You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:55:07 UTC
[18/26] incubator-taverna-server git commit: temporarily empty
repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/ProfileList.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/ProfileList.java b/server-webapp/src/main/java/org/taverna/server/master/common/ProfileList.java
deleted file mode 100644
index 69c3622..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/ProfileList.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright (C) 2012 The University of Manchester
- *
- * See the file "LICENSE.txt" for license terms.
- */
-package org.taverna.server.master.common;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-
-/**
- * Description of the profiles that can apply to a workflow.
- *
- * @author Donal K. Fellows
- */
-@XmlRootElement(name = "profiles")
-@XmlType(name = "ProfileList")
-public class ProfileList {
- public List<ProfileList.Info> profile = new ArrayList<ProfileList.Info>();
-
- /**
- * Description of a single workflow profile.
- *
- * @author Donal Fellows
- */
- @XmlRootElement(name = "profile")
- @XmlType(name = "Profile")
- public static class Info {
- @XmlValue
- public String name;
- /**
- * Whether this is the main profile.
- */
- @XmlAttribute(name = "isMain")
- public Boolean main;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/Roles.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/Roles.java b/server-webapp/src/main/java/org/taverna/server/master/common/Roles.java
deleted file mode 100644
index 8079b1c..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/Roles.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-/**
- * The roles defined in this webapp.
- *
- * @author Donal Fellows
- */
-public interface Roles {
- /** The role of a normal user. */
- static final String USER = "ROLE_tavernauser";
- /**
- * The role of an administrator. Administrators <i>should</i> have the
- * normal user role as well.
- */
- static final String ADMIN = "ROLE_tavernasuperuser";
- /**
- * The role of a workflow accessing itself. Do not give users this role.
- */
- static final String SELF = "ROLE_tavernaworkflow";
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/RunReference.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/RunReference.java b/server-webapp/src/main/java/org/taverna/server/master/common/RunReference.java
deleted file mode 100644
index 3486bf7..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/RunReference.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import static org.taverna.server.master.common.Namespaces.SERVER;
-import static org.taverna.server.master.common.Namespaces.XLINK;
-import static org.taverna.server.master.common.VersionedElement.VERSION;
-
-import java.net.URI;
-
-import javax.ws.rs.core.UriBuilder;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlSeeAlso;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
-
-/**
- * A reference to a single workflow run, described using JAXB.
- *
- * @author Donal Fellows
- * @see org.taverna.server.master.interfaces.TavernaRun TavernaRun
- */
-@XmlRootElement
-@XmlType(name = "TavernaRun")
-@XmlSeeAlso( { Workflow.class, DirEntryReference.class })
-public class RunReference {
- /**
- * Where to get information about the run. For REST.
- */
- @XmlAttribute(name = "href", namespace = XLINK)
- @XmlSchemaType(name = "anyURI")
- public URI link;
- /** What version of server produced this element? */
- @XmlAttribute(namespace = SERVER)
- public String serverVersion;
- /**
- * The name of the run. For SOAP.
- */
- @XmlValue
- public String name;
-
- /**
- * Make a blank run reference.
- */
- public RunReference() {
- }
-
- /**
- * Make a reference to the given workflow run.
- *
- * @param name
- * The name of the run.
- * @param ub
- * A factory for URIs, or <tt>null</tt> if none is to be made.
- */
- public RunReference(String name, UriBuilder ub) {
- this.serverVersion = VERSION;
- this.name = name;
- if (ub != null)
- this.link = ub.build(name);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/Status.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/Status.java b/server-webapp/src/main/java/org/taverna/server/master/common/Status.java
deleted file mode 100644
index 8e360dc..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/Status.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import javax.xml.bind.annotation.XmlEnum;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * 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
- */
-@XmlEnum
-@XmlType(name = "Status")
-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
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/Trust.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/Trust.java b/server-webapp/src/main/java/org/taverna/server/master/common/Trust.java
deleted file mode 100644
index 6d77aa7..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/Trust.java
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * Copyright (C) 2011-2012 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import static org.taverna.server.master.common.Namespaces.XLINK;
-
-import java.io.Serializable;
-import java.security.cert.Certificate;
-import java.util.Collection;
-import java.util.List;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlTransient;
-import javax.xml.bind.annotation.XmlType;
-
-/**
- * A description of a trusted identity or identities. This description is
- * characterised by a file visible to the workflow run that contains one or more
- * certificates.
- *
- * @author Donal Fellows
- */
-@XmlType(name = "TrustDescriptor")
-@XmlRootElement(name = "trustedIdentity")
-@SuppressWarnings("serial")
-public final class Trust implements Serializable {
- /** The location of this descriptor in the REST world. */
- @XmlAttribute(namespace = XLINK)
- public String href;
- /**
- * The location of this descriptor in the SOAP world. Must match corrected
- * with the {@link #href} field.
- */
- @XmlTransient
- public String id;
- /**
- * The file containing the certificate(s). This is resolved with respect to
- * the workflow run working directory.
- */
- @XmlElement
- public String certificateFile;
- /**
- * The type of certificate file. Defaults to <tt>X.509</tt> if unspecified.
- */
- @XmlElement
- public String fileType;
- /**
- * The encoded serialized keystore containing the certificate(s).
- */
- @XmlElement
- public byte[] certificateBytes;
- /**
- * The names of the server(s) identified by this trust.
- */
- @XmlElement
- public List<String> serverName;
- /**
- * The collection of certificates loaded from the specified file. This is
- * always <tt>null</tt> before validation.
- */
- public transient Collection<? extends Certificate> loadedCertificates;
-
- @Override
- public int hashCode() {
- return id.hashCode();
- }
-
- @Override
- public boolean equals(Object o) {
- if (o == null || !(o instanceof Trust))
- return false;
- return id.equals(((Trust) o).id);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/Uri.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/Uri.java b/server-webapp/src/main/java/org/taverna/server/master/common/Uri.java
deleted file mode 100644
index d6d057c..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/Uri.java
+++ /dev/null
@@ -1,432 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import static javax.ws.rs.core.UriBuilder.fromUri;
-import static org.apache.commons.logging.LogFactory.getLog;
-import static org.taverna.server.master.common.Namespaces.XLINK;
-
-import java.lang.reflect.Method;
-import java.net.URI;
-import java.util.Map;
-
-import javax.annotation.PreDestroy;
-import javax.ws.rs.core.UriBuilder;
-import javax.ws.rs.core.UriBuilderException;
-import javax.ws.rs.core.UriInfo;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlType;
-
-import org.apache.commons.logging.Log;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.security.web.PortMapper;
-
-import javax.annotation.Nonnull;
-
-/**
- * A class that makes it simpler to work with an element with a {@link URI} in
- * an <tt>href</tt> attribute. Done with JAXB.
- *
- * @author Donal Fellows
- */
-@XmlType(name = "Location")
-public class Uri {
- static Log log = getLog("Taverna.Server.UriRewriter");
- private static final String SECURE_SCHEME = "https";
- /**
- * This type is characterised by an attribute that is the reference to some
- * other element.
- */
- @XmlAttribute(name = "href", namespace = XLINK)
- @XmlSchemaType(name = "anyURI")
- public URI ref;
-
- /** Make a reference that points nowhere. */
- public Uri() {
- }
-
- /**
- * Make a reference to the given location.
- *
- * @param ref
- * Where to point to.
- */
- public Uri(@Nonnull URI ref) {
- this.ref = secure(ref);
- }
-
- /**
- * Make a reference from the factory with the given parameters.
- *
- * @param ub
- * The configured factory.
- * @param strings
- * The parameters to the factory.
