Run response2run(ClientResponse response) throws ClientException, ServerException {
+ checkError(response);
+ if (response.getClientResponseStatus().getStatusCode() == 201) {
+ String[] path = response.getLocation().getPath().split("/");
+ return new Run(this, path[path.length - 1]);
+ }
+ return null;
+ }
+
+ public Run createWorkflowRun(byte[] t2flowBytes) throws ClientException, ServerException {
+ return response2run(root.runs().postVndTavernaT2flowXmlAsOctetStream(
+ t2flowBytes, ClientResponse.class));
+ }
+
+ public Run createWorkflowRun(File t2flowFile) throws IOException, ClientException, ServerException {
+ return createWorkflowRun(readAllBytes(t2flowFile.toPath()));
+ }
+
+ public Run createWorkflowRun(URI t2flowUri) throws ClientException, ServerException {
+ return response2run(root.runs().postTextUriListAsOctetStream(
+ t2flowUri.toString(), ClientResponse.class));
+ }
+
+
+ public static class ClientException extends Exception {
+ private static final long serialVersionUID = 1L;
+
+ ClientException(String msg, Throwable cause) {
+ super(msg, cause);
+ }
+ }
+ public static class AuthorizationException extends ClientException {
+ private static final long serialVersionUID = 1L;
+
+ AuthorizationException(String msg, Throwable cause) {
+ super(msg, cause);
+ }
+ }
+ static class ServerException extends Exception {
+ private static final long serialVersionUID = 1L;
+
+ ServerException(String msg, Throwable cause) {
+ super(msg, cause);
+ }
+ }
+}
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java
new file mode 100644
index 0000000..b00b075
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/TavernaServerConnectionFactory.java
@@ -0,0 +1,23 @@
+package uk.org.taverna.server.client;
+
+import java.net.URI;
+import java.util.HashMap;
+import java.util.Map;
+
+public class TavernaServerConnectionFactory {
+ private Map<URI, TavernaServer> cache = new HashMap<>();
+
+ public synchronized TavernaServer connectNoAuth(URI uri) {
+ TavernaServer conn = cache.get(uri);
+ if (conn == null)
+ cache.put(uri, conn = new TavernaServer(uri));
+ return conn;
+ }
+
+ public TavernaServer connectAuth(URI uri, String username, String password) {
+ TavernaServer conn = new TavernaServer(uri, username, password);
+ // Force a check of the credentials by getting the server version
+ conn.getServerVersionInfo();
+ return conn;
+ }
+}
diff --git a/server-client/src/main/java/uk/org/taverna/server/client/package-info.java b/server-client/src/main/java/uk/org/taverna/server/client/package-info.java
new file mode 100644
index 0000000..59e809d
--- /dev/null
+++ b/server-client/src/main/java/uk/org/taverna/server/client/package-info.java
@@ -0,0 +1,5 @@
+/**
+ * Implementation of a basic client for Taverna Server.
+ * @author Donal Fellows
+ */
+package uk.org.taverna.server.client;
\ No newline at end of file
diff --git a/server-client/src/main/wadl/tavserv.wadl b/server-client/src/main/wadl/tavserv.wadl
new file mode 100644
index 0000000..2ba8fbe
--- /dev/null
+++ b/server-client/src/main/wadl/tavserv.wadl
@@ -0,0 +1,591 @@
+<application xmlns="http://wadl.dev.java.net/2009/02"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:prefix1="http://ns.taverna.org.uk/2010/xml/server/rest/"
+ xmlns:prefix3="http://ns.taverna.org.uk/2010/xml/server/"
+ xmlns:prefix10="http://ns.taverna.org.uk/2010/port/" xmlns:jxb="http://java.sun.com/xml/ns/jaxb"
+ xsi:schemaLocation="http://java.sun.com/xml/ns/jaxb http://java.sun.com/xml/ns/jaxb/bindingschema_2_0.xsd"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" jxb:version="2.1">
+<grammars>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:admin="http://ns.taverna.org.uk/2010/xml/server/admin/" xmlns:feed="http://ns.taverna.org.uk/2010/xml/server/feed/" xmlns:port="http://ns.taverna.org.uk/2010/port/" xmlns:tns="http://ns.taverna.org.uk/2010/xml/server/rest/" xmlns:ts="http://ns.taverna.org.uk/2010/xml/server/" xmlns:ts-rest="http://ns.taverna.org.uk/2010/xml/server/rest/" xmlns:ts-soap="http://ns.taverna.org.uk/2010/xml/server/soap/" xmlns:xlink="http://www.w3.org/1999/xlink" attributeFormDefault="qualified" elementFormDefault="qualified" targetNamespace="http://ns.taverna.org.uk/2010/xml/server/rest/" jxb:version="2.1">
+ <xs:annotation>
+ <xs:appinfo>
+ <jxb:schemaBindings>
+ <jxb:package name="uk.org.taverna.server.client.rest" />
+ </jxb:schemaBindings>
+ </xs:appinfo>
+ </xs:annotation>
+ <xs:import namespace="http://ns.taverna.org.uk/2010/xml/server/"/>
+ <xs:import namespace="http://www.w3.org/1999/xlink"/>
+ <xs:element name="capabilities">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="capability" type="ts:Capability"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="credential" type="ts-rest:Credential"/>
+ <xs:element name="credentials" type="ts-rest:credentialList"/>
+ <xs:element name="directoryContents" type="ts-rest:DirectoryContents"/>
+ <xs:element name="enabledNotificationFabrics">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="notifier" type="xs:string"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="filesystemOperation" type="ts-rest:FilesystemCreationOperation"/>
+ <xs:element name="listenerDefinition" type="ts-rest:ListenerDefinition"/>
+ <xs:element name="listenerDescription" type="ts-rest:ListenerDescription"/>
+ <xs:element name="listeners">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="listener" type="ts-rest:ListenerDescription"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="mkdir" type="ts-rest:MakeDirectory"/>
+ <xs:element name="permissionUpdate" type="ts-rest:permissionDescription"/>
+ <xs:element name="permissionsDescriptor" type="ts-rest:permissionsDescription"/>
+ <xs:element name="permittedListeners">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="type" type="xs:string"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="permittedWorkflows">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="workflow" type="xs:string"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="policyDescription">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="runLimit" type="ts:Location"/>
+ <xs:element minOccurs="0" name="operatingLimit" type="ts:Location"/>
+ <xs:element minOccurs="0" name="permittedWorkflows" type="ts:Location"/>
+ <xs:element minOccurs="0" name="permittedListenerTypes" type="ts:Location"/>
+ <xs:element minOccurs="0" name="enabledNotificationFabrics" type="ts:Location"/>
+ <xs:element minOccurs="0" name="capabilities" type="ts:Location"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="properties">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="property" type="ts-rest:PropertyDescription"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="runDescription">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="expiry">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute ref="xlink:href"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element minOccurs="0" name="creationWorkflow" type="ts:Location"/>
+ <xs:element minOccurs="0" name="createTime" type="ts:Location"/>
+ <xs:element minOccurs="0" name="startTime" type="ts:Location"/>
+ <xs:element minOccurs="0" name="finishTime" type="ts:Location"/>
+ <xs:element minOccurs="0" name="status" type="ts:Location"/>
+ <xs:element minOccurs="0" name="workingDirectory" type="ts:Location"/>
+ <xs:element minOccurs="0" name="inputs" type="ts:Location"/>
+ <xs:element minOccurs="0" name="output" type="ts:Location"/>
+ <xs:element minOccurs="0" name="securityContext" type="ts:Location"/>
+ <xs:element minOccurs="0" name="listeners">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:Location">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="listener" nillable="true" type="ts:Location"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element minOccurs="0" name="interaction" type="ts:Location"/>
+ <xs:element minOccurs="0" name="name" type="ts:Location"/>
+ <xs:element minOccurs="0" name="stdout" type="ts:Location"/>
+ <xs:element minOccurs="0" name="stderr" type="ts:Location"/>
+ <xs:element minOccurs="0" name="usage" type="ts:Location"/>
+ <xs:element minOccurs="0" name="log" type="ts:Location"/>
+ <xs:element minOccurs="0" name="run-bundle" type="ts:Location"/>
+ <xs:element minOccurs="0" name="generate-provenance" type="ts:Location"/>
+ </xs:sequence>
+ <xs:attribute ref="ts-rest:owner"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="runInput" type="ts-rest:InputDescription"/>
+ <xs:element name="runInputs" type="ts-rest:TavernaRunInputs"/>
+ <xs:element name="runList">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="run" type="ts:TavernaRun"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="securityDescriptor" type="ts-rest:SecurityDescriptor"/>
+ <xs:element name="serverDescription">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="runs" type="ts:Location"/>
+ <xs:element minOccurs="0" name="policy" type="ts:Location"/>
+ <xs:element minOccurs="0" name="feed" type="ts:Location"/>
+ <xs:element minOccurs="0" name="interactionFeed" type="ts:Location"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="trustedIdentities" type="ts-rest:trustList"/>
+ <xs:element name="upload" type="ts-rest:UploadFile"/>
+ <xs:element name="userPermission" type="ts-rest:linkedPermissionDescription"/>
+ <xs:complexType name="InputDescription">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:choice minOccurs="0">
+ <xs:element name="file">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="ts-rest:InputContents"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="reference">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="ts-rest:InputContents"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="value">
+ <xs:complexType>
+ <xs:simpleContent>
+ <xs:extension base="ts-rest:InputContents"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute ref="ts-rest:name"/>
+ <xs:attribute ref="ts-rest:descriptorRef"/>
+ <xs:attribute ref="ts-rest:listDelimiter"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:simpleType name="InputContents">
+ <xs:restriction base="xs:string"/>
+ </xs:simpleType>
+ <xs:complexType name="ListenerDescription">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="configuration" type="ts:Location"/>
+ <xs:element minOccurs="0" name="properties">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="property" type="ts-rest:PropertyDescription"/>
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute ref="xlink:href"/>
+ <xs:attribute ref="ts-rest:name"/>
+ <xs:attribute ref="ts-rest:type"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="PropertyDescription">
+ <xs:complexContent>
+ <xs:extension base="ts:Location">
+ <xs:sequence/>
+ <xs:attribute ref="ts-rest:name"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="TavernaRunInputs">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="expected" type="ts:Location"/>
+ <xs:element minOccurs="0" name="baclava" type="ts:Location"/>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="input" nillable="true" type="ts:Location"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="Credential">
+ <xs:choice>
+ <xs:element ref="ts:keypair"/>
+ <xs:element ref="ts:userpass"/>
+ </xs:choice>
+ </xs:complexType>
+ <xs:complexType name="DirectoryContents">
+ <xs:sequence>
+ <xs:choice maxOccurs="unbounded" minOccurs="0">
+ <xs:element ref="ts:dir"/>
+ <xs:element ref="ts:file"/>
+ </xs:choice>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType name="FilesystemCreationOperation">
+ <xs:simpleContent>
+ <xs:extension base="xs:base64Binary">
+ <xs:attribute ref="ts-rest:name"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="MakeDirectory">
+ <xs:simpleContent>
+ <xs:extension base="ts-rest:FilesystemCreationOperation"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="UploadFile">
+ <xs:simpleContent>
+ <xs:extension base="ts-rest:FilesystemCreationOperation"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="permissionsDescription">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="permission" type="ts-rest:linkedPermissionDescription"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="linkedPermissionDescription">
+ <xs:complexContent>
+ <xs:extension base="ts:Location">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="userName" type="xs:string"/>
+ <xs:element minOccurs="0" name="permission" type="ts:Permission"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="trustList">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="trust" type="ts:TrustDescriptor"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="permissionDescription">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="userName" type="xs:string"/>
+ <xs:element minOccurs="0" name="permission" type="ts:Permission"/>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="SecurityDescriptor">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="owner" type="xs:string"/>
+ <xs:element minOccurs="0" name="permissions" type="ts:Location"/>
+ <xs:element minOccurs="0" name="credentials" type="ts-rest:CredentialCollection"/>
+ <xs:element minOccurs="0" name="trusts" type="ts-rest:TrustCollection"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="CredentialCollection">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" ref="ts-rest:credential"/>
+ </xs:sequence>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="TrustCollection">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="trust" type="ts:TrustDescriptor"/>
+ </xs:sequence>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="credentialList">
+ <xs:complexContent>
+ <xs:extension base="ts:VersionedElement">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" ref="ts-rest:credential"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="ListenerDefinition">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute ref="ts-rest:type"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:attribute name="descriptorRef" type="xs:anyURI"/>
+ <xs:attribute name="listDelimiter" type="xs:string"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="owner" type="xs:string"/>
+ <xs:attribute name="type" type="xs:string"/>
+</xs:schema>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://www.w3.org/1999/xlink" attributeFormDefault="unqualified" elementFormDefault="unqualified" targetNamespace="http://www.w3.org/1999/xlink" jxb:version="2.1">
+ <xs:attribute name="href" type="xs:string"/>
+</xs:schema>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:port="http://ns.taverna.org.uk/2010/port/" xmlns:run="http://ns.taverna.org.uk/2010/run/" xmlns:tns="http://ns.taverna.org.uk/2010/port/" xmlns:xlink="http://www.w3.org/1999/xlink" attributeFormDefault="qualified" elementFormDefault="qualified" targetNamespace="http://ns.taverna.org.uk/2010/port/" jxb:version="2.1">
+ <xs:annotation>
+ <xs:appinfo>
+ <jxb:schemaBindings>
+ <jxb:package name="uk.org.taverna.server.client.generic.port" />
+ </jxb:schemaBindings>
+ </xs:appinfo>
+ </xs:annotation>
+ <xs:import namespace="http://www.w3.org/1999/xlink"/>
+ <xs:element name="inputDescription" type="port:inputDescription"/>
+ <xs:element name="workflowOutputs" type="port:outputDescription"/>
+ <xs:complexType name="outputDescription">
