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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 16:37:08 UTC
[08/49] incubator-taverna-server git commit: taverna-* module names
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegate.java
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diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegate.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegate.java
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@@ -0,0 +1,649 @@
+/*
+ * Copyright (C) 2010-2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.master.worker;
+
+import static java.lang.String.format;
+import static java.util.Arrays.fill;
+import static java.util.UUID.randomUUID;
+import static org.taverna.server.master.defaults.Default.CERTIFICATE_FIELD_NAMES;
+import static org.taverna.server.master.defaults.Default.CERTIFICATE_TYPE;
+import static org.taverna.server.master.defaults.Default.CREDENTIAL_FILE_SIZE_LIMIT;
+import static org.taverna.server.master.identity.WorkflowInternalAuthProvider.PREFIX;
+
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.rmi.RemoteException;
+import java.security.GeneralSecurityException;
+import java.security.Key;
+import java.security.KeyStore;
+import java.security.KeyStoreException;
+import java.security.cert.Certificate;
+import java.security.cert.CertificateException;
+import java.security.cert.CertificateFactory;
+import java.security.cert.X509Certificate;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.annotation.Nullable;
+import javax.security.auth.x500.X500Principal;
+import javax.ws.rs.core.HttpHeaders;
+import javax.ws.rs.core.UriBuilder;
+import javax.xml.ws.handler.MessageContext;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContext;
+import org.taverna.server.localworker.remote.ImplementationException;
+import org.taverna.server.localworker.remote.RemoteSecurityContext;
+import org.taverna.server.master.common.Credential;
+import org.taverna.server.master.common.Trust;
+import org.taverna.server.master.exceptions.FilesystemAccessException;
+import org.taverna.server.master.exceptions.InvalidCredentialException;
+import org.taverna.server.master.exceptions.NoDirectoryEntryException;
+import org.taverna.server.master.interfaces.File;
+import org.taverna.server.master.interfaces.TavernaSecurityContext;
+import org.taverna.server.master.utils.UsernamePrincipal;
+
+/**
+ * Implementation of a security context.
+ *
+ * @author Donal Fellows
+ */
+public abstract class SecurityContextDelegate implements TavernaSecurityContext {
+ Log log = LogFactory.getLog("Taverna.Server.Worker");
+ private final UsernamePrincipal owner;
+ private final List<Credential> credentials = new ArrayList<>();
+ private final List<Trust> trusted = new ArrayList<>();
+ private final RemoteRunDelegate run;
+ private final Object lock = new Object();
+ final SecurityContextFactory factory;
+
+ private transient Keystore keystore;
+ private transient Map<URI, String> uriToAliasMap;
+
+ /**
+ * Initialise the context delegate.
+ *
+ * @param run
+ * What workflow run is this for?
+ * @param owner
+ * Who owns the workflow run?
+ * @param factory
+ * What class built this object?
+ */
+ protected SecurityContextDelegate(RemoteRunDelegate run,
+ UsernamePrincipal owner, SecurityContextFactory factory) {
+ this.run = run;
+ this.owner = owner;
+ this.factory = factory;
+ }
+
+ @Override
+ public SecurityContextFactory getFactory() {
+ return factory;
+ }
+
+ @Override
+ public UsernamePrincipal getOwner() {
+ return owner;
+ }
+
+ @Override
+ public Credential[] getCredentials() {
+ synchronized (lock) {
+ return credentials.toArray(new Credential[credentials.size()]);
+ }
+ }
+
+ /**
+ * Get the human-readable name of a principal.
+ *
+ * @param principal
+ * The principal being decoded.
+ * @return A name.
+ */
+ protected final String getPrincipalName(X500Principal principal) {
+ return factory.x500Utils.getName(principal, CERTIFICATE_FIELD_NAMES);
+ }
+
+ /**
+ * Cause the current state to be flushed to the database.
+ */
+ protected final void flushToDB() {
+ factory.db.flushToDisk(run);
+ }
+
+ @Override
+ public void addCredential(Credential toAdd) {
+ synchronized (lock) {
+ int idx = credentials.indexOf(toAdd);
+ if (idx != -1)
+ credentials.set(idx, toAdd);
+ else
+ credentials.add(toAdd);
+ flushToDB();
+ }
+ }
+
+ @Override
+ public void deleteCredential(Credential toDelete) {
+ synchronized (lock) {
+ credentials.remove(toDelete);
+ flushToDB();
+ }
+ }
+
+ @Override
+ public Trust[] getTrusted() {
+ synchronized (lock) {
+ return trusted.toArray(new Trust[trusted.size()]);
+ }
+ }
+
+ @Override
+ public void addTrusted(Trust toAdd) {
+ synchronized (lock) {
+ int idx = trusted.indexOf(toAdd);
+ if (idx != -1)
+ trusted.set(idx, toAdd);
+ else
+ trusted.add(toAdd);
+ flushToDB();
+ }
+ }
+
+ @Override
+ public void deleteTrusted(Trust toDelete) {
+ synchronized (lock) {
+ trusted.remove(toDelete);
+ flushToDB();
+ }
+ }
+
+ @Override
+ public abstract void validateCredential(Credential c)
+ throws InvalidCredentialException;
+
+ @Override
+ public void validateTrusted(Trust t) throws InvalidCredentialException {
+ InputStream contentsAsStream;
+ if (t.certificateBytes != null && t.certificateBytes.length > 0) {
+ contentsAsStream = new ByteArrayInputStream(t.certificateBytes);
+ t.certificateFile = null;
+ } else if (t.certificateFile == null
+ || t.certificateFile.trim().isEmpty())
+ throw new InvalidCredentialException(
+ "absent or empty certificateFile");
+ else {
+ contentsAsStream = contents(t.certificateFile);
+ t.certificateBytes = null;
+ }
+ t.serverName = null;
+ if (t.fileType == null || t.fileType.trim().isEmpty())
+ t.fileType = CERTIFICATE_TYPE;
+ t.fileType = t.fileType.trim();
+ try {
+ t.loadedCertificates = CertificateFactory.getInstance(t.fileType)
+ .generateCertificates(contentsAsStream);
+ t.serverName = new ArrayList<>(t.loadedCertificates.size());
+ for (Certificate c : t.loadedCertificates)
+ t.serverName.add(getPrincipalName(((X509Certificate) c)
+ .getSubjectX500Principal()));
+ } catch (CertificateException e) {
+ throw new InvalidCredentialException(e);
+ } catch (ClassCastException e) {
+ // Do nothing; truncates the list of server names
+ }
+ }
+
+ @Override
+ public void initializeSecurityFromContext(SecurityContext securityContext)
+ throws Exception {
+ // This is how to get the info from Spring Security
+ Authentication auth = securityContext.getAuthentication();
+ if (auth == null)
+ return;
+ auth.getPrincipal();
+ // do nothing else in this implementation
+ }
+
+ @Override
+ public void initializeSecurityFromSOAPContext(MessageContext context) {
+ // do nothing in this implementation
+ }
+
+ @Override
+ public void initializeSecurityFromRESTContext(HttpHeaders context) {
+ // do nothing in this implementation
+ }
+
+ private UriBuilder getUB() {
+ return factory.uriSource.getRunUriBuilder(run);
+ }
+
+ private RunDatabaseDAO getDAO() {
+ return ((RunDatabase) factory.db).dao;
+ }
+
+ @Nullable
+ private List<X509Certificate> getCerts(URI uri) throws IOException,
+ GeneralSecurityException {
+ return factory.certFetcher.getTrustsForURI(uri);
+ }
+
+ private void installLocalPasswordCredential(List<Credential> credentials,
+ List<Trust> trusts) throws InvalidCredentialException, IOException,
+ GeneralSecurityException {
+ Credential.Password pw = new Credential.Password();
+ pw.id = "run:self";
+ pw.username = PREFIX + run.id;
+ pw.password = getDAO().getSecurityToken(run.id);
+ UriBuilder ub = getUB().segment("").fragment(factory.httpRealm);
+ pw.serviceURI = ub.build();
+ validateCredential(pw);
+ log.info("issuing self-referential credential for " + pw.serviceURI);
+ credentials.add(pw);
+ List<X509Certificate> myCerts = getCerts(pw.serviceURI);
+ if (myCerts != null && myCerts.size() > 0) {
+ Trust t = new Trust();
+ t.loadedCertificates = getCerts(pw.serviceURI);
+ trusts.add(t);
+ }
+ }
+
+ /**
+ * Builds and transfers a keystore with suitable credentials to the back-end
+ * workflow execution engine.