- */
- public Uri(@Nonnull UriBuilder ub, String... strings) {
- ref = secure(ub).build((Object[]) strings);
- }
-
- /**
- * Make a reference from the factory with the given parameters.
- *
- * @param ui
- * The factory factory.
- * @param path
- * The path to configure the factory with.
- * @param strings
- * The parameters to the factory.
- */
- public Uri(@Nonnull UriInfo ui, @Nonnull String path, String... strings) {
- this(ui, true, path, strings);
- }
-
- /**
- * Make a reference from the factory with the given parameters.
- *
- * @param ui
- * The factory factory.
- * @param secure
- * Whether the URI should be required to use HTTPS.
- * @param path
- * The path to configure the factory with.
- * @param strings
- * The parameters to the factory.
- */
- public Uri(@Nonnull UriInfo ui, boolean secure, @Nonnull String path,
- String... strings) {
- UriBuilder ub = ui.getAbsolutePathBuilder();
- if (secure) {
- ub = secure(ub);
- }
- ref = ub.path(path).build((Object[]) strings);
- }
-
- public static UriBuilder secure(UriBuilder ub) {
- return Rewriter.getInstance().getSecuredUriBuilder(ub);
- }
-
- public static UriBuilder secure(UriInfo ui) {
- return secure(ui.getAbsolutePathBuilder());
- }
-
- public static URI secure(URI uri) {
- URI newURI = secure(fromUri(uri)).build();
- if (log.isDebugEnabled())
- log.debug("rewrote " + uri + " to " + newURI);
- return newURI;
- }
-
- public static URI secure(URI base, String uri) {
- URI newURI = secure(fromUri(base.resolve(uri))).build();
- if (log.isDebugEnabled())
- log.debug("rewrote " + uri + " to " + newURI);
- return newURI;
- }
-
- /**
- * A bean that allows configuration of how to rewrite generated URIs to be
- * secure.
- *
- * @author Donal Fellows
- */
- public static class Rewriter {
- private static Rewriter instance;
- private PortMapper portMapper;
- private boolean suppress;
- private String rewriteRE = "://[^/]+/[^/]+";
- private String rewriteTarget;
-
- static Rewriter getInstance() {
- if (instance == null)
- new Rewriter();
- return instance;
- }
-
- @Autowired
- public void setPortMapper(PortMapper portMapper) {
- this.portMapper = portMapper;
- }
-
- /**
- * Whether to suppress rewriting of URIs to be secure.
- *
- * @param suppressSecurity
- * True if no rewriting should be done.
- */
- public void setSuppressSecurity(boolean suppressSecurity) {
- suppress = suppressSecurity;
- }
-
- public void setRewriteRegexp(String rewriteRegexp) {
- this.rewriteRE = rewriteRegexp;
- }
-
- /**
- * What to rewrite the host, port and web-app name to be.
- *
- * @param rewriteTarget
- * What to rewrite to, or "<tt>NONE</tt>" for no rewrite.
- */
- public void setRewriteTarget(String rewriteTarget) {
- if (rewriteTarget.isEmpty())
- this.rewriteTarget = null;
- else if (rewriteTarget.equals("NONE"))
- this.rewriteTarget = null;
- else if (rewriteTarget.startsWith("${"))
- this.rewriteTarget = null;
- else
- this.rewriteTarget = "://" + rewriteTarget;
- }
-
- private Integer lookupHttpsPort(URI uri) {
- if (portMapper != null)
- return portMapper.lookupHttpsPort(uri.getPort());
- return null;
- }
-
- public Rewriter() {
- instance = this;
- }
-
- @PreDestroy
- public void done() {
- instance = null;
- Uri.log = null;
- }
-
- @Nonnull
- URI rewrite(@Nonnull String url) {
- if (rewriteTarget != null)
- url = url.replaceFirst(rewriteRE, rewriteTarget);
- return URI.create(url);
- }
-
- @Nonnull
- public UriBuilder getSecuredUriBuilder(@Nonnull UriBuilder uribuilder) {
- if (suppress)
- return uribuilder.clone();
- UriBuilder ub = new RewritingUriBuilder(uribuilder);
- Integer secPort = null;
- try {
- secPort = lookupHttpsPort(ub.build());
- } catch (Exception e) {
- /*
- * Do not log this; we know why it happens and don't actually
- * care to do anything about it. All it does is fill up the log
- * with pointless scariness!
- */
-
- // log.debug("failed to extract current URI port", e);
- }
- if (secPort == null || secPort.intValue() == -1)
- return ub.scheme(SECURE_SCHEME);
- return ub.scheme(SECURE_SCHEME).port(secPort);
- }
-
- /**
- * {@link UriBuilder} that applies a rewrite rule to the URIs produced
- * by the wrapped builder.
- *
- * @author Donal Fellows
- */
- class RewritingUriBuilder extends UriBuilder {
- private UriBuilder wrapped;
-
- RewritingUriBuilder(UriBuilder builder) {
- wrapped = builder.clone();
- }
-
- private URI rewrite(URI uri) {
- return Rewriter.this.rewrite(uri.toString());
- }
-
- @Override
- public UriBuilder clone() {
- return new RewritingUriBuilder(wrapped);
- }
-
- @Override
- public URI buildFromMap(Map<String, ?> values)
- throws IllegalArgumentException, UriBuilderException {
- return rewrite(wrapped.buildFromMap(values));
- }
-
- @Override
- public URI buildFromEncodedMap(Map<String, ? extends Object> values)
- throws IllegalArgumentException, UriBuilderException {
- return rewrite(wrapped.buildFromEncodedMap(values));
- }
-
- @Override
- public URI build(Object... values) throws IllegalArgumentException,
- UriBuilderException {
- return rewrite(wrapped.build(values));
- }
-
- @Override
- public URI build(Object[] values, boolean encodeSlashInPath)
- throws IllegalArgumentException, UriBuilderException {
- return rewrite(wrapped.build(values, encodeSlashInPath));
- }
-
- @Override
- public URI buildFromEncoded(Object... values)
- throws IllegalArgumentException, UriBuilderException {
- return rewrite(wrapped.buildFromEncoded(values));
- }
-
- @Override
- public URI buildFromMap(Map<String, ?> values,
- boolean encodeSlashInPath) throws IllegalArgumentException,
- UriBuilderException {
- return rewrite(wrapped.buildFromEncoded(values,
- encodeSlashInPath));
- }
-
- @Override
- public UriBuilder uri(URI uri) throws IllegalArgumentException {
- wrapped.uri(uri);
- return this;
- }
-
- @Override
- public UriBuilder uri(String uriTemplate)
- throws IllegalArgumentException {
- wrapped.uri(uriTemplate);
- return this;
- }
-
- @Override
- public String toTemplate() {
- return wrapped.toTemplate();
- }
-
- @Override
- public UriBuilder scheme(String scheme)
- throws IllegalArgumentException {
- wrapped.scheme(scheme);
- return this;
- }
-
- @Override
- public UriBuilder schemeSpecificPart(String ssp)
- throws IllegalArgumentException {
- wrapped.schemeSpecificPart(ssp);
- return this;
- }
-
- @Override
- public UriBuilder userInfo(String ui) {
- wrapped.userInfo(ui);
- return this;
- }
-
- @Override
- public UriBuilder host(String host) throws IllegalArgumentException {
- wrapped.host(host);
- return this;
- }
-
- @Override
- public UriBuilder port(int port) throws IllegalArgumentException {
- wrapped.port(port);
- return this;
- }
-
- @Override
- public UriBuilder replacePath(String path) {
- wrapped.replacePath(path);
- return this;
- }
-
- @Override
- public UriBuilder path(String path) throws IllegalArgumentException {
- wrapped.path(path);
- return this;
- }
-
- @Override
- public UriBuilder path(
- @java.lang.SuppressWarnings("rawtypes") Class resource)
- throws IllegalArgumentException {
- wrapped.path(resource);
- return this;
- }
-
- @Override
- public UriBuilder path(
- @java.lang.SuppressWarnings("rawtypes") Class resource,
- String method) throws IllegalArgumentException {
- wrapped.path(resource, method);
- return this;
- }
-
- @Override
- public UriBuilder path(Method method)
- throws IllegalArgumentException {
- wrapped.path(method);
- return this;