+ <xs:complexContent>
+ <xs:extension base="port:PortDescription">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="output" type="port:OutputPort"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType abstract="true" name="PortDescription">
+ <xs:sequence/>
+ <xs:attribute ref="port:workflowId"/>
+ <xs:attribute ref="port:workflowRun"/>
+ <xs:attribute ref="port:workflowRunId"/>
+ </xs:complexType>
+ <xs:complexType name="OutputPort">
+ <xs:complexContent>
+ <xs:extension base="port:Port">
+ <xs:choice>
+ <xs:element name="value" type="port:LeafValue"/>
+ <xs:element name="list" type="port:ListValue"/>
+ <xs:element name="error" type="port:ErrorValue"/>
+ <xs:element name="absent" type="port:AbsentValue"/>
+ </xs:choice>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="Port">
+ <xs:sequence/>
+ <xs:attribute ref="port:name" use="required"/>
+ <xs:attribute ref="port:depth"/>
+ </xs:complexType>
+ <xs:complexType name="LeafValue">
+ <xs:complexContent>
+ <xs:extension base="port:Value">
+ <xs:sequence/>
+ <xs:attribute ref="port:contentFile"/>
+ <xs:attribute ref="port:contentType"/>
+ <xs:attribute ref="port:contentByteLength"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType abstract="true" name="Value">
+ <xs:sequence/>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:complexType name="ErrorValue">
+ <xs:complexContent>
+ <xs:extension base="port:Value">
+ <xs:sequence/>
+ <xs:attribute ref="port:depth"/>
+ <xs:attribute ref="port:errorFile"/>
+ <xs:attribute ref="port:errorByteLength"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="ListValue">
+ <xs:complexContent>
+ <xs:extension base="port:Value">
+ <xs:sequence>
+ <xs:choice maxOccurs="unbounded" minOccurs="0">
+ <xs:element name="value" type="port:LeafValue"/>
+ <xs:element name="list" type="port:ListValue"/>
+ <xs:element name="error" type="port:ErrorValue"/>
+ <xs:element name="absent" type="port:AbsentValue"/>
+ </xs:choice>
+ </xs:sequence>
+ <xs:attribute ref="port:length"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="AbsentValue">
+ <xs:complexContent>
+ <xs:extension base="port:Value">
+ <xs:sequence/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="inputDescription">
+ <xs:complexContent>
+ <xs:extension base="port:PortDescription">
+ <xs:sequence>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="input" type="port:InputPort"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="InputPort">
+ <xs:complexContent>
+ <xs:extension base="port:Port">
+ <xs:sequence/>
+ <xs:attribute ref="xlink:href"/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:attribute name="contentByteLength" type="xs:long"/>
+ <xs:attribute name="contentFile" type="xs:string"/>
+ <xs:attribute name="contentType" type="xs:string"/>
+ <xs:attribute name="depth" type="xs:int"/>
+ <xs:attribute name="errorByteLength" type="xs:long"/>
+ <xs:attribute name="errorFile" type="xs:string"/>
+ <xs:attribute name="length" type="xs:int"/>
+ <xs:attribute name="name" type="xs:ID"/>
+ <xs:attribute name="workflowId" type="xs:string"/>
+ <xs:attribute name="workflowRun" type="xs:anyURI"/>
+ <xs:attribute name="workflowRunId" type="xs:string"/>
+</xs:schema>
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:admin="http://ns.taverna.org.uk/2010/xml/server/admin/" xmlns:feed="http://ns.taverna.org.uk/2010/xml/server/feed/" xmlns:tns="http://ns.taverna.org.uk/2010/xml/server/" xmlns:ts="http://ns.taverna.org.uk/2010/xml/server/" xmlns:ts-rest="http://ns.taverna.org.uk/2010/xml/server/rest/" xmlns:ts-soap="http://ns.taverna.org.uk/2010/xml/server/soap/" xmlns:xlink="http://www.w3.org/1999/xlink" attributeFormDefault="qualified" elementFormDefault="qualified" targetNamespace="http://ns.taverna.org.uk/2010/xml/server/" jxb:version="2.1">
+ <xs:annotation>
+ <xs:appinfo>
+ <jxb:schemaBindings>
+ <jxb:package name="uk.org.taverna.server.client.generic" />
+ </jxb:schemaBindings>
+ </xs:appinfo>
+ </xs:annotation>
+ <xs:import namespace="http://www.w3.org/1999/xlink"/>
+ <xs:element name="capability" type="ts:Capability"/>
+ <xs:element name="dir" type="ts:DirectoryReference"/>
+ <xs:element name="file" type="ts:FileReference"/>
+ <xs:element name="keypair" type="ts:KeyPairCredential"/>
+ <xs:element name="runReference" type="ts:TavernaRun"/>
+ <xs:element name="trustedIdentity" type="ts:TrustDescriptor"/>
+ <xs:element name="userpass" type="ts:PasswordCredential"/>
+ <xs:element name="workflow" type="ts:Workflow"/>
+ <xs:complexType abstract="true" name="VersionedElement">
+ <xs:sequence/>
+ <xs:attribute ref="ts:serverVersion"/>
+ <xs:attribute ref="ts:serverRevision"/>
+ <xs:attribute ref="ts:serverBuildTimestamp"/>
+ </xs:complexType>
+ <xs:complexType name="Location">
+ <xs:sequence/>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:complexType name="Capability">
+ <xs:sequence/>
+ <xs:attribute ref="ts:capability"/>
+ <xs:attribute ref="ts:version"/>
+ </xs:complexType>
+ <xs:complexType name="KeyPairCredential">
+ <xs:complexContent>
+ <xs:extension base="ts:CredentialDescriptor">
+ <xs:sequence>
+ <xs:element name="credentialName" type="xs:string"/>
+ <xs:element minOccurs="0" name="credentialFile" type="xs:string"/>
+ <xs:element minOccurs="0" name="fileType" type="xs:string"/>
+ <xs:element minOccurs="0" name="unlockPassword" type="xs:string"/>
+ <xs:element minOccurs="0" name="credentialBytes" type="xs:base64Binary"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType abstract="true" name="CredentialDescriptor">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="serviceURI" type="xs:anyURI"/>
+ </xs:sequence>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:complexType name="PasswordCredential">
+ <xs:complexContent>
+ <xs:extension base="ts:CredentialDescriptor">
+ <xs:sequence>
+ <xs:element name="username" type="xs:string"/>
+ <xs:element name="password" type="xs:string"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ <xs:complexType name="DirectoryEntry">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute ref="xlink:href"/>
+ <xs:attribute ref="ts:name"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="DirectoryReference">
+ <xs:simpleContent>
+ <xs:extension base="ts:DirectoryEntry"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="FileReference">
+ <xs:simpleContent>
+ <xs:extension base="ts:DirectoryEntry"/>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="TavernaRun">
+ <xs:simpleContent>
+ <xs:extension base="xs:string">
+ <xs:attribute ref="xlink:href"/>
+ <xs:attribute ref="ts:serverVersion"/>
+ </xs:extension>
+ </xs:simpleContent>
+ </xs:complexType>
+ <xs:complexType name="Workflow">
+ <xs:sequence>
+ <xs:any maxOccurs="unbounded" minOccurs="0" namespace="##other" processContents="lax"/>
+ </xs:sequence>
+ </xs:complexType>
+ <xs:complexType final="extension restriction" name="TrustDescriptor">
+ <xs:sequence>
+ <xs:element minOccurs="0" name="certificateFile" type="xs:string"/>
+ <xs:element minOccurs="0" name="fileType" type="xs:string"/>
+ <xs:element minOccurs="0" name="certificateBytes" type="xs:base64Binary"/>
+ <xs:element maxOccurs="unbounded" minOccurs="0" name="serverName" type="xs:string"/>
+ </xs:sequence>
+ <xs:attribute ref="xlink:href"/>
+ </xs:complexType>
+ <xs:simpleType name="Permission">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="none"/>
+ <xs:enumeration value="read"/>
+ <xs:enumeration value="update"/>
+ <xs:enumeration value="destroy"/>
+ </xs:restriction>
+ </xs:simpleType>
+ <xs:attribute name="capability" type="xs:anyURI"/>
+ <xs:attribute name="name" type="xs:string"/>
+ <xs:attribute name="serverBuildTimestamp" type="xs:string"/>
+ <xs:attribute name="serverRevision" type="xs:string"/>
+ <xs:attribute name="serverVersion" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+</xs:schema>
+</grammars><resources base="http://example.com/taverna/rest"><resource path="/"><method name="GET"><doc>Produces the description of the service.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:serverDescription"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the service.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="runs"><method name="GET"><doc>Produces a list of all runs visible to the user.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:runList"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the operations on the collection of runs.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Accepts (or not) a request to create a new run executing the given workflow.</doc><request><representation mediaType="application/vnd.taverna.t2flow+xml" element="prefix3:workflow"><doc>Accepts (or not) a request to create a new run executing the given workflow.</doc></representation><representation mediaType="application/xml" element="prefix3:workflow"><doc>Accepts (or not) a request to create a new run executing the given workflow.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Accepts a URL to a workflow to download and run. The URL must be hosted on a publicly-accessible service.</doc><request><representation mediaType="text/uri-list"><doc>Accepts a URL to a workflow to download and run. The URL must be hosted on a publicly-accessible service.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/policy"><method name="GET"><doc>Describe the parts of this policy.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:policyDescription"></representation><representation mediaType="application/json"></representation></response></method><resource path="/capabilities"><method name="GET"><doc>Gets a description of the capabilities supported by this installation of Taverna Server.</doc><response><representation mediaType="application/xml" element="prefix1:capabilities"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/enabledNotificationFabrics"><method name="GET"><doc>Gets the list of supported, enabled notification fabrics. Each corresponds (approximately) to a protocol, e.g., email.</doc><response><representation mediaType="application/xml" element="prefix1:enabledNotificationFabrics"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/operatingLimit"><method name="GET"><doc>Gets the maximum number of simultaneously operating runs that the user may have. Note that this is often a global limit; it does not represent a promise that a particular user may be able to have that many operating runs at once.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:int"><doc>Gets the maximum number of simultaneously operating runs that the user may have. Note that this is often a global limit; it does not represent a promise that a particular user may be able to have that many operating runs at once.</doc></param></representation></response></method></resource><resource path="/permittedListenerTypes"><method name="GET"><doc>Gets the list of permitted event listener types.</doc><response><representation mediaType="application/xml" element="prefix1:permittedListeners"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/permittedWorkflows"><method name="GET"><doc>Gets the list of permitted workflows.</doc><response><representation mediaType="application/xml" element="prefix1:permittedWorkflows"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/runLimit"><method name="GET"><doc>Gets the maximum number of simultaneous runs in any state that the user may create.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:int"><doc>Gets the maximum number of simultaneous runs in any state that the user may create.</doc></param></representation></response></method></resource></resource><resource path="/runs/{runName}"><doc>This represents how a Taverna Server workflow run looks to a RESTful API.</doc><param name="runName" style="template" type="xs:string"/><method name="DELETE"><doc>Deletes a workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Describes a workflow run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:runDescription"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="/createTime"><method name="GET"><doc>Gives the time when the workflow run was first submitted to the server.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the time when the workflow run was first submitted to the server.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run create time.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/expiry"><method name="GET"><doc>Gives the time when the workflow run becomes eligible for automatic deletion.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the time when the workflow run becomes eligible for automatic deletion.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run expiry.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Sets the time when the workflow run becomes eligible for automatic deletion.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Sets the time when the workflow run becomes eligible for automatic deletion.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Sets the time when the workflow run becomes eligible for automatic deletion.</doc></param></representation></response></method></resource><resource path="/finishTime"><method name="GET"><doc>Gives the time when the workflow run was first detected as finished, or an empty string if it has not yet finished (including if it has never started).</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the time when the workflow run was first detected as finished, or an empty string if it has not yet finished (including if it has never started).</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run finish time.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/generate-provenance"><method name="GET"><doc>Whether to create the run bundle for the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:boolean"><doc>Whether to create the run bundle for the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Whether to create the run bundle for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Whether to create the run bundle for the workflow run.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:boolean"><doc>Whether to create the run bundle for the workflow run.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:boolean"><doc>Whether to create the run bundle for the workflow run.</doc></param></representation></response></method></resource><resource path="/log"><method name="GET"><doc>Return the log for the workflow run.</doc><response><representation mediaType="text/plain"></representation></response></method><method name="OPTIONS"><doc>Return the log for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/name"><method name="GET"><doc>Gives the descriptive name of the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the descriptive name of the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the operations on the run's descriptive name.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Set the descriptive name of the workflow run. Note that this value may be arbitrarily truncated by the implementation.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Set the descriptive name of the workflow run. Note that this value may be arbitrarily truncated by the implementation.