+ *
+ * @throws GeneralSecurityException
+ * If the manipulation of the keystore, keys or certificates
+ * fails.
+ * @throws IOException
+ * If there are problems building the data (should not happen).
+ * @throws RemoteException
+ * If the conveyancing fails.
+ */
+ @Override
+ public final void conveySecurity() throws GeneralSecurityException,
+ IOException, ImplementationException {
+ RemoteSecurityContext rc = run.run.getSecurityContext();
+
+ List<Trust> trusted = new ArrayList<>(this.trusted);
+ this.trusted.clear();
+ List<Credential> credentials = new ArrayList<>(this.credentials);
+ this.credentials.clear();
+
+ try {
+ installLocalPasswordCredential(credentials, trusted);
+ } catch (Exception e) {
+ log.warn("failed to construct local credential: "
+ + "interaction service will fail", e);
+ }
+
+ char[] password = null;
+ try {
+ password = generateNewPassword();
+
+ log.info("constructing merged keystore");
+ Truststore truststore = new Truststore(password);
+ Keystore keystore = new Keystore(password);
+ Map<URI, String> uriToAliasMap = new HashMap<>();
+ int trustedCount = 0, keyCount = 0;
+
+ synchronized (lock) {
+ try {
+ for (Trust t : trusted) {
+ if (t == null || t.loadedCertificates == null)
+ continue;
+ for (Certificate cert : t.loadedCertificates)
+ if (cert != null) {
+ truststore.addCertificate(cert);
+ trustedCount++;
+ }
+ }
+
+ this.uriToAliasMap = uriToAliasMap;
+ this.keystore = keystore;
+ for (Credential c : credentials) {
+ addCredentialToKeystore(c);
+ keyCount++;
+ }
+ } finally {
+ this.uriToAliasMap = null;
+ this.keystore = null;
+ credentials.clear();
+ trusted.clear();
+ flushToDB();
+ }
+ }
+
+ byte[] trustbytes = null, keybytes = null;
+ try {
+ trustbytes = truststore.serialize();
+ keybytes = keystore.serialize();
+
+ // Now we've built the security information, ship it off...
+
+ log.info("transfering merged truststore with " + trustedCount
+ + " entries");
+ rc.setTruststore(trustbytes);
+
+ log.info("transfering merged keystore with " + keyCount
+ + " entries");
+ rc.setKeystore(keybytes);
+ } finally {
+ if (trustbytes != null)
+ fill(trustbytes, (byte) 0);
+ if (keybytes != null)
+ fill(keybytes, (byte) 0);
+ }
+ rc.setPassword(password);
+
+ log.info("transferring serviceURL->alias map with "
+ + uriToAliasMap.size() + " entries");
+ rc.setUriToAliasMap(uriToAliasMap);
+ } finally {
+ if (password != null)
+ fill(password, ' ');
+ }
+
+ synchronized (lock) {
+ conveyExtraSecuritySettings(rc);
+ }
+ }
+
+ /**
+ * Hook that allows additional information to be conveyed to the remote run.
+ *
+ * @param remoteSecurityContext
+ * The remote resource that information would be passed to.
+ * @throws IOException
+ * If anything goes wrong with the communication.
+ */
+ protected void conveyExtraSecuritySettings(
+ RemoteSecurityContext remoteSecurityContext) throws IOException {
+ // Does nothing by default; overrideable
+ }
+
+ /**
+ * @return A new password with a reasonable level of randomness.
+ */
+ protected final char[] generateNewPassword() {
+ return randomUUID().toString().toCharArray();
+ }
+
+ /**
+ * Adds a credential to the current keystore.
+ *
+ * @param alias
+ * The alias to create within the keystore.
+ * @param c
+ * The key-pair.
+ * @throws KeyStoreException
+ */
+ protected final void addKeypairToKeystore(String alias, Credential c)
+ throws KeyStoreException {
+ if (c.loadedKey == null)
+ throw new KeyStoreException("critical: credential was not verified");
+ if (uriToAliasMap.containsKey(c.serviceURI))
+ log.warn("duplicate URI in alias mapping: " + c.serviceURI);
+ keystore.addKey(alias, c.loadedKey, c.loadedTrustChain);
+ uriToAliasMap.put(c.serviceURI, alias);
+ }
+
+ /**
+ * Adds a credential to the current keystore.
+ *
+ * @param c
+ * The credential to add.
+ * @throws KeyStoreException
+ */
+ public abstract void addCredentialToKeystore(Credential c)
+ throws KeyStoreException;
+
+ /**
+ * Read a file up to {@value #FILE_SIZE_LIMIT}kB in size.
+ *
+ * @param name
+ * The path name of the file, relative to the context run's
+ * working directory.
+ * @return A stream of the file's contents.
+ * @throws InvalidCredentialException
+ * If anything goes wrong.