- }
-
- @Override
- public UriBuilder segment(String... segments)
- throws IllegalArgumentException {
- wrapped.segment(segments);
- return this;
- }
-
- @Override
- public UriBuilder replaceMatrix(String matrix)
- throws IllegalArgumentException {
- wrapped.replaceMatrix(matrix);
- return this;
- }
-
- @Override
- public UriBuilder matrixParam(String name, Object... values)
- throws IllegalArgumentException {
- wrapped.matrixParam(name, values);
- return this;
- }
-
- @Override
- public UriBuilder replaceMatrixParam(String name, Object... values)
- throws IllegalArgumentException {
- wrapped.replaceMatrixParam(name, values);
- return this;
- }
-
- @Override
- public UriBuilder replaceQuery(String query)
- throws IllegalArgumentException {
- wrapped.replaceQuery(query);
- return this;
- }
-
- @Override
- public UriBuilder queryParam(String name, Object... values)
- throws IllegalArgumentException {
- wrapped.queryParam(name, values);
- return this;
- }
-
- @Override
- public UriBuilder replaceQueryParam(String name, Object... values)
- throws IllegalArgumentException {
- wrapped.replaceQueryParam(name, values);
- return this;
- }
-
- @Override
- public UriBuilder fragment(String fragment) {
- wrapped.fragment(fragment);
- return this;
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/VersionedElement.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/VersionedElement.java b/server-webapp/src/main/java/org/taverna/server/master/common/VersionedElement.java
deleted file mode 100644
index 6eddf2d..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/VersionedElement.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import static org.apache.commons.logging.LogFactory.getLog;
-import static org.taverna.server.master.common.Namespaces.SERVER;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Properties;
-
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
-
-import org.apache.commons.logging.Log;
-
-/**
- * The type of an element that declares the version of the server that produced
- * it.
- *
- * @author Donal Fellows
- */
-@XmlType(name = "VersionedElement", namespace = SERVER)
-public abstract class VersionedElement {
- /** What version of server produced this element? */
- @XmlAttribute(namespace = SERVER)
- public String serverVersion;
- /** What revision of server produced this element? Derived from SCM commit. */
- @XmlAttribute(namespace = SERVER)
- public String serverRevision;
- /** When was the server built? */
- @XmlAttribute(namespace = SERVER)
- public String serverBuildTimestamp;
- public static final String VERSION, REVISION, TIMESTAMP;
- static {
- Log log = getLog("Taverna.Server.Webapp");
- Properties p = new Properties();
- try {
- try (InputStream is = VersionedElement.class
- .getResourceAsStream("/version.properties")) {
- p.load(is);
- }
- } catch (IOException e) {
- log.warn("failed to read /version.properties", e);
- }
- VERSION = p.getProperty("tavernaserver.version", "unknownVersion");
- REVISION = String.format("%s (tag: %s)",
- p.getProperty("tavernaserver.branch", "unknownRevision"),
- p.getProperty("tavernaserver.revision.describe", "unknownTag"));
- TIMESTAMP = p
- .getProperty("tavernaserver.timestamp", "unknownTimestamp");
- }
-
- public VersionedElement() {
- }
-
- protected VersionedElement(boolean ignored) {
- serverVersion = VERSION;
- serverRevision = REVISION;
- serverBuildTimestamp = TIMESTAMP;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/Workflow.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/Workflow.java b/server-webapp/src/main/java/org/taverna/server/master/common/Workflow.java
deleted file mode 100644
index ba6a68c..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/Workflow.java
+++ /dev/null
@@ -1,367 +0,0 @@
-/*
- * Copyright (C) 2010-2012 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common;
-
-import static javax.xml.bind.Marshaller.JAXB_ENCODING;
-import static javax.xml.bind.Marshaller.JAXB_FORMATTED_OUTPUT;
-import static javax.xml.bind.annotation.XmlAccessType.NONE;
-import static org.apache.commons.logging.LogFactory.getLog;
-import static org.taverna.server.master.rest.handler.Scufl2DocumentHandler.SCUFL2;
-import static org.taverna.server.master.rest.handler.T2FlowDocumentHandler.T2FLOW;
-import static org.taverna.server.master.rest.handler.T2FlowDocumentHandler.T2FLOW_NS;
-import static org.taverna.server.master.rest.handler.T2FlowDocumentHandler.T2FLOW_ROOTNAME;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.Externalizable;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.ObjectInput;
-import java.io.ObjectOutput;
-import java.io.OutputStreamWriter;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.net.URL;
-
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAnyElement;
-import javax.xml.bind.annotation.XmlRootElement;
-import javax.xml.bind.annotation.XmlTransient;
-import javax.xml.bind.annotation.XmlType;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.taverna.server.master.rest.handler.Scufl2DocumentHandler;
-import org.taverna.server.master.rest.handler.T2FlowDocumentHandler;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.xml.sax.SAXException;
-
-import uk.org.taverna.scufl2.api.common.NamedSet;
-import uk.org.taverna.scufl2.api.container.WorkflowBundle;
-import uk.org.taverna.scufl2.api.io.ReaderException;
-import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
-import uk.org.taverna.scufl2.api.io.WriterException;
-import uk.org.taverna.scufl2.api.profiles.Profile;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-/**
- * Encapsulation of a T2flow or Scufl2 document.
- *
- * @author Donal K. Fellows
- */
-@XmlRootElement(name = "workflow")
-@XmlType(name = "Workflow")
-@XmlAccessorType(NONE)
-public class Workflow implements Serializable, Externalizable {
- /** Literal document, if present. */
- @XmlAnyElement(lax = true)
- private Element content;
- /** SCUFL2 bundle, if present. */
- @XmlTransient
- private WorkflowBundle bundle;
- /** Which came first, the bundle or the t2flow document. */
- @XmlTransient
- private boolean isBundleFirst;
-
- private static Marshaller marshaller;
- private static Unmarshaller unmarshaller;
- private final static String ENCODING = "UTF-8";
- private final static WorkflowBundleIO io;
- static {
- try {
- JAXBContext context = JAXBContext.newInstance(Workflow.class);
- marshaller = context.createMarshaller();
- unmarshaller = context.createUnmarshaller();
- marshaller.setProperty(JAXB_ENCODING, ENCODING);
- marshaller.setProperty(JAXB_FORMATTED_OUTPUT, false);
- } catch (JAXBException e) {
- getLog("Taverna.Server.Webapp").fatal(
- "failed to build JAXB context for working with "
- + Workflow.class, e);
- }
- io = new WorkflowBundleIO();
- }
-
- public enum ContentType {
- T2FLOW(T2FlowDocumentHandler.T2FLOW), SCUFL2(
- Scufl2DocumentHandler.SCUFL2);
- private String type;
-
- ContentType(String type) {
- this.type = type;
- }
-
- public String getContentType() {
- return type;
- }
- }
-
- public Workflow() {
- }
-
- public Workflow(Element element) {
- this.content = element;
- this.isBundleFirst = false;
- }
-
- public Workflow(WorkflowBundle bundle) {
- this.bundle = bundle;
- this.isBundleFirst = true;
- }
-
- public Workflow(URL url) throws ReaderException, IOException {
- this(io.readBundle(url, null));
- }
-
- /**
- * What content type would this workflow "prefer" to be?