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Set the descriptive name of the workflow run. Note that this value may be arbitrarily truncated by the implementation.</doc></param></representation></response></method></resource><resource path="/output"><method name="GET"><doc>Gives the Baclava file where output will be written; empty means use multiple simple files in the out directory.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the Baclava file where output will be written; empty means use multiple simple files in the out directory.</doc></param></representation></response></method><method name="GET"><doc>Gives a description of the outputs, as currently understood</doc><request></request><response><representation mediaType="application/xml" element="prefix10:workflowOutputs"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run output.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Sets the Baclava file where output will be written; empty means use multiple simple files in the out directory.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Sets the Baclava file where output will be written; empty means use multiple simple files in the out directory.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Sets the Baclava file where output will be written; empty means use multiple simple files in the out directory.</doc></param></representation></response></method></resource><resource path="/run-bundle"><method name="GET"><doc>Return the run bundle for the workflow run.</doc><response><representation mediaType="application/vnd.wf4ever.robundle+zip"></representation></response></method><method name="OPTIONS"><doc>Return the run bundle for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/startTime"><method name="GET"><doc>Gives the time when the workflow run was started, or an empty string if the run has not yet started.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the time when the workflow run was started, or an empty string if the run has not yet started.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run start time.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/status"><method name="GET"><doc>Gives the current status of the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the current status of the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run status.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Attempts to update the status of the workflow run.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Attempts to update the status of the workflow run.</doc></param></representation></request><response><representation mediaType="text/plain"></representation></response></method></resource><resource path="/stderr"><method name="GET"><doc>Return the stderr for the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Return the stderr for the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Return the stderr for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/stdout"><method name="GET"><doc>Return the stdout for the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Return the stdout for the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Return the stdout for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/usage"><method name="GET"><doc>Return the usage record for the workflow run.</doc><response><representation mediaType="application/xml"></representation></response></method><method name="OPTIONS"><doc>Return the usage record for the workflow run.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/workflow"><method name="GET"><doc>Gives the workflow document used to create the workflow run.</doc><response><representation mediaType="application/vnd.taverna.t2flow+xml" element="prefix3:workflow"></representation><representation mediaType="application/xml" element="prefix3:workflow"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run workflow.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/input"><doc>This represents how a Taverna Server workflow run's inputs looks to a RESTful API.</doc><method name="GET"><doc>Describe the sub-URIs of this resource.</doc><response><representation mediaType="application/xml" element="prefix1:runInputs"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run's inputs' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="/baclava"><method name="GET"><doc>Gives the Baclava file describing the inputs, or empty if individual files are used.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the Baclava file describing the inputs, or empty if individual files are used.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the inputs' baclava operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Sets the Baclava file describing the inputs.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Sets the Baclava file describing the inputs.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Sets the Baclava file describing the inputs.</doc></param></representation></response></method></resource><resource path="/expected"><method name="GET"><doc>Describe the expected inputs of this workflow run.</doc><response><representation mediaType="application/xml" element="prefix10:inputDescription"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the expected inputs' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/input/{name}"><param name="name" style="template" type="xs:string"/><method name="GET"><doc>Gives a description of what is used to supply a particular input.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:runInput"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the one input's operations.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Sets the source for a particular input port.</doc><request><representation mediaType="application/xml" element="prefix1:runInput"><doc>Sets the source for a particular input port.</doc></representation><representation mediaType="application/json"><doc>Sets the source for a particular input port.</doc></representation></request><response><representation mediaType="application/xml" element="prefix1:runInput"></representation><representation mediaType="application/json"></representation></response></method></resource></resource><resource path="/interaction"><method name="GET"><doc>Get the feed document for this ATOM feed.</doc><response><representation mediaType="application/atom+xml"></representation></response></method><method name="OPTIONS"><doc>Describes what HTTP operations are supported on the feed.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Adds an entry to this ATOM feed.</doc><request><representation mediaType="application/atom+xml"><doc>Adds an entry to this ATOM feed.</doc></representation></request><response><representation mediaType="application/atom+xml"></representation></response></method><resource path="/{id}"><param name="id" style="template" type="xs:string"/><method name="DELETE"><doc>Deletes an entry from this ATOM feed.</doc><request></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Deletes an entry from this ATOM feed.</doc></param></representation></response></method><method name="GET"><doc>Get the entry with a particular ID within this ATOM feed.</doc><request></request><response><representation mediaType="application/atom+xml"></representation></response></method><method name="OPTIONS"><doc>Describes what HTTP operations are supported on an entry.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method></resource></resource><resource path="/listeners"><doc>This represents all the event listeners attached to a workflow run.</doc><method name="GET"><doc>Get the listeners installed in the workflow run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:listeners"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run listeners' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Add a new event listener to the named workflow run.</doc><request><representation mediaType="application/xml" element="prefix1:listenerDefinition"><doc>Add a new event listener to the named workflow run.</doc></representation><representation mediaType="application/json"><doc>Add a new event listener to the named workflow run.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="/{name}"><doc>This represents a single event listener attached to a workflow run.</doc><param name="name" style="template" type="xs:string"/><method name="GET"><doc>Get the description of this listener.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:listenerDescription"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run listener's operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="/configuration"><method name="GET"><doc>Get the configuration for the given event listener that is attached to a workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Get the configuration for the given event listener that is attached to a workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run listener's configuration's operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/properties"><method name="GET"><doc>Get the list of properties supported by a given event listener attached to a workflow run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:properties"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run listener's properties' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/properties/{propertyName}"><doc>This represents a single property attached of an event listener.</doc><param name="propertyName" style="template" type="xs:string"/><method name="GET"><doc>Get the value of the particular property of an event listener attached to a workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Get the value of the particular property of an event listener attached to a workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run listener's property's operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Set the value of the particular property of an event listener attached to a workflow run.</doc><request><representation mediaType="text/plain"><param name="request" style="plain" type="xs:string"><doc>Set the value of the particular property of an event listener attached to a workflow run.</doc></param></representation></request><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Set the value of the particular property of an event listener attached to a workflow run.</doc></param></representation></response></method></resource></resource></resource><resource path="/security"><doc>Manages the security of the workflow run. In general, only the owner of a run may access this resource.</doc><method name="GET"><doc>Gives a description of the security information supported by the workflow run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:securityDescriptor"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run security.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><resource path="/credentials"><method name="DELETE"><doc>Deletes all credentials.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Gives a list of credentials supplied to this workflow run.</doc><response><representation mediaType="application/xml" element="prefix1:credentials"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run credentials' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Creates a new credential.</doc><request><representation mediaType="application/xml" element="prefix1:credential"><doc>Creates a new credential.</doc></representation><representation mediaType="application/json"><doc>Creates a new credential.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/credentials/{id}"><param name="id" style="template" type="xs:string"/><method name="DELETE"><doc>Deletes a particular credential.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Describes a particular credential.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:credential"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run credential's operations.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Updates a particular credential.</doc><request><representation mediaType="application/xml" element="prefix1:credential"><doc>Updates a particular credential.</doc></representation><representation mediaType="application/json"><doc>Updates a particular credential.</doc></representation></request><response><representation mediaType="application/xml" element="prefix1:credential"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/owner"><method name="GET"><doc>Gives the identity of who owns the workflow run.</doc><response><representation mediaType="text/plain"><param name="result" style="plain" type="xs:string"><doc>Gives the identity of who owns the workflow run.</doc></param></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run owner.</doc><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/permissions"><method name="GET"><doc>Gives a list of all non-default permissions associated with the enclosing workflow run. By default, nobody has any access at all except for the owner of the run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:permissionsDescriptor"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run permissions' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Creates a new assignment of permissions to a particular user.</doc><request><representation mediaType="application/xml" element="prefix1:permissionUpdate"><doc>Creates a new assignment of permissions to a particular user.</doc></representation><representation mediaType="application/json"><doc>Creates a new assignment of permissions to a particular user.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/permissions/{id}"><param name="id" style="template" type="xs:string"/><method name="DELETE"><doc>Deletes (by resetting to default) the permissions associated with a particular user.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Describes the permission granted to a particular user.</doc><request></request><response><representation mediaType="text/plain"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run permission's operations.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Updates the permissions granted to a particular user.</doc><request><representation mediaType="text/plain"><doc>Updates the permissions granted to a particular user.</doc></representation></request><response><representation mediaType="text/plain"></representation></response></method></resource><resource path="/trusts"><method name="DELETE"><doc>Deletes all trusted identities.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Gives a list of trusted identities supplied to this workflow run.</doc><response><representation mediaType="application/xml" element="prefix1:trustedIdentities"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the run trusted certificates' operations.</doc><response><representation mediaType="application/octet-stream"></representation></response></method><method name="POST"><doc>Adds a new trusted identity.</doc><request><representation mediaType="application/xml" element="prefix3:trustedIdentity"><doc>Adds a new trusted identity.</doc></representation><representation mediaType="application/json"><doc>Adds a new trusted identity.