+ */
+ final InputStream contents(String name) throws InvalidCredentialException {
+ try {
+ File f = (File) factory.fileUtils.getDirEntry(run, name);
+ long size = f.getSize();
+ if (size > CREDENTIAL_FILE_SIZE_LIMIT * 1024)
+ throw new InvalidCredentialException(CREDENTIAL_FILE_SIZE_LIMIT
+ + "kB limit hit");
+ return new ByteArrayInputStream(f.getContents(0, (int) size));
+ } catch (NoDirectoryEntryException | FilesystemAccessException e) {
+ throw new InvalidCredentialException(e);
+ } catch (ClassCastException e) {
+ throw new InvalidCredentialException("not a file", e);
+ }
+ }
+
+ @Override
+ public Set<String> getPermittedDestroyers() {
+ return run.getDestroyers();
+ }
+
+ @Override
+ public void setPermittedDestroyers(Set<String> destroyers) {
+ run.setDestroyers(destroyers);
+ }
+
+ @Override
+ public Set<String> getPermittedUpdaters() {
+ return run.getWriters();
+ }
+
+ @Override
+ public void setPermittedUpdaters(Set<String> updaters) {
+ run.setWriters(updaters);
+ }
+
+ @Override
+ public Set<String> getPermittedReaders() {
+ return run.getReaders();
+ }
+
+ @Override
+ public void setPermittedReaders(Set<String> readers) {
+ run.setReaders(readers);
+ }
+
+ /**
+ * Reinstall the credentials and the trust extracted from serialization to
+ * the database.
+ *
+ * @param credentials
+ * The credentials to reinstall.
+ * @param trust
+ * The trusted certificates to reinstall.
+ */
+ void setCredentialsAndTrust(Credential[] credentials, Trust[] trust) {
+ synchronized (lock) {
+ this.credentials.clear();
+ if (credentials != null)
+ for (Credential c : credentials)
+ try {
+ validateCredential(c);
+ this.credentials.add(c);
+ } catch (InvalidCredentialException e) {
+ log.warn("failed to revalidate credential: " + c, e);
+ }
+ this.trusted.clear();
+ if (trust != null)
+ for (Trust t : trust)
+ try {
+ validateTrusted(t);
+ this.trusted.add(t);
+ } catch (InvalidCredentialException e) {
+ log.warn("failed to revalidate trust assertion: " + t,
+ e);
+ }
+ }
+ }
+
+ static class SecurityStore {
+ private KeyStore ks;
+ private char[] password;
+
+ SecurityStore(char[] password) throws GeneralSecurityException {
+ this.password = password.clone();
+ ks = KeyStore.getInstance("UBER", "BC");
+ try {
+ ks.load(null, this.password);
+ } catch (IOException e) {
+ throw new GeneralSecurityException(
+ "problem initializing blank truststore", e);
+ }
+ }
+
+ final synchronized void setCertificate(String alias, Certificate c)
+ throws KeyStoreException {
+ if (ks == null)
+ throw new IllegalStateException("store already written");
+ ks.setCertificateEntry(alias, c);
+ }
+
+ final synchronized void setKey(String alias, Key key, Certificate[] trustChain)
+ throws KeyStoreException {
+ if (ks == null)
+ throw new IllegalStateException("store already written");
+ ks.setKeyEntry(alias, key, password, trustChain);
+ }
+
+ final synchronized byte[] serialize(boolean logIt)
+ throws GeneralSecurityException {
+ if (ks == null)
+ throw new IllegalStateException("store already written");
+ try (ByteArrayOutputStream stream = new ByteArrayOutputStream()) {
+ ks.store(stream, password);
+ if (logIt)
+ LogFactory.getLog("Taverna.Server.Worker").debug(
+ "serialized UBER/BC truststore (size: " + ks.size()
+ + ") with password \""
+ + new String(password) + "\"");
+ return stream.toByteArray();
+ } catch (IOException e) {
+ throw new GeneralSecurityException(
+ "problem serializing keystore", e);
+ } finally {
+ ks = null;
+ fill(password, ' ');
+ }
+ }
+
+ @Override
+ protected final void finalize() {
+ fill(password, ' ');
+ ks = null;
+ }
+ }
+
+ /**
+ * A trust store that can only be added to or serialized. Only trusted
+ * certificates can be placed in it.
+ *
+ * @author Donal Fellows
+ */
+ class Truststore extends SecurityStore {
+ Truststore(char[] password) throws GeneralSecurityException {
+ super(password);
+ }
+
+ /**
+ * Add a trusted certificate to the truststore. No certificates can be
+ * added after the truststore is serialized.
+ *
+ * @param cert
+ * The certificate (typically belonging to a root CA) to add.
+ * @throws KeyStoreException
+ * If anything goes wrong.
+ */
+ public void addCertificate(Certificate cert) throws KeyStoreException {
+ X509Certificate c = (X509Certificate) cert;
+ String alias = format("trustedcert#%s#%s#%s",
+ getPrincipalName(c.getSubjectX500Principal()),
+ getPrincipalName(c.getIssuerX500Principal()),
+ factory.x500Utils.getSerial(c));
+ setCertificate(alias, c);
+ if (log.isDebugEnabled() && factory.logSecurityDetails)
+ log.debug("added cert with alias \"" + alias + "\" of type "
+ + c.getClass().getCanonicalName());
+ }
+
+ /**
+ * Get the byte serialization of this truststore. This can only be
+ * fetched exactly once.
+ *
+ * @return The serialization.
+ * @throws GeneralSecurityException
+ * If anything goes wrong.
+ */
+ public byte[] serialize() throws GeneralSecurityException {
+ return serialize(log.isDebugEnabled() && factory.logSecurityDetails);
+ }
+ }
+
+ /**
+ * A key store that can only be added to or serialized. Only keys can be
+ * placed in it.
+ *
+ * @author Donal Fellows
+ */
+ class Keystore extends SecurityStore {
+ Keystore(char[] password) throws GeneralSecurityException {
+ super(password);
+ }
+
+ /**
+ * Add a key to the keystore. No keys can be added after the keystore is
+ * serialized.
+ *
+ * @param alias
+ * The alias of the key.
+ * @param key
+ * The secret/private key to add.
+ * @param trustChain
+ * The trusted certificate chain of the key. Should be
+ * <tt>null</tt> for secret keys.
+ * @throws KeyStoreException
+ * If anything goes wrong.
+ */
+ public void addKey(String alias, Key key, Certificate[] trustChain)
+ throws KeyStoreException {
+ setKey(alias, key, trustChain);
+ if (log.isDebugEnabled() && factory.logSecurityDetails)
+ log.debug("added key with alias \"" + alias + "\" of type "
+ + key.getClass().getCanonicalName());
+ }
+
+ /**
+ * Get the byte serialization of this keystore. This can only be fetched
+ * exactly once.