- */
- public ContentType getPreferredContentType() {
- if (isBundleFirst)
- return ContentType.SCUFL2;
- else
- return ContentType.T2FLOW;
- }
-
- /**
- * Retrieves the workflow as a SCUFL2 document, converting it if necessary.
- *
- * @return The SCUFL2 document.
- * @throws IOException
- * If anything goes wrong.
- */
- public WorkflowBundle getScufl2Workflow() throws IOException {
- try {
- if (bundle == null)
- bundle = io.readBundle(new ByteArrayInputStream(getAsT2Flow()),
- T2FLOW);
- return bundle;
- } catch (IOException e) {
- throw e;
- } catch (Exception e) {
- throw new IOException("problem when converting to SCUFL2", e);
- }
- }
-
- /**
- * Get the bytes of the serialized SCUFL2 workflow.
- *
- * @return Array of bytes.
- * @throws IOException
- * If serialization fails.
- * @throws WriterException
- * If conversion fails.
- */
- public byte[] getScufl2Bytes() throws IOException, WriterException {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- io.writeBundle(getScufl2Workflow(), baos, SCUFL2);
- return baos.toByteArray();
- }
-
- /**
- * Retrieves the workflow as a T2Flow document, converting it if necessary.
- *
- * @return The T2Flow document.
- * @throws IOException
- * If anything goes wrong.
- */
- public Element getT2flowWorkflow() throws IOException {
- try {
- if (content != null)
- return content;
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- io.writeBundle(bundle, baos, T2FLOW);
- Document doc;
- try {
- DocumentBuilderFactory dbf = DocumentBuilderFactory
- .newInstance();
- dbf.setNamespaceAware(true);
- doc = dbf.newDocumentBuilder().parse(
- new ByteArrayInputStream(baos.toByteArray()));
- } catch (SAXException e) {
- throw new IOException("failed to convert to DOM tree", e);
- }
- Element e = doc.getDocumentElement();
- if (e.getNamespaceURI().equals(T2FLOW_NS)
- && e.getNodeName().equals(T2FLOW_ROOTNAME))
- return content = e;
- throw new IOException(
- "unexpected element when converting to T2Flow: {"
- + e.getNamespaceURI() + "}" + e.getNodeName());
- } catch (IOException e) {
- throw e;
- } catch (Exception e) {
- throw new IOException("problem when converting to SCUFL2", e);
- }
- }
-
- /**
- * @return The name of the main workflow profile, or <tt>null</tt> if there
- * is none.
- */
- public String getMainProfileName() {
- try {
- return getScufl2Workflow().getMainProfile().getName();
- } catch (IOException e) {
- return null;
- }
- }
-
- /**
- * @return The set of profiles supported over this workflow.
- */
- public NamedSet<Profile> getProfiles() {
- try {
- return getScufl2Workflow().getProfiles();
- } catch (IOException e) {
- return new NamedSet<Profile>();
- }
- }
-
- /**
- * Convert from marshalled form.
- *
- * @throws JAXBException
- * If the conversion fails.
- */
- public static Workflow unmarshal(String representation)
- throws JAXBException {
- StringReader sr = new StringReader(representation);
- return (Workflow) unmarshaller.unmarshal(sr);
- }
-
- /**
- * Convert to marshalled form.
- */
- public String marshal() throws JAXBException {
- StringWriter sw = new StringWriter();
- marshaller.marshal(this, sw);
- return sw.toString();
- }
-
- @Override
- public void readExternal(ObjectInput in) throws IOException,
- ClassNotFoundException {
- try {
- ByteArrayInputStream bytes = readbytes(in);
- if (bytes != null)
- try (Reader r = new InputStreamReader(bytes, ENCODING)) {
- content = ((Workflow) unmarshaller.unmarshal(r)).content;
- }
- bytes = readbytes(in);
- if (bytes != null)
- bundle = io.readBundle(bytes, SCUFL2);
- isBundleFirst = in.readBoolean();
- return;
- } catch (JAXBException e) {
- throw new IOException("failed to unmarshal", e);
- } catch (ClassCastException e) {
- throw new IOException("bizarre result of unmarshalling", e);
- } catch (ReaderException e) {
- throw new IOException("failed to unmarshal", e);
- }
- }
-
- private byte[] getAsT2Flow() throws IOException, JAXBException {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- OutputStreamWriter w = new OutputStreamWriter(baos, ENCODING);
- marshaller.marshal(this, w);
- w.close();
- return baos.toByteArray();
- }
-
- private byte[] getAsScufl2() throws IOException, WriterException {
- ByteArrayOutputStream baos = new ByteArrayOutputStream();
- io.writeBundle(bundle, baos, SCUFL2);
- baos.close();
- return baos.toByteArray();
- }
-
- @Override
- public void writeExternal(ObjectOutput out) throws IOException {
- try {
- writebytes(out, (content != null) ? getAsT2Flow() : null);
- } catch (JAXBException e) {
- throw new IOException("failed to marshal t2flow", e);
- }
- try {
- writebytes(out, (bundle != null) ? getAsScufl2() : null);
- } catch (WriterException e) {
- throw new IOException("failed to marshal scufl2", e);
- }
- out.writeBoolean(isBundleFirst);
- }
-
- private ByteArrayInputStream readbytes(ObjectInput in) throws IOException {
- int len = in.readInt();
- if (len > 0) {
- byte[] bytes = new byte[len];
- in.readFully(bytes);
- return new ByteArrayInputStream(bytes);
- }
- return null;
- }
-
- private void writebytes(ObjectOutput out, byte[] data) throws IOException {
- out.writeInt(data == null ? 0 : data.length);
- if (data != null && data.length > 0)
- out.write(data);
- }
-
- /**
- * Make up for the lack of an integrated XPath engine.
- *
- * @param name
- * The element names to look up from the root of the contained
- * document.
- * @return The looked up element, or <tt>null</tt> if it doesn't exist.
- */
- private Element getEl(String... name) {
- Element el = content;
- boolean skip = true;
- for (String n : name) {
- if (skip) {
- skip = false;
- continue;
- }
- if (el == null)
- return null;
- NodeList nl = el.getElementsByTagNameNS(T2FLOW_NS, n);
- if (nl.getLength() == 0)
- return null;
- Node node = nl.item(0);
- if (node instanceof Element)
- el = (Element) node;
- else
- return null;
- }
- return el;
- }
-
- /**
- * @return The content of the embedded
- * <tt><workflow><dataflow><name></tt> element.
- */
- @XmlTransient
- public String getName() {
- return getEl("workflow", "dataflow", "name").getTextContent();
- }
-
- /**
- * @return The embedded <tt><workflow></tt> element.
- */
- @XmlTransient
- public Element getWorkflowRoot() {
- return getEl("workflow");
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/common/package-info.java
deleted file mode 100644
index fd040de..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/package-info.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-/**
- * This package contains the common XML elements used throughout Taverna Server's various interfaces.