</doc></representation></request><response><representation mediaType="application/octet-stream"></representation></response></method></resource><resource path="/trusts/{id}"><param name="id" style="template" type="xs:string"/><method name="DELETE"><doc>Deletes a particular trusted identity.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="GET"><doc>Describes a particular trusted identity.</doc><request></request><response><representation mediaType="application/xml" element="prefix3:trustedIdentity"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of one run trusted certificate's operations.</doc><request></request><response><representation mediaType="application/octet-stream"></representation></response></method><method name="PUT"><doc>Updates a particular trusted identity.</doc><request><representation mediaType="application/xml" element="prefix3:trustedIdentity"><doc>Updates a particular trusted identity.</doc></representation><representation mediaType="application/json"><doc>Updates a particular trusted identity.</doc></representation></request><response><representation mediaType="application/xml" element="prefix3:trustedIdentity"></representation><representation mediaType="application/json"></representation></response></method></resource></resource><resource path="/wd"><doc>Representation of how a workflow run's working directory tree looks.</doc><method name="GET"><doc>Describes the working directory of the workflow run.</doc><request></request><response><representation mediaType="application/xml" element="prefix1:directoryContents"></representation><representation mediaType="application/json"></representation></response></method><resource path="/{path:(.*)}"><param name="path" style="template" repeating="true"/><method name="POST"><doc>Creates or updates a file in a particular location beneath the working directory of the workflow run with the contents of a publicly readable URL.</doc><request><representation mediaType="text/uri-list"><doc>Creates or updates a file in a particular location beneath the working directory of the workflow run with the contents of a publicly readable URL.</doc></representation></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation></response></method><method name="PUT"><doc>Creates or updates a file in a particular location beneath the working directory of the workflow run.</doc><request><representation mediaType="application/octet-stream"><doc>Creates or updates a file in a particular location beneath the working directory of the workflow run.</doc></representation><representation mediaType="*/*"><doc>Creates or updates a file in a particular location beneath the working directory of the workflow run.</doc></representation></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/{path:.*}"><param name="path" style="template" repeating="true"/><method name="DELETE"><doc>Deletes a file or directory that is in or below the working directory of a workflow run.</doc><request></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation></response></method><method name="OPTIONS"><doc>Produces the description of the files/directories' baclava operations.</doc><request></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation></response></method><method name="POST"><doc>Creates a directory in the filesystem beneath the working directory of the workflow run, or creates or updates a file's contents, where that file is in or below the working directory of a workflow run.</doc><request><representation mediaType="application/xml" element="prefix1:filesystemOperation"><doc>Creates a directory in the filesystem beneath the working directory of the workflow run, or creates or updates a file's contents, where that file is in or below the working directory of a workflow run.</doc></representation><representation mediaType="application/json"><doc>Creates a directory in the filesystem beneath the working directory of the workflow run, or creates or updates a file's contents, where that file is in or below the working directory of a workflow run.</doc></representation></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation></response></method></resource><resource path="/{path:.+}"><param name="path" style="template" repeating="true"/><method name="GET"><doc>Gives a description of the named entity in or beneath the working directory of the workflow run (either a Directory or File).</doc><request></request><response><representation mediaType="application/xml"></representation><representation mediaType="application/json"></representation><representation mediaType="application/octet-stream"></representation><representation mediaType="application/zip"></representation><representation mediaType="*/*"></representation></response></method></resource></resource></resource></resource></resources></application>
\ No newline at end of file
diff --git a/server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java b/server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
index 19c2bcd..fa68b81 100644
--- a/server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
+++ b/server-runinterface/src/main/java/org/taverna/server/localworker/remote/RemoteSingleRun.java
@@ -221,11 +221,15 @@
* 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) throws RemoteException;
+ @Nonnull URL webdavPath, @Nullable URL publishUrlBase) throws RemoteException;
/**
* A do-nothing method, used to check the general reachability of the
diff --git a/server-usagerecord/src/main/java/org/ogf/usage/JobUsageRecord.java b/server-usagerecord/src/main/java/org/ogf/usage/JobUsageRecord.java
index cf7799a..d12d3d8 100644
--- a/server-usagerecord/src/main/java/org/ogf/usage/JobUsageRecord.java
+++ b/server-usagerecord/src/main/java/org/ogf/usage/JobUsageRecord.java
@@ -19,6 +19,7 @@
import javax.xml.bind.annotation.XmlTransient;
import javax.xml.datatype.DatatypeConfigurationException;
import javax.xml.datatype.DatatypeFactory;
+import javax.xml.transform.dom.DOMSource;
import org.ogf.usage.v1_0.Charge;
import org.ogf.usage.v1_0.ConsumableResourceType;
@@ -45,6 +46,7 @@
import org.ogf.usage.v1_0.TimeInstant;
import org.ogf.usage.v1_0.UserIdentity;
import org.ogf.usage.v1_0.WallDuration;
+import org.w3c.dom.Element;
@XmlRootElement(name = "UsageRecord", namespace = "http://schema.ogf.org/urf/2003/09/urf")
public class JobUsageRecord extends org.ogf.usage.v1_0.UsageRecordType {
@@ -277,10 +279,25 @@
return writer.toString();
}
+ private static JAXBContext context;
+ static {
+ try {
+ context = JAXBContext.newInstance(JobUsageRecord.class);
+ } catch (JAXBException e) {
+ throw new RuntimeException("failed to handle JAXB annotated class",
+ e);
+ }
+ }
+
public static JobUsageRecord unmarshal(String s) throws JAXBException {
- StringReader reader = new StringReader(s);
- return (JobUsageRecord) JAXBContext.newInstance(JobUsageRecord.class)
- .createUnmarshaller().unmarshal(reader);
+ return (JobUsageRecord) context.createUnmarshaller().unmarshal(
+ new StringReader(s));
+ }
+
+ public static JobUsageRecord unmarshal(Element elem) throws JAXBException {
+ return context.createUnmarshaller()
+ .unmarshal(new DOMSource(elem), JobUsageRecord.class)
+ .getValue();
}
// TODO: Add signing support
diff --git a/server-webapp/pom.xml b/server-webapp/pom.xml
index f56b9c5..15f1eb4 100644
--- a/server-webapp/pom.xml
+++ b/server-webapp/pom.xml
@@ -520,6 +520,19 @@
<ignore />
</action>
</pluginExecution>
+ <pluginExecution>
+ <pluginExecutionFilter>
+ <groupId>net.alchim31.maven</groupId>
+ <artifactId>yuicompressor-maven-plugin</artifactId>
+ <versionRange>[1.0.0,)</versionRange>
+ <goals>
+ <goal>compress</goal>
+ </goals>
+ </pluginExecutionFilter>
+ <action>
+ <execute/>
+ </action>
+ </pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
@@ -664,6 +677,14 @@
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-war-plugin</artifactId>
+ <version>2.4</version>
+ <configuration>
+ <webXml>src/main/webapp/WEB-INF/web-sec.xml</webXml>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-eclipse-plugin</artifactId>
<configuration>
<additionalProjectnatures>
@@ -735,6 +756,24 @@
</configuration>
</plugin>
<plugin>
+ <groupId>net.alchim31.maven</groupId>
+ <artifactId>yuicompressor-maven-plugin</artifactId>
+ <version>1.4.0</version>
+ <executions>
+ <execution>
+ <goals>
+ <goal>compress</goal>
+ </goals>
+ </execution>
+ </executions>
+ <configuration>
+ <excludes>
+ <exclude>**/*.min.js</exclude>
+ </excludes>
+ <nosuffix>true</nosuffix>
+ </configuration>
+ </plugin>
+ <plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<executions>
@@ -810,5 +849,33 @@
<forker.module>server-win-forker</forker.module>
</properties>
</profile>
+ <profile>
+ <id>nosec</id>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-war-plugin</artifactId>
+ <configuration>
+ <webXml>src/main/webapp/WEB-INF/web-nosec.xml</webXml>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
+ <profile>
+ <id>partsec</id>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-war-plugin</artifactId>
+ <configuration>
+ <webXml>src/main/webapp/WEB-INF/web-partsec.xml</webXml>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ </profile>
</profiles>
</project>
diff --git a/server-webapp/src/main/java/org/taverna/server/master/ContentsDescriptorBuilder.java b/server-webapp/src/main/java/org/taverna/server/master/ContentsDescriptorBuilder.java
index ab43827..f5259bd 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/ContentsDescriptorBuilder.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/ContentsDescriptorBuilder.java
@@ -8,7 +8,7 @@
import static eu.medsea.util.MimeUtil.getMimeType;
import static javax.ws.rs.core.MediaType.APPLICATION_OCTET_STREAM_TYPE;
import static javax.ws.rs.core.UriBuilder.fromUri;
-import static org.taverna.server.master.TavernaServerSupport.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import static org.taverna.server.master.common.Uri.secure;
import java.io.ByteArrayInputStream;
@@ -21,6 +21,7 @@
import javax.ws.rs.core.UriBuilder;
import javax.ws.rs.core.UriInfo;
+import org.apache.commons.logging.Log;
import org.springframework.beans.factory.annotation.Required;
import org.taverna.server.master.exceptions.FilesystemAccessException;
import org.taverna.server.master.exceptions.NoDirectoryEntryException;
@@ -53,6 +54,7 @@
* @author Donal Fellows
*/
public class ContentsDescriptorBuilder {
+ private Log log = getLog("Taverna.Server.Webapp");
private FilenameUtils fileUtils;
private UriBuilderFactory uriBuilderFactory;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/DirectoryREST.java b/server-webapp/src/main/java/org/taverna/server/master/DirectoryREST.java
index 5bd6f30..48969fa 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/DirectoryREST.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/DirectoryREST.java
@@ -11,7 +11,7 @@
import static javax.ws.rs.core.Response.ok;
import static javax.ws.rs.core.Response.seeOther;
import static javax.ws.rs.core.Response.status;
-import static org.taverna.server.master.TavernaServer.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import static org.taverna.server.master.api.ContentTypes.APPLICATION_ZIP_TYPE;
import static org.taverna.server.master.api.ContentTypes.DIRECTORY_VARIANTS;
import static org.taverna.server.master.api.ContentTypes.INITIAL_FILE_VARIANTS;
@@ -37,6 +37,7 @@
import javax.ws.rs.core.Variant;
import javax.xml.ws.Holder;
+import org.apache.commons.logging.Log;
import org.springframework.beans.factory.annotation.Required;
import org.taverna.server.master.api.DirectoryBean;
import org.taverna.server.master.exceptions.FilesystemAccessException;
@@ -61,6 +62,7 @@
* @author Donal Fellows
*/
class DirectoryREST implements TavernaServerDirectoryREST, DirectoryBean {
+ private Log log = getLog("Taverna.Server.Webapp");
private TavernaServerSupport support;
private TavernaRun run;
private FilenameUtils fileUtils;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/ListenerPropertyREST.java b/server-webapp/src/main/java/org/taverna/server/master/ListenerPropertyREST.java
index 2822de3..3e983a9 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/ListenerPropertyREST.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/ListenerPropertyREST.java
@@ -5,11 +5,12 @@
*/
package org.taverna.server.master;
-import static org.taverna.server.master.TavernaServer.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import static org.taverna.server.master.utils.RestUtils.opt;
import javax.ws.rs.core.Response;
+import org.apache.commons.logging.Log;
import org.taverna.server.master.api.ListenerPropertyBean;
import org.taverna.server.master.exceptions.NoListenerException;
import org.taverna.server.master.exceptions.NoUpdateException;
@@ -26,6 +27,7 @@
*/
class ListenerPropertyREST implements TavernaServerListenersREST.Property,
ListenerPropertyBean {
+ private Log log = getLog("Taverna.Server.Webapp");
private TavernaServerSupport support;
private Listener listen;
private String propertyName;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/RunREST.java b/server-webapp/src/main/java/org/taverna/server/master/RunREST.java
index eb7b38e..563a822 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/RunREST.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/RunREST.java
@@ -10,9 +10,9 @@
import static javax.ws.rs.core.Response.noContent;
import static javax.ws.rs.core.Response.ok;
import static javax.ws.rs.core.Response.status;
+import static org.apache.commons.logging.LogFactory.getLog;
import static org.joda.time.format.ISODateTimeFormat.dateTime;
import static org.joda.time.format.ISODateTimeFormat.dateTimeParser;
-import static org.taverna.server.master.TavernaServer.log;
import static org.taverna.server.master.common.Roles.SELF;
import static org.taverna.server.master.common.Roles.USER;
import static org.taverna.server.master.common.Status.Initialized;
@@ -26,6 +26,7 @@
import javax.ws.rs.core.UriInfo;
import javax.xml.bind.JAXBException;
+import org.apache.commons.logging.Log;
import org.joda.time.DateTime;
import org.ogf.usage.JobUsageRecord;
import org.springframework.beans.factory.annotation.Required;
@@ -58,6 +59,7 @@
* @author Donal Fellows
*/
abstract class RunREST implements TavernaServerRunREST, RunBean {
+ private Log log = getLog("Taverna.Server.Webapp");
private String runName;
private TavernaRun run;
private TavernaServerSupport support;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/TavernaServer.java b/server-webapp/src/main/java/org/taverna/server/master/TavernaServer.java
index 7c83c75..0f98da6 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/TavernaServer.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/TavernaServer.java
@@ -128,7 +128,7 @@
+ Version.JAVA + ",name=";
/** The logger for the server framework. */
- public static Log log = getLog("Taverna.Server.Webapp");
+ public Log log = getLog("Taverna.Server.Webapp");
@PreDestroy
void closeLog() {
diff --git a/server-webapp/src/main/java/org/taverna/server/master/TavernaServerSupport.java b/server-webapp/src/main/java/org/taverna/server/master/TavernaServerSupport.java
index 5c6d938..ce36bd3 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/TavernaServerSupport.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/TavernaServerSupport.java
@@ -91,7 +91,7 @@
+ Version.JAVA + " web-application interface.")