+ *
+ * @return The serialization.
+ * @throws GeneralSecurityException
+ * If anything goes wrong.
+ */
+ public byte[] serialize() throws GeneralSecurityException {
+ return serialize(log.isDebugEnabled() && factory.logSecurityDetails);
+ }
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegateImpl.java
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diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegateImpl.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegateImpl.java
new file mode 100644
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+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextDelegateImpl.java
@@ -0,0 +1,298 @@
+/*
+ * Copyright (C) 2010-2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.master.worker;
+
+import static java.lang.String.format;
+import static javax.xml.ws.handler.MessageContext.HTTP_REQUEST_HEADERS;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.Charset;
+import java.rmi.RemoteException;
+import java.security.Key;
+import java.security.KeyStore;
+import java.security.KeyStoreException;
+import java.security.NoSuchAlgorithmException;
+import java.security.UnrecoverableKeyException;
+import java.security.cert.CertificateException;
+import java.security.cert.X509Certificate;
+import java.util.List;
+import java.util.Map;
+
+import javax.crypto.spec.SecretKeySpec;
+import javax.ws.rs.core.HttpHeaders;
+import javax.ws.rs.core.MultivaluedMap;
+import javax.xml.ws.handler.MessageContext;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.taverna.server.localworker.remote.RemoteSecurityContext;
+import org.taverna.server.master.common.Credential;
+import org.taverna.server.master.exceptions.InvalidCredentialException;
+import org.taverna.server.master.utils.UsernamePrincipal;
+import org.taverna.server.master.utils.X500Utils;
+
+/**
+ * Factoring out of the part of the security context handling that actually
+ * deals with the different types of credentials.
+ *
+ * @author Donal Fellows
+ */
+class SecurityContextDelegateImpl extends SecurityContextDelegate {
+ private static final char USERNAME_PASSWORD_SEPARATOR = '\u0000';
+ private static final String USERNAME_PASSWORD_KEY_ALGORITHM = "DUMMY";
+ /** What passwords are encoded as. */
+ private static final Charset UTF8 = Charset.forName("UTF-8");
+
+ private X500Utils x500Utils;
+
+ /**
+ * Initialise the context delegate.
+ *
+ * @param run
+ * What workflow run is this for?
+ * @param owner
+ * Who owns the workflow run?
+ * @param factory
+ * What class built this object?
+ */
+ protected SecurityContextDelegateImpl(RemoteRunDelegate run,
+ UsernamePrincipal owner, SecurityContextFactory factory) {
+ super(run, owner, factory);
+ this.x500Utils = factory.x500Utils;
+ }
+
+ @Override
+ public void validateCredential(Credential c)
+ throws InvalidCredentialException {
+ try {
+ if (c instanceof Credential.Password)
+ validatePasswordCredential((Credential.Password) c);
+ else if (c instanceof Credential.KeyPair)
+ validateKeyCredential((Credential.KeyPair) c);
+ else
+ throw new InvalidCredentialException("unknown credential type");
+ } catch (InvalidCredentialException e) {
+ throw e;
+ } catch (Exception e) {
+ throw new InvalidCredentialException(e);
+ }
+ }
+
+ @Override
+ public void addCredentialToKeystore(Credential c) throws KeyStoreException {
+ try {
+ if (c instanceof Credential.Password)
+ addUserPassToKeystore((Credential.Password) c);
+ else if (c instanceof Credential.KeyPair)
+ addKeypairToKeystore((Credential.KeyPair) c);
+ else
+ throw new KeyStoreException("unknown credential type");
+ } catch (KeyStoreException e) {
+ throw e;
+ } catch (Exception e) {
+ throw new KeyStoreException(e);
+ }
+ }
+
+ // -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
+
+ /**
+ * Tests whether the given username+password credential descriptor is valid.
+ * If it is invalid, an exception will be thrown describing what the problem
+ * is. Validation mainly consists of listing what the username is.
+ *
+ * @param passwordDescriptor
+ * The credential descriptor to validate.
+ * @throws InvalidCredentialException
+ * If the username is empty. NB: the password may be empty!
+ * That's legal (if unwise).
+ */
+ protected void validatePasswordCredential(
+ Credential.Password passwordDescriptor)
+ throws InvalidCredentialException {
+ if (passwordDescriptor.username == null
+ || passwordDescriptor.username.trim().isEmpty())
+ throw new InvalidCredentialException("absent or empty username");
+ if (passwordDescriptor.serviceURI == null)
+ throw new InvalidCredentialException("absent service URI");
+ String keyToSave = passwordDescriptor.username
+ + USERNAME_PASSWORD_SEPARATOR + passwordDescriptor.password;
+ passwordDescriptor.loadedKey = encodeKey(keyToSave);
+ passwordDescriptor.loadedTrustChain = null;
+ }
+
+ private static Key encodeKey(String key) {
+ return new SecretKeySpec(key.getBytes(UTF8),
+ USERNAME_PASSWORD_KEY_ALGORITHM);
+ }
+
+ /**
+ * Adds a username/password credential pair to the current keystore.
+ *
+ * @param userpassCredential
+ * The username and password.
+ * @throws KeyStoreException
+ */
+ protected void addUserPassToKeystore(Credential.Password userpassCredential)
+ throws KeyStoreException {
+ String alias = format("password#%s",
+ userpassCredential.serviceURI.toASCIIString());
+ addKeypairToKeystore(alias, userpassCredential);
+ }
+
+ // -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
+
+ /**
+ * Tests whether the given key-pair credential descriptor is valid. If it is
+ * invalid, an exception will be thrown describing what the problem is.
+ *
+ * @param keypairDescriptor
+ * The descriptor to validate.