- * @author Donal Fellows
- */
-@XmlSchema(namespace = SERVER, elementFormDefault = QUALIFIED, attributeFormDefault = QUALIFIED, xmlns = {
- @XmlNs(prefix = "xlink", namespaceURI = XLINK),
- @XmlNs(prefix = "ts", namespaceURI = SERVER),
- @XmlNs(prefix = "ts-rest", namespaceURI = SERVER_REST),
- @XmlNs(prefix = "ts-soap", namespaceURI = SERVER_SOAP),
- @XmlNs(prefix = "feed", namespaceURI = FEED),
- @XmlNs(prefix = "admin", namespaceURI = ADMIN) })
-package org.taverna.server.master.common;
-
-import static javax.xml.bind.annotation.XmlNsForm.QUALIFIED;
-import static org.taverna.server.master.common.Namespaces.ADMIN;
-import static org.taverna.server.master.common.Namespaces.FEED;
-import static org.taverna.server.master.common.Namespaces.SERVER;
-import static org.taverna.server.master.common.Namespaces.SERVER_REST;
-import static org.taverna.server.master.common.Namespaces.SERVER_SOAP;
-import static org.taverna.server.master.common.Namespaces.XLINK;
-
-import javax.xml.bind.annotation.XmlNs;
-import javax.xml.bind.annotation.XmlSchema;
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/common/version/Version.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/common/version/Version.java b/server-webapp/src/main/java/org/taverna/server/master/common/version/Version.java
deleted file mode 100644
index e9c58a9..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/common/version/Version.java
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.common.version;
-
-import static org.taverna.server.master.common.version.Constants.PATCH;
-import static org.taverna.server.master.common.version.Constants.VERSION;
-
-/**
- * Common location for describing the version of the server.
- *
- * @author Donal Fellows
- */
-public interface Version {
- public static final String JAVA = VERSION + Constants.releaseChar + PATCH;
- public static final String HTML = VERSION + Constants.releaseHEnt + PATCH;
- public static final String XML = VERSION + Constants.releaseXEnt + PATCH;
-}
-
-/**
- * The pieces of a version string.
- *
- * @author Donal Fellows
- */
-interface Constants {
- static final String MAJOR = "2";
- static final String MINOR = "5";
- static final String PATCH = "4";
-
- static final char alphaChar = '\u03b1';
- static final char betaChar = '\u03b2';
- static final char releaseChar = '.';
- static final String alphaHEnt = "α";
- static final String betaHEnt = "β";
- static final String releaseHEnt = ".";
- static final String alphaXEnt = "α";
- static final String betaXEnt = "β";
- static final String releaseXEnt = ".";
-
- static final String VERSION = MAJOR + "." + MINOR;
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/defaults/Default.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/defaults/Default.java b/server-webapp/src/main/java/org/taverna/server/master/defaults/Default.java
deleted file mode 100644
index c2a2bc9..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/defaults/Default.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.defaults;
-
-import org.taverna.server.master.common.Status;
-import org.taverna.server.master.localworker.LocalWorkerState;
-
-/**
- * This defines a collection of default values, collecting them from various
- * parts of the server.
- *
- * @author Donal Fellows
- */
-public interface Default {
- /** The default value of the <tt>prefix</tt> property. */
- static final String AUTHORITY_PREFIX = "LOCALUSER_";
-
- /**
- * The name of the resource that is the implementation of the subprocess
- * that this class will fork off.
- */
- static final String SERVER_WORKER_IMPLEMENTATION_JAR = "util/server.worker.jar";
-
- /**
- * The name of the resource that is the implementation of the subprocess
- * that manages secure forking.
- */
- static final String SECURE_FORK_IMPLEMENTATION_JAR = "util/secure.fork.jar";
-
- /**
- * The name of the resource that is the implementation of the subprocess
- * that acts as the RMI registry.
- */
- static final String REGISTRY_JAR = "util/rmi.daemon.jar";
-
- /** Initial lifetime of runs, in minutes. */
- static final int RUN_LIFE_MINUTES = 20;
-
- /**
- * Maximum number of runs to exist at once. Note that this includes when
- * they are just existing for the purposes of file transfer (
- * {@link Status#Initialized}/{@link Status#Finished} states).
- */
- static final int RUN_COUNT_MAX = 5;
-
- /**
- * Prefix to use for RMI names.
- */
- static final String RMI_PREFIX = "ForkRunFactory.";
-
- /** Default value for {@link LocalWorkerState#passwordFile}. */
- static final String PASSWORD_FILE = null;
-
- /**
- * The extra arguments to pass to the subprocess.
- */
- static final String[] EXTRA_ARGUMENTS = new String[0];
-
- /**
- * How long to wait for subprocess startup, in seconds.
- */
- static final int SUBPROCESS_START_WAIT = 40;
-
- /**
- * Polling interval to use during startup, in milliseconds.
- */
- static final int SUBPROCESS_START_POLL_SLEEP = 1000;
-
- /**
- * Maximum number of {@link Status#Operating} runs at any time.
- */
- static final int RUN_OPERATING_LIMIT = 10;
-
- /**
- * What fields of a certificate we look at when understanding who it is
- * talking about, in the order that we look.
- */
- static final String[] CERTIFICATE_FIELD_NAMES = { "CN", "COMMONNAME",
- "COMMON NAME", "COMMON_NAME", "OU", "ORGANIZATIONALUNITNAME",
- "ORGANIZATIONAL UNIT NAME", "O", "ORGANIZATIONNAME",
- "ORGANIZATION NAME" };
-
- /** The type of certificates that are processed if we don't say otherwise. */
- static final String CERTIFICATE_TYPE = "X.509";
-
- /** Max size of credential file, in kiB. */
- static final int CREDENTIAL_FILE_SIZE_LIMIT = 20;
-
- /**
- * The notification message format to use if none is configured.
- */
- public static final String NOTIFY_MESSAGE_FORMAT = "Your job with ID={0} has finished with exit code {1,number,integer}.";
-
- /** The address of the SMS gateway service used. */
- public static final String SMS_GATEWAY_URL = "https://www.intellisoftware.co.uk/smsgateway/sendmsg.aspx";
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/defaults/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/defaults/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/defaults/package-info.java
deleted file mode 100644
index 239b260..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/defaults/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * This package contains information about the various default values supported by the server.
- * @author Donal Fellows
- */
-package org.taverna.server.master.defaults;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadInputPortNameException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadInputPortNameException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadInputPortNameException.java
deleted file mode 100644
index 0b6247e..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadInputPortNameException.java
+++ /dev/null
@@ -1,21 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Indicates that the port name was not recognized.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "BadInputPortNameFault")
-@SuppressWarnings("serial")
-public class BadInputPortNameException extends Exception {
- public BadInputPortNameException(String msg) {
- super(msg);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadPropertyValueException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadPropertyValueException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadPropertyValueException.java
deleted file mode 100644
index 303b19b..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadPropertyValueException.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Indicates a bad property value.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "BadPropertyValueFault")
-public class BadPropertyValueException extends NoListenerException {
- private static final long serialVersionUID = -8459491388504556875L;
-
- public BadPropertyValueException(String msg) {
- super(msg);
- }
-
- public BadPropertyValueException(String msg, Throwable e) {
- super(msg, e);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadStateChangeException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadStateChangeException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadStateChangeException.java
deleted file mode 100644
index 4b843e2..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/BadStateChangeException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Exception that is thrown to indicate that the state change requested for a
- * run is impossible.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoUpdateFault")
-public class BadStateChangeException extends NoUpdateException {
- private static final long serialVersionUID = -4490826388447601775L;
-
- public BadStateChangeException() {
- super("cannot do that state change");
- }
-
- public BadStateChangeException(Throwable t) {
- super("cannot do that state change", t);
- }
-
- public BadStateChangeException(String msg, Throwable t) {
- super(msg, t);
- }
-
- public BadStateChangeException(String message) {
- super(message);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/FilesystemAccessException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/FilesystemAccessException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/FilesystemAccessException.java
deleted file mode 100644
index 0b6cf07..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/FilesystemAccessException.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import java.rmi.RemoteException;
-
-import javax.xml.ws.WebFault;
-
-/**
- * An exception that happened when the underlying filesystem was accessed.