public class TavernaServerSupport {
/** The main webapp log. */
- public static Log log = getLog("Taverna.Server.Webapp");
+ private Log log = getLog("Taverna.Server.Webapp");
private Log accessLog = getLog("Taverna.Server.Webapp.Access");;
/** Bean used to log counts of external calls. */
private InvocationCounter counter;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/UserStore.java b/server-webapp/src/main/java/org/taverna/server/master/identity/UserStore.java
index fdd615b..054d932 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/UserStore.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/identity/UserStore.java
@@ -50,7 +50,7 @@
public class UserStore extends JDOSupport<User> implements UserDetailsService,
UserStoreAPI {
/** The logger for the user store. */
- private static Log log = getLog("Taverna.Server.UserDB");
+ private transient Log log = getLog("Taverna.Server.UserDB");
public UserStore() {
super(User.class);
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/WorkflowInternalAuthProvider.java b/server-webapp/src/main/java/org/taverna/server/master/identity/WorkflowInternalAuthProvider.java
index d8361e5..9219a60 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/WorkflowInternalAuthProvider.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/identity/WorkflowInternalAuthProvider.java
@@ -54,7 +54,7 @@
*/
public class WorkflowInternalAuthProvider extends
AbstractUserDetailsAuthenticationProvider {
- private static Log log = LogFactory.getLog("Taverna.Server.UserDB");
+ private Log log = LogFactory.getLog("Taverna.Server.UserDB");
private static final boolean logDecisions = true;
public static final String PREFIX = "wfrun_";
private RunDatabaseDAO dao;
@@ -265,7 +265,7 @@
}
public static class WorkflowSelfIDMapper implements LocalIdentityMapper {
- private static Log log = LogFactory.getLog("Taverna.Server.UserDB");
+ private Log log = LogFactory.getLog("Taverna.Server.UserDB");
private RunStore runStore;
@PreDestroy
diff --git a/server-webapp/src/main/java/org/taverna/server/master/interaction/InteractionFeedSupport.java b/server-webapp/src/main/java/org/taverna/server/master/interaction/InteractionFeedSupport.java
index 3a9808b..99e1d99 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/interaction/InteractionFeedSupport.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/interaction/InteractionFeedSupport.java
@@ -5,18 +5,31 @@
*/
package org.taverna.server.master.interaction;
+import static java.lang.management.ManagementFactory.getPlatformMBeanServer;
import static java.util.Collections.reverse;
+import static javax.management.Query.attr;
+import static javax.management.Query.match;
+import static javax.management.Query.value;
+import static org.apache.commons.logging.LogFactory.getLog;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URI;
+import java.net.URL;
import java.util.ArrayList;
import java.util.Date;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.concurrent.atomic.AtomicInteger;
+import javax.annotation.Nullable;
+import javax.annotation.PostConstruct;
+import javax.management.MBeanServer;
+import javax.management.ObjectName;
+
import org.apache.abdera.Abdera;
import org.apache.abdera.factory.Factory;
import org.apache.abdera.i18n.iri.IRI;
@@ -97,6 +110,28 @@
this.uriBuilder = uriBuilder;
}
+ private final Map<String, URL> endPoints = new HashMap<>();
+
+ @PostConstruct
+ void determinePorts() {
+ try {
+ MBeanServer mbs = getPlatformMBeanServer();
+ for (ObjectName obj : mbs.queryNames(new ObjectName(
+ "*:type=Connector,*"),
+ match(attr("protocol"), value("HTTP/1.1")))) {
+ String scheme = mbs.getAttribute(obj, "scheme").toString();
+ String port = obj.getKeyProperty("port");
+ endPoints.put(scheme, new URL(scheme + "://localhost:" + port));
+ }
+ getLog(getClass()).info(
+ "installed feed port publication mapping for "
+ + endPoints.keySet());
+ } catch (Exception e) {
+ getLog(getClass()).error(
+ "failure in determining local port mapping", e);
+ }
+ }
+
/**
* @param run
* The workflow run that defines which feed we are operating on.
@@ -106,6 +141,13 @@
return uriBuilder.getRunUriBuilder(run).path(FEED_URL_DIR).build();
}
+ @Nullable
+ public URL getLocalFeedBase(URI feedURI) {
+ if (feedURI == null)
+ return null;
+ return endPoints.get(feedURI.getScheme());
+ }
+
/**
* @param run
* The workflow run that defines which feed we are operating on.
diff --git a/server-webapp/src/main/java/org/taverna/server/master/localworker/AbstractRemoteRunFactory.java b/server-webapp/src/main/java/org/taverna/server/master/localworker/AbstractRemoteRunFactory.java
index d2c9c91..fc7f881 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/localworker/AbstractRemoteRunFactory.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/localworker/AbstractRemoteRunFactory.java
@@ -17,6 +17,7 @@
import java.io.IOException;
import java.io.ObjectInputStream;
+import java.net.URI;
import java.net.URL;
import java.rmi.MarshalledObject;
import java.rmi.RMISecurityManager;
@@ -29,14 +30,14 @@
import java.util.List;
import java.util.UUID;
+import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
import javax.annotation.Resource;
import javax.xml.bind.JAXBException;
import org.apache.commons.io.IOUtils;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Required;
import org.springframework.beans.factory.annotation.Value;
-import org.springframework.core.task.TaskExecutor;
import org.springframework.jmx.export.annotation.ManagedResource;
import org.taverna.server.localworker.remote.RemoteRunFactory;
import org.taverna.server.localworker.remote.RemoteSingleRun;
@@ -142,6 +143,19 @@
}
}
+ protected static final Process launchSubprocess(ProcessBuilder b)
+ throws IOException {
+ Thread t = Thread.currentThread();
+ ClassLoader ccl = t.getContextClassLoader();
+ try {
+ t.setContextClassLoader(null);
+ return b.start();
+ } finally {
+ t.setContextClassLoader(ccl);
+ }
+ }
+
+ /** Get a handle to a new instance of the RMI registry. */
private Registry makeRegistry(int port) throws RemoteException {
ProcessBuilder p = new ProcessBuilder(getJavaBinary());
p.command().add("-jar");
@@ -149,7 +163,7 @@
p.command().add(Integer.toString(port));
p.command().add(Boolean.toString(rmiLocalhostOnly));
try {
- Process proc = p.start();
+ Process proc = launchSubprocess(p);
Thread.sleep(getSleepTime());
try {
if (proc.exitValue() == 0)
@@ -240,7 +254,6 @@
public static final String SECURITY_POLICY_FILE = "security.policy";
private SecurityContextFactory securityFactory;
UsageRecordRecorder usageRecordSink;
- TaskExecutor urProcessorPool;
private EventDAO masterEventFeed;
@Autowired(required = true)
@@ -258,12 +271,6 @@
this.usageRecordSink = usageRecordSink;
}
- @Resource(name = "URThreads")
- @Required
- void setURProcessorPool(TaskExecutor urProcessorPool) {
- this.urProcessorPool = urProcessorPool;
- }
-
/**
* Configures the Java security model. Not currently used, as it is
* viciously difficult to get right!
@@ -337,10 +344,16 @@
state.getDefaultLifetime(), runDB, id,
state.getGenerateProvenance(), this);
run.setSecurityContext(securityFactory.create(run, creator));
- URL feedUrl = interactionFeedSupport.getFeedURI(run).toURL();
+ @Nonnull
+ URI feed = interactionFeedSupport.getFeedURI(run);
+ @Nonnull
+ URL feedUrl = feed.toURL();
+ @Nonnull
URL webdavUrl = baseurifactory.getRunUriBuilder(run)
.path(DIR + "/interactions").build().toURL();
- rsr.setInteractionServiceDetails(feedUrl, webdavUrl);
+ @Nullable
+ URL pub = interactionFeedSupport.getLocalFeedBase(feed);
+ rsr.setInteractionServiceDetails(feedUrl, webdavUrl, pub);
return run;
} catch (NoCreateException e) {
log.warn("failed to build run instance", e);
@@ -386,6 +399,12 @@
}
}
+ private void acceptUsageRecord(String usageRecord) {
+ if (usageRecordSink != null)
+ usageRecordSink.storeUsageRecord(usageRecord);
+ runDB.checkForFinishNow();
+ }
+
/**
* Make a Remote object that can act as a consumer for usage records.
*
@@ -403,20 +422,8 @@
}
@Override
- public void acceptUsageRecord(final String usageRecord) {
- if (usageRecordSink != null && urProcessorPool != null)
- urProcessorPool.execute(new Runnable() {
- @Override
- public void run() {
- usageRecordSink.storeUsageRecord(usageRecord);
- }
- });
- urProcessorPool.execute(new Runnable() {
- @Override
- public void run() {
- runDB.checkForFinishNow();
- }
- });
+ public void acceptUsageRecord(String usageRecord) {
+ AbstractRemoteRunFactory.this.acceptUsageRecord(usageRecord);
}
}
return new URReceiver();
diff --git a/server-webapp/src/main/java/org/taverna/server/master/localworker/ForkRunFactory.java b/server-webapp/src/main/java/org/taverna/server/master/localworker/ForkRunFactory.java
index dccfeac..b67e121 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/localworker/ForkRunFactory.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/localworker/ForkRunFactory.java
@@ -10,13 +10,9 @@
import static java.util.Arrays.asList;
import static java.util.Calendar.SECOND;
import static java.util.UUID.randomUUID;
-import static org.apache.commons.logging.LogFactory.getLog;
import static org.taverna.server.master.TavernaServer.JMX_ROOT;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
import java.rmi.ConnectException;
import java.rmi.ConnectIOException;
import java.rmi.NotBoundException;
@@ -26,9 +22,9 @@
import javax.annotation.Nonnull;
import javax.annotation.PostConstruct;
+import javax.annotation.PreDestroy;
import javax.xml.bind.JAXBException;
-import org.apache.commons.logging.Log;
import org.springframework.jmx.export.annotation.ManagedAttribute;
import org.springframework.jmx.export.annotation.ManagedResource;
import org.taverna.server.localworker.remote.RemoteRunFactory;
@@ -145,15 +141,20 @@
// Spawn the subprocess
log.info("about to create subprocess: " + p.command());
- factoryProcess = p.start();
- Thread logger = new Thread(new OutputLogger(factoryProcessName,
- factoryProcess), factoryProcessName + ".Logger");
- logger.setDaemon(true);
- logger.start();
- Thread logger2 = new Thread(new ErrorLogger(factoryProcessName,
- factoryProcess), factoryProcessName + ".Logger");
- logger2.setDaemon(true);
- logger2.start();
+
+ factoryProcess = launchSubprocess(p);
+ outlog = new StreamLogger("FactoryStdout", factoryProcess.getInputStream()) {
+ @Override
+ protected void write(String msg) {
+ log.info(msg);
+ }
+ };
+ errlog = new StreamLogger("FactoryStderr", factoryProcess.getErrorStream()) {
+ @Override
+ protected void write(String msg) {
+ log.info(msg);
+ }
+ };
// Wait for the subprocess to register itself in the RMI registry
Calendar deadline = Calendar.getInstance();
@@ -192,6 +193,17 @@
throw lastException;
}
+ private StreamLogger outlog, errlog;
+
+ private void stopLoggers() {
+ if (outlog != null)
+ outlog.stop();
+ outlog = null;
+ if (errlog != null)
+ errlog.stop();
+ errlog = null;
+ }
+
private RemoteRunFactory getRemoteFactoryHandle(String name)
throws RemoteException, NotBoundException {
log.info("about to look up resource called " + name);
@@ -207,81 +219,10 @@
return rrf;
}
- private static class OutputLogger implements Runnable {
- private final Log log;
-
- OutputLogger(String name, Process process) {
- log = getLog("Taverna.Server.LocalWorker." + name);
- this.uniqueName = name;
- this.br = new BufferedReader(new InputStreamReader(
- process.getInputStream()));
- }
-
- private String uniqueName;
- private BufferedReader br;
-
- @Override
- public void run() {
- try {
- String line;
- while (true) {
- line = br.readLine();
- if (line == null)
- break;
- log.info(uniqueName + " subprocess output: " + line);
- }
- } catch (IOException e) {
- // Do nothing...
- } catch (Exception e) {
- log.warn("failure in reading from " + uniqueName, e);
- } finally {
- try {
- br.close();
- } catch (Throwable e) {
- }
- }
- }
- }
-
- private static class ErrorLogger implements Runnable {
- private final Log log;
-
- ErrorLogger(String name, Process process) {
- log = getLog("Taverna.Server.LocalWorker." + name);
- this.uniqueName = name;
- this.br = new BufferedReader(new InputStreamReader(
- process.getErrorStream()));
- }
-
- private String uniqueName;
- private BufferedReader br;
-
- @Override
- public void run() {
- try {
- String line;
- while (true) {
- line = br.readLine();
- if (line == null)
- break;
- log.info(uniqueName + " subprocess error: " + line);
- }
- } catch (IOException e) {
- // Do nothing...
- } catch (Exception e) {
- log.warn("failure in reading from " + uniqueName, e);
- } finally {
- try {
- br.close();
- } catch (Throwable e) {
- }
- }
- }
- }
-
/**
* Destroys the subprocess that manufactures runs.