+ * @throws InvalidCredentialException
+ * If the descriptor is invalid
+ * @throws KeyStoreException
+ * If we don't understand the keystore type or the contents of
+ * the keystore
+ * @throws NoSuchAlgorithmException
+ * If the keystore is of a known type but we can't comprehend
+ * its security
+ * @throws CertificateException
+ * If the keystore does not include enough information about the
+ * trust chain of the keypair
+ * @throws UnrecoverableKeyException
+ * If we can't get the key out of the keystore
+ * @throws IOException
+ * If we can't read the keystore for prosaic reasons (e.g., file
+ * absent)
+ */
+ protected void validateKeyCredential(Credential.KeyPair keypairDescriptor)
+ throws InvalidCredentialException, KeyStoreException,
+ NoSuchAlgorithmException, CertificateException, IOException,
+ UnrecoverableKeyException {
+ if (keypairDescriptor.credentialName == null
+ || keypairDescriptor.credentialName.trim().isEmpty())
+ throw new InvalidCredentialException(
+ "absent or empty credentialName");
+
+ InputStream contentsAsStream;
+ if (keypairDescriptor.credentialBytes != null
+ && keypairDescriptor.credentialBytes.length > 0) {
+ contentsAsStream = new ByteArrayInputStream(
+ keypairDescriptor.credentialBytes);
+ keypairDescriptor.credentialFile = null;
+ } else if (keypairDescriptor.credentialFile == null
+ || keypairDescriptor.credentialFile.trim().isEmpty())
+ throw new InvalidCredentialException(
+ "absent or empty credentialFile");
+ else {
+ contentsAsStream = contents(keypairDescriptor.credentialFile);
+ keypairDescriptor.credentialBytes = new byte[0];
+ }
+ if (keypairDescriptor.fileType == null
+ || keypairDescriptor.fileType.trim().isEmpty())
+ keypairDescriptor.fileType = KeyStore.getDefaultType();
+ keypairDescriptor.fileType = keypairDescriptor.fileType.trim();
+
+ KeyStore ks = KeyStore.getInstance(keypairDescriptor.fileType);
+ char[] password = keypairDescriptor.unlockPassword.toCharArray();
+ ks.load(contentsAsStream, password);
+
+ try {
+ keypairDescriptor.loadedKey = ks.getKey(
+ keypairDescriptor.credentialName, password);
+ } catch (UnrecoverableKeyException ignored) {
+ keypairDescriptor.loadedKey = ks.getKey(
+ keypairDescriptor.credentialName, new char[0]);
+ }
+ if (keypairDescriptor.loadedKey == null)
+ throw new InvalidCredentialException(
+ "no such credential in key store");
+ keypairDescriptor.loadedTrustChain = ks
+ .getCertificateChain(keypairDescriptor.credentialName);
+ if (keypairDescriptor.loadedTrustChain == null
+ || keypairDescriptor.loadedTrustChain.length == 0)
+ throw new InvalidCredentialException(
+ "could not establish trust chain for credential");
+ }
+
+ /**
+ * Adds a key-pair to the current keystore.
+ *
+ * @param c
+ * The key-pair.
+ * @throws KeyStoreException
+ */
+ protected void addKeypairToKeystore(Credential.KeyPair c)
+ throws KeyStoreException {
+ X509Certificate subjectCert = (X509Certificate) c.loadedTrustChain[0];
+ String alias = format("keypair#%s#%s#%s",
+ getPrincipalName(subjectCert.getSubjectX500Principal()),
+ getPrincipalName(subjectCert.getIssuerX500Principal()),
+ x500Utils.getSerial(subjectCert));
+ addKeypairToKeystore(alias, c);
+ }
+}
+
+/**
+ * Special subclass that adds support for HELIO project security tokens.
+ *
+ * @author Donal Fellows
+ */
+class HelioSecurityContextDelegateImpl extends SecurityContextDelegateImpl {
+ /**
+ * Initialise the context delegate.
+ *
+ * @param run
+ * What workflow run is this for?
+ * @param owner
+ * Who owns the workflow run?
+ * @param factory
+ * What class built this object?
+ */
+ protected HelioSecurityContextDelegateImpl(RemoteRunDelegate run,
+ UsernamePrincipal owner, SecurityContextFactory factory) {
+ super(run, owner, factory);
+ }
+
+ private Log log = LogFactory.getLog("Taverna.Server.Worker");
+ /** The name of the HTTP header holding the CIS token. */
+ private static final String HELIO_CIS_TOKEN = "X-Helio-CIS";
+ private transient String helioToken;
+
+ @Override
+ public void initializeSecurityFromSOAPContext(MessageContext context) {
+ // does nothing
+ @SuppressWarnings("unchecked")
+ Map<String, List<String>> headers = (Map<String, List<String>>) context
+ .get(HTTP_REQUEST_HEADERS);
+ if (factory.supportHelioToken && headers.containsKey(HELIO_CIS_TOKEN))
+ helioToken = headers.get(HELIO_CIS_TOKEN).get(0);
+ }
+
+ @Override
+ public void initializeSecurityFromRESTContext(HttpHeaders context) {
+ // does nothing
+ MultivaluedMap<String, String> headers = context.getRequestHeaders();
+ if (factory.supportHelioToken && headers.containsKey(HELIO_CIS_TOKEN))
+ helioToken = headers.get(HELIO_CIS_TOKEN).get(0);
+ }
+
+ @Override
+ protected void conveyExtraSecuritySettings(RemoteSecurityContext rc)
+ throws RemoteException {
+ try {
+ if (factory.supportHelioToken && helioToken != null) {
+ if (factory.logSecurityDetails)
+ log.info("transfering HELIO CIS token: " + helioToken);
+ rc.setHelioToken(helioToken);
+ }
+ } finally {
+ helioToken = null;
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextFactory.java
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextFactory.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextFactory.java
new file mode 100644
index 0000000..cbccf34
--- /dev/null
+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SecurityContextFactory.java
@@ -0,0 +1,154 @@
+/*
+ * Copyright (C) 2011-2012 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.master.worker;
+
+import static java.security.Security.addProvider;
+import static java.security.Security.getProvider;
+import static java.security.Security.removeProvider;
+import static org.apache.commons.logging.LogFactory.getLog;
+import static org.bouncycastle.jce.provider.BouncyCastleProvider.PROVIDER_NAME;
+
+import java.io.Serializable;
+
+import javax.annotation.PostConstruct;
+import javax.annotation.PreDestroy;
+
+import org.apache.commons.logging.Log;
+import org.bouncycastle.jce.provider.BouncyCastleProvider;
+import org.springframework.beans.factory.annotation.Required;
+import org.springframework.beans.factory.annotation.Value;
+import org.taverna.server.master.interfaces.TavernaRun;
+import org.taverna.server.master.interfaces.UriBuilderFactory;
+import org.taverna.server.master.utils.CertificateChainFetcher;
+import org.taverna.server.master.utils.FilenameUtils;
+import org.taverna.server.master.utils.UsernamePrincipal;
+import org.taverna.server.master.utils.X500Utils;
+
+/**
+ * Singleton factory. Really is a singleton (and is also very trivial); the
+ * singleton-ness is just about limiting the number of instances of this around
+ * even when lots of serialization is going on.
+ *
+ * @see Serializable
+ * @author Donal Fellows
+ */
+public class SecurityContextFactory implements
+ org.taverna.server.master.interfaces.SecurityContextFactory {
+ private static final long serialVersionUID = 12345678987654321L;
+ private static SecurityContextFactory instance;
+ transient RunDBSupport db;
+ transient FilenameUtils fileUtils;
+ transient X500Utils x500Utils;
+ transient UriBuilderFactory uriSource;
+ transient CertificateChainFetcher certFetcher;
+ transient String httpRealm;
+ private transient PasswordIssuer passwordIssuer;
+ private transient BouncyCastleProvider provider;
+
+ /**
+ * Whether to support HELIO CIS tokens.