- * @author Donal Fellows
- */
-@WebFault(name = "FilesystemAccessFault")
-public class FilesystemAccessException extends Exception {
- private static final long serialVersionUID = 8715937300989820318L;
-
- public FilesystemAccessException(String msg) {
- super(msg);
- }
-
- public FilesystemAccessException(String string, Throwable cause) {
- super(string, getRealCause(cause));
- }
-
- private static Throwable getRealCause(Throwable t) {
- if (t instanceof RemoteException) {
- RemoteException remote = (RemoteException) t;
- if (remote.detail != null)
- return remote.detail;
- }
- if (t.getCause() != null)
- return t.getCause();
- return t;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/GeneralFailureException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/GeneralFailureException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/GeneralFailureException.java
deleted file mode 100644
index 11d47c7..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/GeneralFailureException.java
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import static org.taverna.server.master.common.Namespaces.SERVER_SOAP;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Some sort of exception that occurred which we can't map any other way. This
- * is generally indicative of a problem server-side.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "GeneralFailureFault", targetNamespace = SERVER_SOAP)
-@SuppressWarnings("serial")
-public class GeneralFailureException extends RuntimeException {
- public GeneralFailureException(Throwable cause) {
- super(cause.getMessage(), cause);
- }
-
- public GeneralFailureException(String message, Throwable cause) {
- super(message, cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/InvalidCredentialException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/InvalidCredentialException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/InvalidCredentialException.java
deleted file mode 100644
index 67ba551..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/InvalidCredentialException.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-/**
- * An exception that is thrown to indicate that a credential-descriptor or
- * trust-descriptor supplied as part of a credential or trust management
- * operation is invalid.
- *
- * @author Donal Fellows
- *
- */
-@SuppressWarnings("serial")
-public class InvalidCredentialException extends Exception {
- private static final String MSG = "that credential is invalid";
-
- public InvalidCredentialException() {
- super(MSG);
- }
-
- public InvalidCredentialException(String reason) {
- super(MSG + ": " + reason);
- }
-
- public InvalidCredentialException(String reason, Throwable cause) {
- this(reason);
- initCause(cause);
- }
-
- public InvalidCredentialException(Throwable cause) {
- this(cause.getMessage(), cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCreateException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCreateException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCreateException.java
deleted file mode 100644
index e2ddf4c..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCreateException.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-
-/**
- * Exception that is thrown to indicate that the user is not permitted to
- * create something.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoCreateFault")
-public class NoCreateException extends NoUpdateException {
- private static final long serialVersionUID = 270413810410167235L;
-
- public NoCreateException() {
- super("not permitted to create");
- }
-
- public NoCreateException(String string) {
- super(string);
- }
-
- public NoCreateException(String string, Throwable e) {
- super(string, e);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCredentialException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCredentialException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCredentialException.java
deleted file mode 100644
index 7077fc4..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoCredentialException.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-/**
- * Exception that indicates the absence of an expected credential.
- *
- * @author Donal Fellows
- */
-@SuppressWarnings("serial")
-public class NoCredentialException extends Exception {
- public NoCredentialException() {
- super("no such credential");
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDestroyException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDestroyException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDestroyException.java
deleted file mode 100644
index d7b0d29..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDestroyException.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-
-/**
- * Exception that is thrown to indicate that the user is not permitted to
- * destroy something.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoDestroyFault")
-public class NoDestroyException extends NoUpdateException {
- private static final long serialVersionUID = 6207448533265237933L;
-
- public NoDestroyException() {
- super("not permitted to destroy");
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDirectoryEntryException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDirectoryEntryException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDirectoryEntryException.java
deleted file mode 100644
index 0d6ca63..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoDirectoryEntryException.java
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Indicates that the file or directory name was not recognized.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoDirectoryEntryFault")
-@SuppressWarnings("serial")
-public class NoDirectoryEntryException extends Exception {
- public NoDirectoryEntryException(String msg) {
- super(msg);
- }
- public NoDirectoryEntryException(String msg,Exception cause) {
- super(msg, cause);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoListenerException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoListenerException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoListenerException.java
deleted file mode 100644
index f4b8e81..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoListenerException.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.bind.annotation.XmlSeeAlso;
-import javax.xml.ws.WebFault;
-
-/**
- * Exception thrown to indicate that no listener by that name exists, or that
- * some other problem with listeners has occurred.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoListenerFault")
-@XmlSeeAlso(BadPropertyValueException.class)
-public class NoListenerException extends Exception {
- private static final long serialVersionUID = -2550897312787546547L;
-
- public NoListenerException() {
- super("no such listener");
- }
-
- public NoListenerException(String msg) {
- super(msg);
- }
-
- public NoListenerException(String msg, Throwable t) {
- super(msg, t);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoUpdateException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoUpdateException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoUpdateException.java
deleted file mode 100644
index c49d111..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NoUpdateException.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.bind.annotation.XmlSeeAlso;
-import javax.xml.ws.WebFault;
-
-/**
- * Exception that is thrown to indicate that the user is not permitted to update
- * something.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NoUpdateFault")
-@XmlSeeAlso( { NoCreateException.class, NoDestroyException.class, BadStateChangeException.class })
-public class NoUpdateException extends Exception {
- private static final long serialVersionUID = 4230987102653846379L;
-
- public NoUpdateException() {
- super("not permitted to update");
- }
-
- public NoUpdateException(String msg) {
- super(msg);
- }
-
- public NoUpdateException(String string, Throwable e) {
- super(string, e);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/NotOwnerException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NotOwnerException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/NotOwnerException.java
deleted file mode 100644
index 6e1f792..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/NotOwnerException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * An exception thrown when an operation is attempted which only the owner is
- * permitted to do. Notably, permissions may <i>only</i> be manipulated by the
- * owner.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "NotOwnerFault")
-@SuppressWarnings("serial")
-public class NotOwnerException extends Exception {
- public NotOwnerException() {
- super("not permitted; not the owner");
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/OverloadedException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/OverloadedException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/OverloadedException.java
deleted file mode 100644
index dda371e..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/OverloadedException.java
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Exception that is thrown to indicate that the state change requested for a
- * run is currently impossible due to excessive server load.
- *
- * @author Donal Fellows
- */
-@WebFault(name = "OverloadedFault")
-public class OverloadedException extends BadStateChangeException {
- private static final long serialVersionUID = 490826388447601776L;
-
- public OverloadedException() {
- super("server too busy; try later please");
- }
-
- public OverloadedException(Throwable t) {
- super("server too busy; try later please", t);
- }
-
- public OverloadedException(String msg, Throwable t) {
- super(msg, t);
- }
-
- public OverloadedException(String message) {
- super(message);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/UnknownRunException.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/UnknownRunException.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/UnknownRunException.java
deleted file mode 100644
index 4632d4a..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/UnknownRunException.java
+++ /dev/null
@@ -1,27 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.exceptions;
-
-import javax.xml.ws.WebFault;
-
-/**
- * Exception thrown to indicate that the handle of the run is unknown (or
- * unacceptable to the current user).
- *
- * @author Donal Fellows
- */
-@WebFault(name = "UnknownRunFault")
-public class UnknownRunException extends Exception {
- private static final long serialVersionUID = -3028749401786242841L;
-
- public UnknownRunException() {
- super("unknown run UUID");
- }
-
- public UnknownRunException(Throwable t) {
- super("implementation problems", t);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/exceptions/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/exceptions/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/exceptions/package-info.java
deleted file mode 100644
index 29ccacd..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/exceptions/package-info.java
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-/**
- * This package contains the exceptions/faults thrown by Taverna Server.