*/
+ @PreDestroy
public void killFactory() {
if (factory != null) {
log.info("requesting shutdown of " + factoryProcessName);
@@ -315,6 +256,7 @@
}
} finally {
factoryProcess = null;
+ stopLoggers();
}
if (code > 128) {
log.info(factoryProcessName + " died with signal="
@@ -327,12 +269,6 @@
}
}
- @Override
- protected void finalize() throws Throwable {
- killFactory();
- super.finalize();
- }
-
/**
* The real core of the run builder, factored out from its reliability
* support.
@@ -347,6 +283,7 @@
*/
private RemoteSingleRun getRealRun(@Nonnull UsernamePrincipal creator,
@Nonnull byte[] wf, UUID id) throws RemoteException {
+ @Nonnull
String globaluser = "Unknown Person";
if (creator != null)
globaluser = creator.getName();
@@ -359,6 +296,7 @@
@Override
protected RemoteSingleRun getRealRun(UsernamePrincipal creator,
Workflow workflow, UUID id) throws Exception {
+ @Nonnull
byte[] wf = serializeWorkflow(workflow);
for (int i = 0; i < 3; i++) {
initFactory();
diff --git a/server-webapp/src/main/java/org/taverna/server/master/localworker/IdAwareForkRunFactory.java b/server-webapp/src/main/java/org/taverna/server/master/localworker/IdAwareForkRunFactory.java
index 1115f25..e449373 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/localworker/IdAwareForkRunFactory.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/localworker/IdAwareForkRunFactory.java
@@ -10,15 +10,12 @@
import static java.util.Arrays.asList;
import static java.util.Calendar.SECOND;
import static java.util.UUID.randomUUID;
-import static org.apache.commons.logging.LogFactory.getLog;
import static org.taverna.server.master.TavernaServer.JMX_ROOT;
+import static org.taverna.server.master.localworker.AbstractRemoteRunFactory.launchSubprocess;
-import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.rmi.ConnectException;
@@ -335,72 +332,6 @@
}
}
-abstract class StreamLogger {
- protected final Log log;
-
- protected StreamLogger(String name, InputStream is) {
- log = getLog("Taverna.Server.LocalWorker." + name);
- final String uniqueName = name;
- final BufferedReader br = new BufferedReader(new InputStreamReader(is));
- Thread t = new Thread(new Runnable() {
- @Override
- public void run() {
- String line;
- try {
- while ((line = br.readLine()) != null)
- if (!line.isEmpty())
- write(line);
- } catch (IOException e) {
- // Do nothing...
- } catch (Exception e) {
- log.warn("failure in reading from " + uniqueName, e);
- } finally {
- try {
- br.close();
- } catch (Throwable e) {
- }
- }
- }
- }, name + ".StreamLogger");
- t.setDaemon(true);
- t.start();
- }
-
- /**
- * Write a line read from the subproces to the log.
- * <p>
- * This needs to be implemented by subclasses in order for the log to be
- * correctly written with the class name.
- *
- * @param msg
- * The message to write. Guaranteed to have no newline characters
- * in it and to be non-empty.
- */
- protected abstract void write(String msg);
-}
-
-class StdOut extends StreamLogger {
- StdOut(Process process) {
- super("forker", process.getInputStream());
- }
-
- @Override
- protected void write(String msg) {
- log.info(msg);
- }
-}
-
-class StdErr extends StreamLogger {
- StdErr(Process process) {
- super("forker", process.getErrorStream());
- }
-
- @Override
- protected void write(String msg) {
- log.info(msg);
- }
-}
-
/**
* The connector that handles the secure fork process itself.
*
@@ -414,6 +345,7 @@
private Integer lastExitCode;
private Log log;
private LocalWorkerState state;
+ private StreamLogger out, err;
/**
* Construct the command to run the meta-factory process.
@@ -452,12 +384,22 @@
// Spawn the subprocess
log.info("about to create subprocess: " + p.command());
log.info("subprocess directory: " + p.directory());
- process = p.start();
+ process = launchSubprocess(p);
channel = new PrintWriter(new BufferedWriter(new OutputStreamWriter(
process.getOutputStream())), true);
// Log the responses
- new StdOut(process);
- new StdErr(process);
+ out = new StreamLogger("ForkedStdout", process.getInputStream()) {
+ @Override
+ protected void write(String msg) {
+ log.info(msg);
+ }
+ };
+ err = new StreamLogger("ForkedStderr", process.getErrorStream()) {
+ @Override
+ protected void write(String msg) {
+ log.info(msg);
+ }
+ };
}
@Override
@@ -495,6 +437,8 @@
} finally {
process = null;
channel = null;
+ out.stop();
+ err.stop();
}
}
diff --git a/server-webapp/src/main/java/org/taverna/server/master/localworker/StreamLogger.java b/server-webapp/src/main/java/org/taverna/server/master/localworker/StreamLogger.java
new file mode 100644
index 0000000..f361e17
--- /dev/null
+++ b/server-webapp/src/main/java/org/taverna/server/master/localworker/StreamLogger.java
@@ -0,0 +1,62 @@
+package org.taverna.server.master.localworker;
+
+import static java.lang.Thread.interrupted;
+import static org.apache.commons.logging.LogFactory.getLog;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+import org.apache.commons.logging.Log;
+
+abstract class StreamLogger {
+ protected final Log log;
+ private Thread t;
+ private InputStream in;
+
+ protected StreamLogger(final String name, InputStream is) {
+ log = getLog("Taverna.Server.LocalWorker." + name);
+ in = is;
+ t = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ try (BufferedReader br = new BufferedReader(
+ new InputStreamReader(in))) {
+ String line;
+ while (!interrupted() && (line = br.readLine()) != null)
+ if (!line.isEmpty())
+ write(line);
+ } catch (IOException e) {
+ // Do nothing...
+ } catch (Exception e) {
+ log.warn("failure in reading from " + name, e);
+ }
+ }
+ }, name + ".StreamLogger");
+ t.setContextClassLoader(null);
+ t.setDaemon(true);
+ t.start();
+ }
+
+ /**
+ * Write a line read from the subprocess to the log.
+ * <p>
+ * This needs to be implemented by subclasses in order for the log to be
+ * correctly written with the class name.
+ *
+ * @param msg
+ * The message to write. Guaranteed to have no newline characters
+ * in it and to be non-empty.
+ */
+ protected abstract void write(String msg);
+
+ public void stop() {
+ log.info("trying to close down " + t.getName());
+ t.interrupt();
+ try {
+ in.close();
+ } catch (IOException e) {
+ }
+ }
+}
diff --git a/server-webapp/src/main/java/org/taverna/server/master/notification/atom/EventDAO.java b/server-webapp/src/main/java/org/taverna/server/master/notification/atom/EventDAO.java
index ac33133..56f25ff 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/notification/atom/EventDAO.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/notification/atom/EventDAO.java
@@ -5,6 +5,10 @@
*/
package org.taverna.server.master.notification.atom;
+import static java.lang.Thread.interrupted;
+import static java.lang.Thread.sleep;
+import static java.util.Arrays.asList;
+
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.Date;
@@ -13,6 +17,7 @@
import java.util.concurrent.BlockingQueue;
import javax.annotation.Nonnull;
+import javax.annotation.PreDestroy;
import javax.jdo.annotations.PersistenceAware;
import org.apache.commons.logging.Log;
@@ -155,25 +160,41 @@
messageSubject, messageContent));
}
+ private Thread eventDaemon;
+ private boolean shuttingDown = false;
+
@Required
public void setSelf(final EventDAO dao) {
- Thread t = new Thread(new Runnable() {
+ eventDaemon = new Thread(new Runnable() {
@Override
public void run() {
try {
- while (true) {
- ArrayList<Event> e = new ArrayList<>();
- e.add(insertQueue.take());
- insertQueue.drainTo(e);
- dao.storeEvents(e);
- Thread.sleep(5000);
+ while (!shuttingDown && !interrupted()) {
+ transferEvents(dao, new ArrayList<Event>(
+ asList(insertQueue.take())));
+ sleep(5000);
}
} catch (InterruptedException e) {
+ } finally {
+ transferEvents(dao, new ArrayList<Event>());
}
}
- });
- t.setDaemon(true);
- t.start();
+ }, "ATOM event daemon");
+ eventDaemon.setContextClassLoader(null);
+ eventDaemon.setDaemon(true);
+ eventDaemon.start();
+ }
+
+ private void transferEvents(EventDAO dao, List<Event> e) {
+ insertQueue.drainTo(e);
+ dao.storeEvents(e);
+ }
+
+ @PreDestroy
+ void stopDaemon() {
+ shuttingDown = true;
+ if (eventDaemon != null)
+ eventDaemon.interrupt();
}
@WithinSingleTransaction
diff --git a/server-webapp/src/main/java/org/taverna/server/master/rest/handler/FileMessageHandler.java b/server-webapp/src/main/java/org/taverna/server/master/rest/handler/FileMessageHandler.java
index f181a61..0aeb816 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/rest/handler/FileMessageHandler.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/rest/handler/FileMessageHandler.java
@@ -5,7 +5,7 @@
*/
package org.taverna.server.master.rest.handler;
-import static org.taverna.server.master.TavernaServer.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import java.io.IOException;
import java.io.OutputStream;
@@ -18,6 +18,7 @@
import javax.ws.rs.ext.MessageBodyWriter;
import javax.ws.rs.ext.Provider;
+import org.apache.commons.logging.Log;
import org.taverna.server.master.exceptions.FilesystemAccessException;
import org.taverna.server.master.interfaces.File;
@@ -28,6 +29,7 @@
*/
@Provider
public class FileMessageHandler implements MessageBodyWriter<File> {
+ private Log log = getLog("Taverna.Server.Webapp");
/** How much to pull from the worker in one read. */
private int maxChunkSize;
diff --git a/server-webapp/src/main/java/org/taverna/server/master/rest/handler/HandlerCore.java b/server-webapp/src/main/java/org/taverna/server/master/rest/handler/HandlerCore.java
index efaf47d..0e3fb51 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/rest/handler/HandlerCore.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/rest/handler/HandlerCore.java
@@ -7,10 +7,11 @@
import static javax.ws.rs.core.MediaType.TEXT_PLAIN_TYPE;
import static javax.ws.rs.core.Response.status;
-import static org.taverna.server.master.TavernaServer.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import javax.ws.rs.core.Response;
+import org.apache.commons.logging.Log;
import org.taverna.server.master.api.ManagementModel;
/**
@@ -20,6 +21,7 @@
* @author Donal Fellows
*/
public class HandlerCore {
+ private Log log = getLog("Taverna.Server.Webapp");
private ManagementModel managementModel;
/**
diff --git a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java b/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
index 16f8689..12de304 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/usage/UsageRecordRecorder.java
@@ -5,7 +5,7 @@
*/
package org.taverna.server.master.usage;
-import static org.taverna.server.master.TavernaServer.log;
+import static org.apache.commons.logging.LogFactory.getLog;
import java.io.FileWriter;
import java.io.IOException;
@@ -17,6 +17,7 @@
import javax.annotation.PreDestroy;
import javax.xml.bind.JAXBException;
+import org.apache.commons.logging.Log;
import org.ogf.usage.JobUsageRecord;
import org.springframework.beans.factory.annotation.Required;
import org.taverna.server.master.api.ManagementModel;
@@ -30,6 +31,7 @@
* @author Donal Fellows
*/
public class UsageRecordRecorder extends JDOSupport<UsageRecord> {
+ private Log log = getLog("Taverna.Server.Webapp");
public UsageRecordRecorder() {
super(UsageRecord.class);
}
@@ -153,10 +155,8 @@
return result;
}
- @Override
@PreDestroy
public void close() {
- super.close();
if (writer != null)
writer.close();
}
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java b/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
index f94d497..c27502f 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
@@ -165,8 +165,20 @@
return null;
synchronized (this) {
if (!cache.containsKey(uri)) {
+ int port = uri.getPort();
+ if (port == -1)
+ switch (uri.getScheme()) {
+ case "http":
+ port = 80;
+ break;
+ case "https":
+ port = 443;
+ break;
+ default:
+ return null;
+ }
X509Certificate[] chain = getCertificateChainForService(
- uri.getHost(), uri.getPort());
+ uri.getHost(), port);
if (chain != null)
cache.put(uri, unmodifiableList(asList(chain)));
else
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java b/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
index 1b41ab7..f8b39e3 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
@@ -1,5 +1,6 @@
package org.taverna.server.master.utils;
+import java.io.EOFException;
import java.io.IOException;
import java.io.Writer;
@@ -26,30 +27,42 @@
}
class DBLog extends Writer {
- Log log = LogFactory.getLog("Taverna.Server.Database");
- StringBuilder sb = new StringBuilder();
+ private Log log = LogFactory.getLog("Taverna.Server.Database");
+ private StringBuilder sb = new StringBuilder();
+ private boolean closed = false;
@Override
public void write(char[] cbuf, int off, int len) throws IOException {
+ if (closed)
+ throw new EOFException();
if (!log.isInfoEnabled())
return;
sb.append(cbuf, off, len);
- while (true) {
- int idx = sb.indexOf("\n");
+ while (!closed) {
+ int idx = sb.indexOf("\n"), realIdx = idx;
if (idx < 0)
break;
- if (idx > 0 && sb.charAt(idx - 1) == '\r')
+ char ch;
+ while (idx > 0 && ((ch = sb.charAt(idx - 1)) == '\r' || ch == ' ' || ch == '\t'))
idx--;
- log.info(sb.substring(0, idx));
- sb.delete(0, idx + 1);
+ if (idx > 0)
+ log.info(sb.substring(0, idx));
+ sb.delete(0, realIdx + 1);
}
}
@Override
public void flush() throws IOException {
+ if (sb.length() > 0) {
+ log.info(sb.toString());
+ sb = new StringBuilder();
+ }
}
@Override
public void close() throws IOException {
+ flush();
+ closed = true;
+ sb = null;
}
}
\ No newline at end of file
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java b/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
index 9bfe8b4..ba9ec81 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
@@ -9,8 +9,10 @@
import static java.lang.annotation.RetentionPolicy.RUNTIME;
import static org.apache.commons.logging.LogFactory.getLog;
+import java.lang.annotation.Documented;
import java.lang.annotation.Retention;
import java.lang.annotation.Target;
+import java.util.WeakHashMap;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
@@ -37,7 +39,7 @@
*/
public abstract class JDOSupport<T> {
private Class<T> contextClass;
- PersistenceManager pm;
+ private PersistenceManagerBuilder pmb;
/**
* Instantiate this class, supplying it a handle to the class that will be
@@ -51,18 +53,19 @@
}
/**
- * @param persistenceManagerFactory
+ * @param persistenceManagerBuilder
* The JDO engine to use for managing persistence.