+ */
+ @Value("${helio.cis.enableTokenPassing}")
+ boolean supportHelioToken;
+
+ /**
+ * Whether to log the details of security (passwords, etc).
+ */
+ @Value("${log.security.details}")
+ boolean logSecurityDetails;
+
+ private Log log() {
+ return getLog("Taverna.Server.Worker.Security");
+ }
+
+ private void installAsInstance(SecurityContextFactory handle) {
+ instance = handle;
+ }
+
+ @PreDestroy
+ void removeAsSingleton() {
+ installAsInstance(null);
+ try {
+ if (provider != null)
+ removeProvider(provider.getName());
+ } catch (SecurityException e) {
+ log().warn(
+ "failed to remove BouncyCastle security provider; "
+ + "might be OK if configured in environment", e);
+ }
+ }
+
+ @PostConstruct
+ void setAsSingleton() {
+ installAsInstance(this);
+ if (getProvider(PROVIDER_NAME) == null)
+ try {
+ provider = new BouncyCastleProvider();
+ if (addProvider(provider) == -1)
+ provider = null;
+ } catch (SecurityException e) {
+ log().warn(
+ "failed to install BouncyCastle security provider; "
+ + "might be OK if already configured", e);
+ provider = null;
+ }
+ }
+
+ @Required
+ public void setRunDatabase(RunDBSupport db) {
+ this.db = db;
+ }
+
+ @Required
+ public void setCertificateFetcher(CertificateChainFetcher fetcher) {
+ this.certFetcher = fetcher;
+ }
+
+ @Required
+ public void setFilenameConverter(FilenameUtils fileUtils) {
+ this.fileUtils = fileUtils;
+ }
+
+ @Required
+ public void setX500Utils(X500Utils x500Utils) {
+ this.x500Utils = x500Utils;
+ }
+
+ @Required
+ public void setUriSource(UriBuilderFactory uriSource) {
+ this.uriSource = uriSource;
+ }
+
+ @Required
+ public void setHttpRealm(String realm) {
+ this.httpRealm = realm; //${http.realmName}
+ }
+
+ @Required
+ public void setPasswordIssuer(PasswordIssuer issuer) {
+ this.passwordIssuer = issuer;
+ }
+
+ @Override
+ public SecurityContextDelegate create(TavernaRun run,
+ UsernamePrincipal owner) throws Exception {
+ Log log = log();
+ if (log.isDebugEnabled())
+ log.debug("constructing security context delegate for " + owner);
+ RemoteRunDelegate rrd = (RemoteRunDelegate) run;
+ return new HelioSecurityContextDelegateImpl(rrd, owner, this);
+ }
+
+ private Object readResolve() {
+ if (instance == null)
+ installAsInstance(this);
+ return instance;
+ }
+
+ public String issueNewPassword() {
+ return passwordIssuer.issue();
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SimpleFormattedCompletionNotifier.java
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SimpleFormattedCompletionNotifier.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SimpleFormattedCompletionNotifier.java
new file mode 100644
index 0000000..793d291
--- /dev/null
+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/SimpleFormattedCompletionNotifier.java
@@ -0,0 +1,64 @@
+/*
+ * Copyright (C) 2010-2011 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.master.worker;
+
+import static org.taverna.server.master.defaults.Default.NOTIFY_MESSAGE_FORMAT;
+
+import java.text.MessageFormat;
+
+import org.springframework.beans.factory.annotation.Required;
+
+/**
+ * Completion notifier that sends messages by email.
+ *
+ * @author Donal Fellows
+ */
+public class SimpleFormattedCompletionNotifier implements CompletionNotifier {
+ @Required
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @param subject
+ * The subject of the notification email.
+ */
+ @Required
+ public void setSubject(String subject) {
+ this.subject = subject;
+ }
+
+ /**
+ * @param messageFormat
+ * The template for the body of the message to send. Parameter #0
+ * will be substituted with the ID of the job, and parameter #1
+ * will be substituted with the exit code.
+ */
+ public void setMessageFormat(String messageFormat) {
+ this.format = new MessageFormat(messageFormat);
+ }
+
+ private String name;
+ private String subject;
+ private MessageFormat format = new MessageFormat(NOTIFY_MESSAGE_FORMAT);
+
+ @Override
+ public String makeCompletionMessage(String name, RemoteRunDelegate run,
+ int code) {
+ return format.format(new Object[] { name, code });
+ }
+
+ @Override
+ public String makeMessageSubject(String name, RemoteRunDelegate run,
+ int code) {
+ return subject;
+ }
+
+ @Override
+ public String getName() {
+ return name;
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/VelocityCompletionNotifier.java
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/VelocityCompletionNotifier.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/VelocityCompletionNotifier.java
new file mode 100644
index 0000000..cf67853
--- /dev/null
+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/VelocityCompletionNotifier.java
@@ -0,0 +1,105 @@
+package org.taverna.server.master.worker;
+
+import java.io.StringWriter;
+
+import org.apache.velocity.Template;
+import org.apache.velocity.VelocityContext;
+import org.apache.velocity.app.VelocityEngine;
+import org.springframework.beans.factory.annotation.Required;
+import org.taverna.server.master.common.version.Version;
+import org.taverna.server.master.exceptions.NoListenerException;
+import org.taverna.server.master.interfaces.Listener;
+import org.taverna.server.master.interfaces.UriBuilderFactory;
+
+public class VelocityCompletionNotifier implements CompletionNotifier {
+ private String subject;
+ private VelocityEngine engine;
+ private Template template;
+ private String name;
+ private String templateName;
+ private UriBuilderFactory ubf;
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param subject
+ * The subject of the notification email.
+ */
+ @Required
+ public void setSubject(String subject) {
+ this.subject = subject;
+ }
+
+ /**
+ * @param engine
+ * The configured Apache Velocity engine.
+ */
+ @Required
+ public void setVelocityEngine(VelocityEngine engine) {
+ this.engine = engine;
+ }
+
+ /**
+ * @param uriBuilderFactory
+ * The configured URI builder factory.
+ */
+ @Required
+ public void setUriBuilderFactory(UriBuilderFactory uriBuilderFactory) {
+ this.ubf = uriBuilderFactory;
+ }
+
+ /**
+ * @param name
+ * The name of the template.