- * @author Donal Fellows
- */
-@XmlSchema(namespace = SERVER, elementFormDefault = QUALIFIED, attributeFormDefault = QUALIFIED, xmlns = {
- @XmlNs(prefix = "xlink", namespaceURI = XLINK),
- @XmlNs(prefix = "ts", namespaceURI = SERVER),
- @XmlNs(prefix = "ts-rest", namespaceURI = SERVER_REST),
- @XmlNs(prefix = "ts-soap", namespaceURI = SERVER_SOAP),
- @XmlNs(prefix = "feed", namespaceURI = FEED),
- @XmlNs(prefix = "admin", namespaceURI = ADMIN) })
-package org.taverna.server.master.exceptions;
-
-import static javax.xml.bind.annotation.XmlNsForm.QUALIFIED;
-import static org.taverna.server.master.common.Namespaces.ADMIN;
-import static org.taverna.server.master.common.Namespaces.FEED;
-import static org.taverna.server.master.common.Namespaces.SERVER;
-import static org.taverna.server.master.common.Namespaces.SERVER_REST;
-import static org.taverna.server.master.common.Namespaces.SERVER_SOAP;
-import static org.taverna.server.master.common.Namespaces.XLINK;
-
-import javax.xml.bind.annotation.XmlNs;
-import javax.xml.bind.annotation.XmlSchema;
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/facade/Facade.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/facade/Facade.java b/server-webapp/src/main/java/org/taverna/server/master/facade/Facade.java
deleted file mode 100644
index 0015754..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/facade/Facade.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.facade;
-
-import static javax.ws.rs.core.MediaType.TEXT_HTML_TYPE;
-import static javax.ws.rs.core.Response.ok;
-
-import java.io.IOException;
-import java.net.URL;
-
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.Produces;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.UriInfo;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.springframework.beans.factory.annotation.Required;
-import org.taverna.server.master.utils.Contextualizer;
-
-/**
- * This is a simple class that is used to serve up a file (with a simple
- * substitution applied) as the root of the T2Server webapp.
- *
- * @author Donal Fellows
- */
-@Path("/")
-public class Facade {
- private Log log = LogFactory.getLog("Taverna.Server.Utils");
- private String welcome;
- private Contextualizer contextualizer;
-
- /**
- * Set what resource file to use as the template for the response.
- *
- * @param file
- * The file from which to load the data (presumed HTML) to serve
- * up as the root content.
- * @throws IOException
- * If the file doesn't exist.
- */
- public void setFile(String file) throws IOException {
- URL full = Facade.class.getResource(file);
- log.info("setting " + full + " as source of root page");
- this.welcome = IOUtils.toString(full);
- }
-
- @Required
- public void setContextualizer(Contextualizer contextualizer) {
- this.contextualizer = contextualizer;
- }
-
- /**
- * Serve up some HTML as the root of the service.
- *
- * @param ui
- * A reference to how we were accessed by the service.
- * @return The response, containing the HTML.
- */
- @GET
- @Path("{dummy:.*}")
- @Produces("text/html")
- public Response get(@Context UriInfo ui) {
- return ok(contextualizer.contextualize(ui, welcome), TEXT_HTML_TYPE)
- .build();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/facade/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/facade/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/facade/package-info.java
deleted file mode 100644
index 73c884f..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/facade/package-info.java
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-/**
- * Simple facade used at the top level of the Taverna Server in order to
- * provide an entry splash page.
- */
-package org.taverna.server.master.facade;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/factories/ConfigurableRunFactory.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/factories/ConfigurableRunFactory.java b/server-webapp/src/main/java/org/taverna/server/master/factories/ConfigurableRunFactory.java
deleted file mode 100644
index 954b6f1..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/factories/ConfigurableRunFactory.java
+++ /dev/null
@@ -1,133 +0,0 @@
-/*
- * Copyright (C) 2012 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.factories;
-
-/**
- * Interface to run factories for the purpose of configuration.
- *
- * @author Donal Fellows
- */
-public interface ConfigurableRunFactory extends RunFactory {
- /** Where is the registry? Getter */
- String getRegistryHost();
-
- /** Where is the registry? Setter */
- void setRegistryHost(String host);
-
- /** Where is the registry? Getter */
- int getRegistryPort();
-
- /** Where is the registry? Setter */
- void setRegistryPort(int port);
-
- /** How much can be done at once? Getter */
- int getMaxRuns();
-
- /** How much can be done at once? Setter */
- void setMaxRuns(int maxRuns);
-
- /** How long will things live? Getter */
- int getDefaultLifetime();
-
- /** How long will things live? Setter */
- void setDefaultLifetime(int defaultLifetime);
-
- /** How often do we probe for info? Getter */
- int getSleepTime();
-
- /** How often do we probe for info? Setter */
- void setSleepTime(int sleepTime);
-
- /** How long do we allow for actions? Getter */
- int getWaitSeconds();
-
- /** How long do we allow for actions? Setter */
- void setWaitSeconds(int seconds);
-
- /** How do we start the workflow engine? Getter */
- String getExecuteWorkflowScript();
-
- /** How do we start the workflow engine? Setter */
- void setExecuteWorkflowScript(String executeWorkflowScript);
-
- /** How do we start the file system access process? Getter */
- String getServerWorkerJar();
-
- /** How do we start the file system access process? Setter */
- void setServerWorkerJar(String serverWorkerJar);
-
- /**
- * How do we start the file system access process? Extra arguments to pass.
- * Getter
- */
- String[] getExtraArguments();
-
- /**
- * How do we start the file system access process? Extra arguments to pass.
- * Setter
- */
- void setExtraArguments(String[] firstArguments);
-
- /** Where is Java? Getter */
- String getJavaBinary();
-
- /** Where is Java? Setter */
- void setJavaBinary(String javaBinary);
-
- /** Where do we get passwords from? Getter */
- String getPasswordFile();
-
- /** Where do we get passwords from? Setter */
- void setPasswordFile(String newValue);
-
- /** How do we switch users? Getter */
- String getServerForkerJar();
-
- /** How do we switch users? Setter */
- void setServerForkerJar(String newValue);
-
- /** How many runs have there been? */
- int getTotalRuns();
-
- /** How long did the last subprocess startup take? */
- int getLastStartupCheckCount();
-
- /** What are the current runs? */
- String[] getCurrentRunNames();
-
- /** What is the RMI ID of the factory process? */
- String getFactoryProcessName();
-
- /** What was the last observed exit code? */
- Integer getLastExitCode();
-
- /** What factory process to use for a particular user? */
- String[] getFactoryProcessMapping();
-
- /** How many runs can be operating at once? Setter */
- void setOperatingLimit(int operatingLimit);
-
- /** How many runs can be operating at once? Getter */
- int getOperatingLimit();
-
- /**
- * How many runs are actually operating?
- *
- * @throws Exception
- * if anything goes wrong
- */
- int getOperatingCount() throws Exception;
-
- /** How do we start the RMI registry process? Getter */
- String getRmiRegistryJar();
-
- /** How do we start the RMI registry process? Setter */
- void setRmiRegistryJar(String rmiRegistryJar);
-
- boolean getGenerateProvenance();
-
- void setGenerateProvenance(boolean generateProvenance);
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/factories/ListenerFactory.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/factories/ListenerFactory.java b/server-webapp/src/main/java/org/taverna/server/master/factories/ListenerFactory.java
deleted file mode 100644
index ecc13cd..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/factories/ListenerFactory.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright (C) 2010 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.factories;
-
-import java.util.List;
-
-import org.taverna.server.master.exceptions.NoListenerException;
-import org.taverna.server.master.interfaces.Listener;
-import org.taverna.server.master.interfaces.TavernaRun;
-
-/**
- * How to make event listeners of various types that are attached to a workflow
- * instance.