*/
@Required
- public void setPersistenceManagerFactory(
- PersistenceManagerFactory persistenceManagerFactory) {
- pm = persistenceManagerFactory.getPersistenceManagerProxy();
+ public void setPersistenceManagerBuilder(
+ PersistenceManagerBuilder persistenceManagerBuilder) {
+ pmb = persistenceManagerBuilder;
}
- @PreDestroy
- public void close() {
- pm.close();
+ private PersistenceManager pm() {
+ if (isPersistent())
+ return pmb.getPersistenceManager();
+ return null;
}
/**
@@ -72,7 +75,7 @@
* @return Whether there is a persistence manager installed.
*/
protected boolean isPersistent() {
- return pm != null;
+ return pmb != null;
}
/**
@@ -84,7 +87,7 @@
*/
@Nonnull
protected Query query(@Nonnull String filter) {
- return pm.newQuery(contextClass, filter);
+ return pm().newQuery(contextClass, filter);
}
/**
@@ -98,7 +101,7 @@
*/
@Nonnull
protected Query namedQuery(@Nonnull String name) {
- return pm.newNamedQuery(contextClass, name);
+ return pm().newNamedQuery(contextClass, name);
}
/**
@@ -113,7 +116,7 @@
protected T persist(@Nullable T value) {
if (value == null)
return null;
- return pm.makePersistent(value);
+ return pm().makePersistent(value);
}
/**
@@ -128,7 +131,7 @@
protected T detach(@Nullable T value) {
if (value == null)
return null;
- return pm.detachCopy(value);
+ return pm().detachCopy(value);
}
/**
@@ -141,7 +144,7 @@
@Nullable
protected T getById(Object id) {
try {
- return pm.getObjectById(contextClass, id);
+ return pm().getObjectById(contextClass, id);
} catch (Exception e) {
return null;
}
@@ -155,7 +158,7 @@
*/
protected void delete(@Nullable T value) {
if (value != null)
- pm.deletePersistent(value);
+ pm().deletePersistent(value);
}
/**
@@ -173,9 +176,9 @@
Object applyTransaction(ProceedingJoinPoint pjp, JDOSupport<?> support)
throws Throwable {
synchronized (lock) {
+ PersistenceManager pm = support.pm();
int id = ++txid;
- Transaction tx = support.pm == null ? null : support.pm
- .currentTransaction();
+ Transaction tx = (pm == null) ? null : pm.currentTransaction();
if (tx != null && tx.isActive())
tx = null;
if (tx != null) {
@@ -217,6 +220,51 @@
*/
@Target(METHOD)
@Retention(RUNTIME)
+ @Documented
public @interface WithinSingleTransaction {
}
+
+ /**
+ * Manages {@linkplain PersistenceManager persistence managers} in a way
+ * that doesn't cause problems when the web application is unloaded.
+ *
+ * @author Donal Fellows
+ */
+ public static class PersistenceManagerBuilder {
+ private PersistenceManagerFactory pmf;
+ private WeakHashMap<Thread, PersistenceManager> cache = new WeakHashMap<>();
+
+ /**
+ * @param persistenceManagerFactory
+ * The JDO engine to use for managing persistence.
+ */
+ @Required
+ public void setPersistenceManagerFactory(
+ PersistenceManagerFactory persistenceManagerFactory) {
+ pmf = persistenceManagerFactory;
+ }
+
+ @Nonnull
+ public PersistenceManager getPersistenceManager() {
+ if (cache == null)
+ return pmf.getPersistenceManager();
+ Thread t = Thread.currentThread();
+ PersistenceManager pm = cache.get(t);
+ if (pm == null && pmf != null) {
+ pm = pmf.getPersistenceManager();
+ cache.put(t, pm);
+ }
+ return pm;
+ }
+
+ @PreDestroy
+ void clearThreadCache() {
+ WeakHashMap<Thread, PersistenceManager> cache = this.cache;
+ this.cache = null;
+ for (PersistenceManager pm : cache.values())
+ if (pm != null)
+ pm.close();
+ cache.clear();
+ }
+ }
}
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java b/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
index 5abb18f..a8aa937 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
@@ -44,9 +44,9 @@
ddl.append(item);
if (!item.endsWith("\n"))
ddl.append('\n');
- timeout = currentTimeMillis() + 15000;
+ timeout = currentTimeMillis() + 5000;
if (timer == null)
- (timer = new Thread(new Runnable() {
+ timer = new OneShotThread("DDL logger timeout", new Runnable() {
@Override
public void run() {
try {
@@ -57,7 +57,7 @@
}
logDDL();
}
- })).start();
+ });
}
/**
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java b/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java
new file mode 100644
index 0000000..68b813d
--- /dev/null
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java
@@ -0,0 +1,10 @@
+package org.taverna.server.master.utils;
+
+public class OneShotThread extends Thread {
+ public OneShotThread(String name, Runnable target) {
+ super(target, name);
+ setContextClassLoader(null);
+ setDaemon(true);
+ start();
+ }
+}
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java b/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
index ca1f19f..03fc749 100644
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
+++ b/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
@@ -5,12 +5,17 @@
*/
package org.taverna.server.master.utils;
+import static java.lang.Thread.currentThread;
+import static java.sql.DriverManager.deregisterDriver;
+import static java.sql.DriverManager.getDrivers;
import static org.taverna.server.master.utils.Contextualizer.ROOT_PLACEHOLDER;
import java.io.PrintWriter;
import java.sql.Connection;
+import java.sql.Driver;
import java.sql.DriverManager;
import java.sql.SQLException;
+import java.util.Enumeration;
import javax.annotation.PreDestroy;
@@ -49,6 +54,7 @@
private void doInit() {
synchronized (this) {
if (!init) {
+ setDriverClassLoader(currentThread().getContextClassLoader());
String url = getUrl();
if (url.contains(ROOT_PLACEHOLDER)) {
String newurl = ctxt.contextualize(url);
@@ -108,5 +114,21 @@
// Expected; ignore it
}
log = null;
+ dropDriver();
+ }
+
+ private void dropDriver() {
+ Enumeration<Driver> drivers = getDrivers();
+ while (drivers.hasMoreElements()) {
+ Driver d = drivers.nextElement();
+ if (d.getClass().getClassLoader() == getDriverClassLoader()
+ && d.getClass().getName().equals(getDriverClassName())) {
+ try {
+ deregisterDriver(d);
+ } catch (SQLException e) {
+ }
+ break;
+ }
+ }
}
}
diff --git a/server-webapp/src/main/replacementscripts/executeworkflow.sh b/server-webapp/src/main/replacementscripts/executeworkflow.sh
index e698aa1..10d73b2 100644
--- a/server-webapp/src/main/replacementscripts/executeworkflow.sh
+++ b/server-webapp/src/main/replacementscripts/executeworkflow.sh
@@ -54,6 +54,9 @@
INTERACTION_PROPS="$INTERACTION_PROPS -Dtaverna.interaction.port=$INTERACTION_PORT"
INTERACTION_PROPS="$INTERACTION_PROPS -Dtaverna.interaction.webdav_path=$INTERACTION_WEBDAV"
INTERACTION_PROPS="$INTERACTION_PROPS -Dtaverna.interaction.feed_path=$INTERACTION_FEED"
+ if test x != "x$INTERACTION_PUBLISH"; then
+ INTERACTION_PROPS="$INTERACTION_PROPS -Dtaverna.interaction.publishAddressOverride=$INTERACTION_PUBLISH"
+ fi
fi
MainClass=net.sf.taverna.t2.commandline.CommandLineLauncher
@@ -62,7 +65,7 @@
exec "$javabin" $memlimit $permsize \
"-Dlog4j.configuration=file://$taverna_home/conf/log4j.properties " \
"-Djava.util.logging.config.file=$taverna_home/conf/logging.properties " \
- "-Dtaverna.app.startup=$taverna_home" \
- $APPHOME_PROP $RUNID_PROP $INTERACTION_PROPS $pre \
+ "-Dtaverna.app.startup=$taverna_home" -Dtaverna.interaction.ignore_requests=true \
+ $APPHOME_PROP $RUNID_PROP $INTERACTION_PROPS -Djava.awt.headless=true $pre \
-jar "$taverna_home/lib/taverna-command-line-0.1.1.jar" \
${1+"$@"}
diff --git a/server-webapp/src/main/resources/admin.html b/server-webapp/src/main/resources/admin.html
index 8ebbd7e..a80a783 100644
--- a/server-webapp/src/main/resources/admin.html
+++ b/server-webapp/src/main/resources/admin.html
@@ -94,7 +94,7 @@
<br>
<textarea title="Workflow URIs to limit execution to." rows="5" cols="60" id="workflows"></textarea>
<p>
-<button id="saveWorkflows">Save</button> <button id="refreshWorkflows">Refresh</button>
+<button id="saveWorkflows">Save</button> <button id="refreshWorkflows">Refresh</button> <button id="emptyWorkflows">Empty URIs list</button>
</div>
<div id="t-usage">
diff --git a/server-webapp/src/main/resources/static/admin.js b/server-webapp/src/main/resources/static/admin.js
index c2b4406..c2c41bf 100644
--- a/server-webapp/src/main/resources/static/admin.js
+++ b/server-webapp/src/main/resources/static/admin.js
@@ -194,8 +194,9 @@
/** How to get the list of permitted workflows; called on demand */
function refreshWorkflows() {
- var wftable = $("#workflows"), wfbut = $("#saveWorkflows"), wfref = $("#refreshWorkflows");
+ var wftable = $("#workflows"), wfbut = $("#saveWorkflows"), wfbut1 = $("#emptyWorkflows"), wfref = $("#refreshWorkflows");
wfbut.button("disable");
+ wfbut1.button("disable");
wfref.button("disable");
getJSON(where("permittedWorkflowURIs"), function(data) {
var s = "";
@@ -204,19 +205,32 @@
});
wftable.val($.trim(s));
wfbut.button("enable");
+ wfbut1.button("enable");
wfref.button("enable");
});
}
/** How to set the list of permitted workflows; called when the user clicks */
function saveWorkflows() {
- var wftable = $("#workflows"), wfbut = $("#saveWorkflows");
+ var wftable = $("#workflows"), wfbut = $("#saveWorkflows"), wfbut1 = $("#emptyWorkflows");
var xml = NodeAll("stringList", "string", wftable.val().split("\n"));
wfbut.button("disable");
+ wfbut1.button("disable");
putXML(where("permittedWorkflowURIs"), xml, function() {
refreshWorkflows();
});
}
+/** How to empty the list of permitted workflows; called when the user clicks */
+function emptyWorkflows() {
+ var wftable = $("#workflows"), wfbut = $("#saveWorkflows"), wfbut1 = $("#emptyWorkflows");
+ var xml = NodeAll("stringList", "string", "");
+ wfbut.button("disable");
+ wfbut1.button("disable");
+ putXML(where("permittedWorkflowURIs"), xml, function() {
+ refreshWorkflows();
+ });
+}
+
/** How to update the table of users; called on demand */
function refreshUsers() {
var usertable = $("#userList");
@@ -497,6 +511,12 @@
refreshWorkflows();
event.preventDefault();
});
+ $("#emptyWorkflows").button({
+ disabled : true
+ }).click(function(event) {
+ emptyWorkflows();
+ event.preventDefault();
+ });
// Make the link to the list of usage records point correctly
// Original plan called for browsable table, but that's too slow
diff --git a/server-webapp/src/main/webapp/WEB-INF/beans.xml b/server-webapp/src/main/webapp/WEB-INF/beans.xml
index af0d8cf..73990a7 100644
--- a/server-webapp/src/main/webapp/WEB-INF/beans.xml