+ */
+ @Required
+ public void setName(String name) {
+ this.name = name;
+ this.templateName = getClass().getName() + "_" + name + ".vtmpl";
+ }
+
+ private Template getTemplate() {
+ if (template == null)
+ synchronized(this) {
+ if (template == null)
+ template = engine.getTemplate(templateName);
+ }
+ return template;
+ }
+
+ @Override
+ public String makeCompletionMessage(String name, RemoteRunDelegate run,
+ int code) {
+ VelocityContext ctxt = new VelocityContext();
+ ctxt.put("id", name);
+ ctxt.put("uriBuilder", ubf.getRunUriBuilder(run));
+ ctxt.put("name", run.getName());
+ ctxt.put("creationTime", run.getCreationTimestamp());
+ ctxt.put("startTime", run.getStartTimestamp());
+ ctxt.put("finishTime", run.getFinishTimestamp());
+ ctxt.put("expiryTime", run.getExpiry());
+ ctxt.put("serverVersion", Version.JAVA);
+ for (Listener l : run.getListeners())
+ if (l.getName().equals("io")) {
+ for (String p : l.listProperties())
+ try {
+ ctxt.put("prop_" + p, l.getProperty(p));
+ } catch (NoListenerException e) {
+ // Ignore...
+ }
+ break;
+ }
+ StringWriter sw = new StringWriter();
+ getTemplate().merge(ctxt, sw);
+ return sw.toString();
+ }
+
+ @Override
+ public String makeMessageSubject(String name, RemoteRunDelegate run,
+ int code) {
+ return subject;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/WorkerModel.java
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/WorkerModel.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/WorkerModel.java
new file mode 100644
index 0000000..1abe617
--- /dev/null
+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/WorkerModel.java
@@ -0,0 +1,203 @@
+/*
+ * Copyright (C) 2010-2013 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+package org.taverna.server.master.worker;
+
+import java.net.URI;
+import java.util.List;
+
+import org.taverna.server.master.common.Status;
+
+/**
+ * Profile of the getters and setters in a worker system. Ensures that the
+ * persisted state matches the public view on the state model at least fairly
+ * closely.
+ *
+ * @author Donal Fellows
+ */
+public interface WorkerModel extends PolicyLimits {
+
+ /**
+ * @param defaultLifetime
+ * how long a workflow run should live by default, in minutes.
+ */
+ public abstract void setDefaultLifetime(int defaultLifetime);
+
+ /**
+ * @return how long a workflow run should live by default, in minutes.
+ */
+ public abstract int getDefaultLifetime();
+
+ /**
+ * @param maxRuns
+ * the maximum number of extant workflow runs
+ */
+ public abstract void setMaxRuns(int maxRuns);
+
+ /**
+ * @param factoryProcessNamePrefix
+ * the prefix used for factory processes in RMI
+ */
+ public abstract void setFactoryProcessNamePrefix(
+ String factoryProcessNamePrefix);
+
+ /**
+ * @return the prefix used for factory processes in RMI
+ */
+ public abstract String getFactoryProcessNamePrefix();
+
+ /**
+ * @param executeWorkflowScript
+ * the script to run to actually run a workflow
+ */
+ public abstract void setExecuteWorkflowScript(String executeWorkflowScript);
+
+ /**
+ * @return the script to run to actually run a workflow
+ */
+ public abstract String getExecuteWorkflowScript();
+
+ /**
+ * @param extraArgs
+ * the extra arguments to pass into the workflow runner
+ */
+ public abstract void setExtraArgs(String[] extraArgs);
+
+ /**
+ * @return the extra arguments to pass into the workflow runner
+ */
+ public abstract String[] getExtraArgs();
+
+ /**
+ * @param waitSeconds
+ * the number of seconds to wait for subprocesses to start
+ */
+ public abstract void setWaitSeconds(int waitSeconds);
+
+ /**
+ * @return the number of seconds to wait for subprocesses to start
+ */
+ public abstract int getWaitSeconds();
+
+ /**
+ * @param sleepMS
+ * milliseconds to wait between polling for a started
+ * subprocess's status
+ */
+ public abstract void setSleepMS(int sleepMS);
+
+ /**
+ * @return milliseconds to wait between polling for a started subprocess's
+ * status
+ */
+ public abstract int getSleepMS();
+
+ /**
+ * @param serverWorkerJar
+ * the full path name of the file system access worker
+ * subprocess's implementation JAR
+ */
+ public abstract void setServerWorkerJar(String serverWorkerJar);
+
+ /**
+ * @return the full path name of the file system access worker subprocess's
+ * implementation JAR
+ */
+ public abstract String getServerWorkerJar();
+
+ /**
+ * @param javaBinary
+ * the full path name to the Java binary to use
+ */
+ public abstract void setJavaBinary(String javaBinary);
+
+ /**
+ * @return the full path name to the Java binary to use
+ */
+ public abstract String getJavaBinary();
+
+ /**
+ * @param registryPort
+ * what port is the RMI registry on
+ */
+ public abstract void setRegistryPort(int registryPort);
+
+ /**
+ * @return what port is the RMI registry on
+ */
+ public abstract int getRegistryPort();
+
+ /**
+ * @param registryHost
+ * what host (network interface) is the RMI registry on
+ */
+ public abstract void setRegistryHost(String registryHost);
+
+ /**
+ * @return what host (network interface) is the RMI registry on
+ */
+ public abstract String getRegistryHost();
+
+ /**
+ * @param serverForkerJar
+ * the full path name of the impersonation engine's
+ * implementation JAR
+ */
+ public abstract void setServerForkerJar(String serverForkerJar);
+
+ /**
+ * @return the full path name of the impersonation engine's implementation
+ * JAR
+ */
+ public abstract String getServerForkerJar();
+
+ /**
+ * @param passwordFile
+ * the full path name of a file containing a password to use with
+ * sudo (or empty for none)
+ */
+ public abstract void setPasswordFile(String passwordFile);
+
+ /**
+ * @return the full path name of a file containing a password to use with
+ * sudo (or empty for none)
+ */
+ public abstract String getPasswordFile();
+
+ /**
+ * @param operatingLimit
+ * the maximum number of runs in the
+ * {@linkplain Status#Operating operating} state at once
+ */
+ public abstract void setOperatingLimit(int operatingLimit);
+
+ @Override
+ void setPermittedWorkflowURIs(List<URI> permittedWorkflows);
+
+ /**
+ * @return the full path name of the RMI registry subprocess's
+ * implementation JAR
+ */
+ String getRegistryJar();
+
+ /**
+ * @param rmiRegistryJar
+ * the full path name of the RMI registry subprocess's
+ * implementation JAR
+ */
+ void setRegistryJar(String rmiRegistryJar);
+
+ /**
+ * @return whether a run should generate provenance information by default
+ */
+ boolean getGenerateProvenance();
+
+ /**
+ * @param generateProvenance
+ * whether a run should generate provenance information by
+ * default
+ */
+ void setGenerateProvenance(boolean generateProvenance);
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/package-info.java
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/package-info.java b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/package-info.java
new file mode 100644
index 0000000..6007f88
--- /dev/null
+++ b/taverna-server-webapp/src/main/java/org/taverna/server/master/worker/package-info.java
@@ -0,0 +1,10 @@
+/*
+ * Copyright (C) 2013 The University of Manchester
+ *
+ * See the file "LICENSE" for license terms.