- *
- * @author Donal Fellows
- */
-public interface ListenerFactory {
- /**
- * Make an event listener.
- *
- * @param run
- * The workflow instance to attach the event listener to.
- * @param listenerType
- * The type of event listener to create. Must be one of the
- * strings returned by {@link #getSupportedListenerTypes()}.
- * @param configuration
- * A configuration document to pass to the listener.
- * @return The event listener that was created.
- * @throws NoListenerException
- * If the <b>listenerType</b> is unrecognized or the
- * <b>configuration</b> is bad in some way.
- */
- public Listener makeListener(TavernaRun run, String listenerType,
- String configuration) throws NoListenerException;
-
- /**
- * What types of listener are supported? Note that we assume that the list
- * of types is the same for all users and all workflow instances.
- *
- * @return A list of supported listener types.
- */
- public List<String> getSupportedListenerTypes();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/factories/RunFactory.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/factories/RunFactory.java b/server-webapp/src/main/java/org/taverna/server/master/factories/RunFactory.java
deleted file mode 100644
index eeacad7..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/factories/RunFactory.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright (C) 2010-2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.factories;
-
-import org.taverna.server.master.common.Workflow;
-import org.taverna.server.master.exceptions.NoCreateException;
-import org.taverna.server.master.interfaces.TavernaRun;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * How to construct a Taverna Server Workflow Run.
- *
- * @author Donal Fellows
- */
-public interface RunFactory {
- /**
- * Make a Taverna Server workflow run that is bound to a particular user
- * (the "creator") and able to run a particular workflow.
- *
- * @param creator
- * The user creating the workflow instance.
- * @param workflow
- * The workflow to instantiate
- * @return An object representing the run.
- * @throws NoCreateException
- * On failure.
- */
- TavernaRun create(UsernamePrincipal creator, Workflow workflow)
- throws NoCreateException;
-
- /**
- * Check whether the factory is permitting runs to actually start operating.
- *
- * @return Whether a run should start.
- */
- boolean isAllowingRunsToStart();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/factories/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/factories/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/factories/package-info.java
deleted file mode 100644
index 39b9ac6..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/factories/package-info.java
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-/**
- * These interfaces define the principal way for the <i>factories</i> of
- * worker classes to be invoked.
- */
-package org.taverna.server.master.factories;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/identity/AuthorityDerivedIDMapper.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/AuthorityDerivedIDMapper.java b/server-webapp/src/main/java/org/taverna/server/master/identity/AuthorityDerivedIDMapper.java
deleted file mode 100644
index 63402ef..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/AuthorityDerivedIDMapper.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.identity;
-
-import static org.taverna.server.master.defaults.Default.AUTHORITY_PREFIX;
-
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.GrantedAuthority;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.taverna.server.master.interfaces.LocalIdentityMapper;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * Extracts the local user id from the set of Spring Security authorities
- * granted to the current user. This is done by scanning the set of authorities
- * to see if any of them start with the substring listed in the <tt>prefix</tt>
- * property; the username is the rest of the authority string in that case.
- *
- * @author Donal Fellows
- */
-public class AuthorityDerivedIDMapper implements LocalIdentityMapper {
- private String prefix = AUTHORITY_PREFIX;
-
- public String getPrefix() {
- return prefix;
- }
-
- public void setPrefix(String prefix) {
- this.prefix = prefix;
- }
-
- @Override
- public String getUsernameForPrincipal(UsernamePrincipal user) {
- Authentication auth = SecurityContextHolder.getContext()
- .getAuthentication();
- if (auth == null || !auth.isAuthenticated())
- return null;
- for (GrantedAuthority authority : auth.getAuthorities()) {
- String token = authority.getAuthority();
- if (token == null)
- continue;
- if (token.startsWith(prefix))
- return token.substring(prefix.length());
- }
- return null;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/identity/CompositeIDMapper.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/CompositeIDMapper.java b/server-webapp/src/main/java/org/taverna/server/master/identity/CompositeIDMapper.java
deleted file mode 100644
index b5fcd5a..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/CompositeIDMapper.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.identity;
-
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.util.List;
-import java.util.Map.Entry;
-
-import org.apache.commons.logging.Log;
-import org.springframework.beans.BeansException;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.taverna.server.master.interfaces.LocalIdentityMapper;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * An identity mapper that composes the results from other mappers, using the
- * identity mappers in order until one can provide a non-<tt>null</tt> answer.
- *
- * @author Donal Fellows.
- */
-public class CompositeIDMapper implements LocalIdentityMapper,
- ApplicationContextAware {
- private Log log = getLog("Taverna.Server.IdentityMapper");
- private List<LocalIdentityMapper> mappers;
- private ApplicationContext context;
-
- /**
- * @param mappers
- * The list of mappers to delegate to. Order is significant.
- */
- public void setIdentityMappers(List<LocalIdentityMapper> mappers) {
- this.mappers = mappers;
- }
-
- @Override
- public void setApplicationContext(ApplicationContext applicationContext)
- throws BeansException {
- context = applicationContext;
- }
-
- @Override
- public String getUsernameForPrincipal(UsernamePrincipal user) {
- if (mappers == null)
- return null;
- for (LocalIdentityMapper m : mappers) {
- String u = m.getUsernameForPrincipal(user);
- if (u == null)
- continue;
- for (Entry<String, ? extends LocalIdentityMapper> entry : context
- .getBeansOfType(m.getClass()).entrySet())
- if (m == entry.getValue()) {
- log.info("used " + entry.getKey() + " LIM to map " + user
- + " to " + u);
- break;
- }
- return u;
- }
- return null;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/identity/ConstantIDMapper.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/ConstantIDMapper.java b/server-webapp/src/main/java/org/taverna/server/master/identity/ConstantIDMapper.java
deleted file mode 100644
index e81f926..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/ConstantIDMapper.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.identity;
-
-import org.taverna.server.master.interfaces.LocalIdentityMapper;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * A trivial principal to user mapper that always uses the same ID.
- * @author Donal Fellows
- */
-public class ConstantIDMapper implements LocalIdentityMapper {
- private String id;
-
- /**
- * Sets what local user ID all users should be mapped to.
- *
- * @param id
- * The local user ID.
- */
- public void setConstantId(String id) {
- this.id = id;
- }
-
- @Override
- public String getUsernameForPrincipal(UsernamePrincipal user) {
- return id;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/identity/NameIDMapper.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/identity/NameIDMapper.java b/server-webapp/src/main/java/org/taverna/server/master/identity/NameIDMapper.java
deleted file mode 100644
index 42a3874..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/identity/NameIDMapper.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.identity;
-
-import static java.util.regex.Pattern.compile;
-
-import java.security.Principal;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.regex.PatternSyntaxException;
-
-import org.taverna.server.master.interfaces.LocalIdentityMapper;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * A trivial identity mapper that just uses the name out of the
- * {@link Principal}, or uses a regular expression to extract it from the string
- * representation of the principal.
- *
- * @author Donal Fellows
- */
-public class NameIDMapper implements LocalIdentityMapper {
- private Pattern pat;
-
- /**
- * @param regexp
- * The regular expression to use. The first capturing group
- * within the RE will be the result of the extraction.
- * @throws PatternSyntaxException
- * If the pattern is invalid.
- */
- public void setRegexp(String regexp) throws PatternSyntaxException {
- pat = compile(regexp);
- }
-
- @Override
- public String getUsernameForPrincipal(UsernamePrincipal user) {
- if (pat != null) {
- Matcher m = pat.matcher(user.toString());
- if (m.find() && m.groupCount() > 0) {
- return m.group(1);
- }
- return null;
- }
- return user.getName();
- }
-}