+++ b/server-webapp/src/main/webapp/WEB-INF/beans.xml
@@ -62,7 +62,7 @@
<property name="logIncomingWorkflows" value="${default.logworkflows}" />
<property name="allowNewWorkflowRuns" value="${default.permitsubmit}" />
<property name="logOutgoingExceptions" value="${default.logexceptions}" />
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<property name="self" ref="webapp.state" />
</bean>
@@ -179,7 +179,7 @@
<bean id="passwordEncoder"
class="org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder" />
<bean class="org.taverna.server.master.identity.UserStore" id="userStore">
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<property name="baselineUserProperties">
<util:properties location="/WEB-INF/security/users.properties" />
</property>
@@ -192,24 +192,28 @@
<props> <prop key="hibernate.dialect">org.hibernate.dialect.DerbyDialect</prop>
<prop key="hibernate.hbm2ddl.auto">create</prop> </props> </property> <property
name="annotatedClasses"> <list> </list> </property> </bean> -->
- <bean id="pmf" class="org.datanucleus.api.jdo.JDOPersistenceManagerFactory"
- destroy-method="close">
- <property name="connectionFactory" ref="dataSource" />
- <property name="nontransactionalRead" value="true" />
- <property name="persistenceProperties">
- <props>
- <prop key="datanucleus.storeManagerType">rdbms</prop>
- <prop key="datanucleus.autoCreateTables">true</prop>
- <prop key="datanucleus.autoCreateTables">true</prop>
- <prop key="datanucleus.validateTables">true</prop>
- <prop key="datanucleus.autoCreateColumns">true</prop>
- <prop key="datanucleus.autoCreateConstraints">true</prop>
- <prop key="datanucleus.validateConstraints">true</prop>
- <prop key="datanucleus.autoCreateSchema">true</prop>
- <prop key="datanucleus.PersistenceUnitName">TavernaServer</prop>
- <prop key="datanucleus.rdbms.datastoreAdapterClassName"
- >org.taverna.server.master.utils.LoggingDerbyAdapter</prop>
- </props>
+ <bean id="pmb" class="org.taverna.server.master.utils.JDOSupport.PersistenceManagerBuilder">
+ <property name="persistenceManagerFactory">
+ <bean id="pmf" class="org.datanucleus.api.jdo.JDOPersistenceManagerFactory"
+ destroy-method="close">
+ <property name="connectionFactory" ref="dataSource" />
+ <property name="nontransactionalRead" value="true" />
+ <property name="persistenceProperties">
+ <props>
+ <prop key="datanucleus.storeManagerType">rdbms</prop>
+ <prop key="datanucleus.autoCreateTables">true</prop>
+ <prop key="datanucleus.autoCreateTables">true</prop>
+ <prop key="datanucleus.validateTables">true</prop>
+ <prop key="datanucleus.autoCreateColumns">true</prop>
+ <prop key="datanucleus.autoCreateConstraints">true</prop>
+ <prop key="datanucleus.validateConstraints">true</prop>
+ <prop key="datanucleus.autoCreateSchema">true</prop>
+ <prop key="datanucleus.PersistenceUnitName">TavernaServer</prop>
+ <prop key="datanucleus.rdbms.datastoreAdapterClassName"
+ >org.taverna.server.master.utils.LoggingDerbyAdapter</prop>
+ </props>
+ </property>
+ </bean>
</property>
</bean>
<bean id="transactionAspect"
@@ -245,7 +249,7 @@
<bean id="usageRecordSink" class="org.taverna.server.master.usage.UsageRecordRecorder">
<property name="state" ref="webapp.state" />
<property name="contextualizer" ref="contextualizer" />
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<property name="self" ref="usageRecordSink" />
<property name="disableDB" value="${usage.disableDB}" />
<property name="logFile" value="${usage.logFile}" />
@@ -269,7 +273,7 @@
/> <property name="usageRecordSink" ref="usageRecordSink" /> <property name="URProcessorPool"
ref="URThreads" /> </bean> -->
- <task:executor id="URThreads" pool-size="${pool.size}" />
+ <!-- <task:executor id="URThreads" pool-size="${pool.size}" /> -->
<bean id="worker.securityContext"
class="org.taverna.server.master.worker.SecurityContextFactory">
@@ -326,7 +330,7 @@
the subprocess to complete its registration.
</description>
</property>
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<!-- <property name="javaBinary"> <description>The name of the java executable
used to run the server worker. Defaults to the executable used to run the
hosting environment.</description> </property> -->
@@ -388,7 +392,7 @@
The implementation of the catalog of workflow runs
supported by the localworker run engine.
</description>
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<property name="facade" ref="worker.rundb" />
</bean>
<task:scheduled-tasks scheduler="taskScheduler">
@@ -451,7 +455,7 @@
<bean id="dispatch.atom" class="org.taverna.server.master.notification.atom.EventDAO">
<property name="expiryAgeDays" value="${atom.lifespan}" />
- <property name="persistenceManagerFactory" ref="pmf" />
+ <property name="persistenceManagerBuilder" ref="pmb" />
<property name="uriBuilderFactory" ref="feed" />
<property name="self" ref="dispatch.atom" />
</bean>
diff --git a/server-webapp/src/main/webapp/WEB-INF/web.xml b/server-webapp/src/main/webapp/WEB-INF/web-nosec.xml
similarity index 95%
copy from server-webapp/src/main/webapp/WEB-INF/web.xml
copy to server-webapp/src/main/webapp/WEB-INF/web-nosec.xml
index 335a5d3..d6c6ee7 100644
--- a/server-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/server-webapp/src/main/webapp/WEB-INF/web-nosec.xml
@@ -10,8 +10,7 @@
<description>This is the front-end engine for Taverna 2.5.4 Server.</description>
<context-param>
<param-name>contextConfigLocation</param-name>
- <param-value>WEB-INF/secure.xml</param-value>
- <!-- <param-value>WEB-INF/insecure.xml</param-value> -->
+ <param-value>WEB-INF/insecure.xml</param-value>
<description>Where Spring is to load its bean definitions from. DO NOT
CHANGE WITHOUT CONSULTING DOCUMENTATION.</description>
</context-param>
diff --git a/server-webapp/src/main/webapp/WEB-INF/web.xml b/server-webapp/src/main/webapp/WEB-INF/web-partsec.xml
similarity index 95%
copy from server-webapp/src/main/webapp/WEB-INF/web.xml
copy to server-webapp/src/main/webapp/WEB-INF/web-partsec.xml
index 335a5d3..a2b545e 100644
--- a/server-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/server-webapp/src/main/webapp/WEB-INF/web-partsec.xml
@@ -10,8 +10,7 @@
<description>This is the front-end engine for Taverna 2.5.4 Server.</description>
<context-param>
<param-name>contextConfigLocation</param-name>
- <param-value>WEB-INF/secure.xml</param-value>
- <!-- <param-value>WEB-INF/insecure.xml</param-value> -->
+ <param-value>WEB-INF/partsecure.xml</param-value>
<description>Where Spring is to load its bean definitions from. DO NOT
CHANGE WITHOUT CONSULTING DOCUMENTATION.</description>
</context-param>
diff --git a/server-webapp/src/main/webapp/WEB-INF/web.xml b/server-webapp/src/main/webapp/WEB-INF/web-sec.xml
similarity index 97%
rename from server-webapp/src/main/webapp/WEB-INF/web.xml
rename to server-webapp/src/main/webapp/WEB-INF/web-sec.xml
index 335a5d3..9a5395a 100644
--- a/server-webapp/src/main/webapp/WEB-INF/web.xml
+++ b/server-webapp/src/main/webapp/WEB-INF/web-sec.xml
@@ -11,7 +11,6 @@
<context-param>
<param-name>contextConfigLocation</param-name>
<param-value>WEB-INF/secure.xml</param-value>
- <!-- <param-value>WEB-INF/insecure.xml</param-value> -->
<description>Where Spring is to load its bean definitions from. DO NOT
CHANGE WITHOUT CONSULTING DOCUMENTATION.</description>
</context-param>
diff --git a/server-webapp/src/main/webapp/WEB-INF/webappBeans.xml b/server-webapp/src/main/webapp/WEB-INF/webappBeans.xml
index 1b979b4..22e74b3 100644
--- a/server-webapp/src/main/webapp/WEB-INF/webappBeans.xml
+++ b/server-webapp/src/main/webapp/WEB-INF/webappBeans.xml
@@ -97,6 +97,9 @@
<ref bean="jsonProvider" />
<ref bean="atomEntryHandler" />
<ref bean="atomFeedHandler" />
+ <bean class="org.apache.cxf.jaxrs.model.wadl.WadlGenerator">
+ <property name="addResourceAndMethodIds" value="true"/>
+ </bean>
</jaxrs:providers>
<jaxrs:outInterceptors>
<ref bean="Interceptor.FlushThreadLocalCache" />
diff --git a/server-worker/src/main/java/org/taverna/server/localworker/impl/LocalWorker.java b/server-worker/src/main/java/org/taverna/server/localworker/impl/LocalWorker.java
index 05f9b1b..adf3ea7 100644
--- a/server-worker/src/main/java/org/taverna/server/localworker/impl/LocalWorker.java
+++ b/server-worker/src/main/java/org/taverna/server/localworker/impl/LocalWorker.java
@@ -166,6 +166,7 @@
List<String> runtimeSettings = new ArrayList<>();
URL interactionFeedURL;
URL webdavURL;
+ URL publishURL;//FIXME
private boolean doProvenance = true;
// ----------------------- METHODS -----------------------
@@ -755,9 +756,10 @@
}
@Override
- public void setInteractionServiceDetails(URL feed, URL webdav) {
+ public void setInteractionServiceDetails(URL feed, URL webdav, URL publish) {
interactionFeedURL = feed;
webdavURL = webdav;
+ publishURL = publish;
}
@Override
diff --git a/server-worker/src/main/java/org/taverna/server/localworker/impl/WorkerCore.java b/server-worker/src/main/java/org/taverna/server/localworker/impl/WorkerCore.java
index 7a24cd5..1a6cff8 100644
--- a/server-worker/src/main/java/org/taverna/server/localworker/impl/WorkerCore.java
+++ b/server-worker/src/main/java/org/taverna/server/localworker/impl/WorkerCore.java
@@ -54,6 +54,8 @@
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.io.Writer;
+import java.net.URI;
+import java.net.URISyntaxException;
import java.net.URL;
import java.rmi.RemoteException;
import java.rmi.server.UnicastRemoteObject;
@@ -442,6 +444,9 @@
env.put("INTERACTION_WEBDAV",
local.webdavURL != null ? local.webdavURL.getPath()
: interactionWebdavPath);
+ String pub = makeInterPublish(local.publishURL);
+ if (pub != null && !pub.isEmpty())
+ env.put("INTERACTION_PUBLISH", pub);
}
return pb;
}
@@ -464,6 +469,23 @@
}
@Nullable
+ private static String makeInterPublish(@Nullable URL url)
+ throws IOException {
+ if (url == null)
+ return null;
+ try {
+ URI uri = url.toURI();
+ int port = uri.getPort();
+ if (port == -1)
+ return uri.getScheme() + "://" + uri.getHost();
+ else
+ return uri.getScheme() + "://" + uri.getHost() + ":" + port;
+ } catch (URISyntaxException e) {
+ throw new IOException("problem constructing publication url", e);
+ }
+ }
+
+ @Nullable
private static String makeInterPath(@Nullable URL url) {
if (url == null)
return interactionFeedPath;