+ */
+/**
+ * A Taverna Server back-end that works by forking off workflow executors.
+ */
+package org.taverna.server.master.worker;
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/replacementscripts/executeworkflow.bat
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/replacementscripts/executeworkflow.bat b/taverna-server-webapp/src/main/replacementscripts/executeworkflow.bat
new file mode 100644
index 0000000..c678855
--- /dev/null
+++ b/taverna-server-webapp/src/main/replacementscripts/executeworkflow.bat
@@ -0,0 +1,25 @@
+@ECHO OFF
+
+REM Taverna startup script
+
+REM distribution directory
+set TAVERNA_HOME=%~dp0
+
+REM 300 MB memory, 140 MB for classes
+set ARGS=-Xmx300m -XX:MaxPermSize=140m
+
+REM Taverna system properties
+set ARGS=%ARGS% "-Draven.profile=file:%TAVERNA_HOME%conf/current-profile.xml"
+set ARGS=%ARGS% -Djava.system.class.loader=net.sf.taverna.raven.prelauncher.BootstrapClassLoader
+set ARGS=%ARGS% -Draven.launcher.app.main=net.sf.taverna.t2.commandline.CommandLineLauncher
+set ARGS=%ARGS% -Draven.launcher.show_splashscreen=false
+set ARGS=%ARGS% -Djava.awt.headless=true
+set ARGS=%ARGS% "-Dtaverna.startup=%TAVERNA_HOME%."
+IF NOT x%RAVEN_APPHOME%==x SET ARGS=%ARGS% "-Draven.launcher.app.home=%RAVEN_APPHOME%"
+IF NOT x%TAVERNA_RUN_ID%==x SET ARGS=%ARGS% "-Dtaverna.runid=%TAVERNA_RUN_ID%"
+IF NOT x%INTERACTION_HOST%==x SET ARGS=%ARGS% "-Dtaverna.interaction.host=%INTERACTION_HOST%"
+IF NOT x%INTERACTION_PORT%==x SET ARGS=%ARGS% "-Dtaverna.interaction.port=%INTERACTION_PORT%"
+IF NOT x%INTERACTION_WEBDAV%==x SET ARGS=%ARGS% "-Dtaverna.interaction.webdav_path=%INTERACTION_WEBDAV%"
+IF NOT x%INTERACTION_FEED%==x SET ARGS=%ARGS% "-Dtaverna.interaction.feed_path=%INTERACTION_FEED%"
+
+java %ARGS% -jar "%TAVERNA_HOME%lib\prelauncher-2.3.jar" %*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/replacementscripts/executeworkflow.sh
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/replacementscripts/executeworkflow.sh b/taverna-server-webapp/src/main/replacementscripts/executeworkflow.sh
new file mode 100644
index 0000000..e9e1d36
--- /dev/null
+++ b/taverna-server-webapp/src/main/replacementscripts/executeworkflow.sh
@@ -0,0 +1,72 @@
+#!/bin/sh
+
+set -e
+
+# 300 MB memory, 140 MB for classes
+memlimit=-Xmx300m
+permsize=-XX:MaxPermSize=140m
+
+## Parse the command line to extract the pieces to move around to before or
+## after the JAR filename...
+pre=-Djava.awt.headless=true
+post=
+for arg
+do
+ case $arg in
+ -JXmx*) memlimit=`echo $arg | sed 's/-JX/-X/'` ;;
+ -JXX:MaxPermSize=*) permsize=`echo $arg | sed 's/-JXX/-XX/'` ;;
+ -J*) pre="$pre `echo $arg | sed 's/-J/-/'`" ;;
+ -D*) pre="$pre $arg" ;;
+ *) post="$post \"$arg\"" ;;
+ esac
+done
+if test "xx" = "x${post}x"; then
+ echo "Missing arguments! Bug in argument processing?" >&2
+ exit 1
+fi
+eval set x $post
+shift
+
+## resolve links - $0 may be a symlink
+prog="$0"
+
+real_path() {
+ readlink -m "$1" 2>/dev/null || python -c 'import os,sys;print os.path.realpath(sys.argv[1])' "$1"
+}
+
+realprog=`real_path "$prog"`
+taverna_home=`dirname "$realprog"`
+javabin=java
+if test -x "$JAVA_HOME/bin/java"; then
+ javabin="$JAVA_HOME/bin/java"
+fi
+APPHOME_PROP=
+if test x != "x$TAVERNA_APPHOME"; then
+ APPHOME_PROP="-Dtaverna.app.home=$TAVERNA_APPHOME"
+fi
+RUNID_PROP=
+if test x != "x$TAVERNA_RUN_ID"; then
+ RUNID_PROP="-Dtaverna.runid=$TAVERNA_RUN_ID"
+fi
+INTERACTION_PROPS=-Dtaverna.interaction.ignore_requests=true
+if test x != "x$INTERACTION_HOST"; then
+ INTERACTION_PROPS="$INTERACTION_PROPS -Dtaverna.interaction.host=$INTERACTION_HOST"
+ 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
+
+echo "pid:$$"
+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" -Dtaverna.interaction.ignore_requests=true \
+ $APPHOME_PROP $RUNID_PROP $INTERACTION_PROPS -Djava.awt.headless=true \
+ -Dcom.sun.net.ssl.enableECC=false -Djsse.enableSNIExtension=false $pre \
+ -jar "$taverna_home/lib/taverna-command-line-0.1.1.jar" \
+ ${1+"$@"}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/resources/admin.html
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/resources/admin.html b/taverna-server-webapp/src/main/resources/admin.html
new file mode 100644
index 0000000..a80a783
--- /dev/null
+++ b/taverna-server-webapp/src/main/resources/admin.html
@@ -0,0 +1,240 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<title>Taverna Server ${project.version} Administration Interface</title>
+<link id="admin" href="admin" />
+<script type="text/javascript" src="admin/static/jquery-1.8.0.min.js"></script>
+<script type="text/javascript" src="admin/static/jquery-ui-1.8.23.custom.min.js"></script>
+<script type="text/javascript" src="admin/static/admin.js"></script>
+<link href="admin/static/jquery-ui-1.8.23.custom.css" rel="stylesheet" type="text/css" />
+
+</head>
+<body>
+<img height="70" style="float:left" src="admin/static/t2cogs.png">
+<h1>Taverna Server ${project.version} Administration Interface</h1>
+<br clear="left"/>
+<div id="body">
+<ul>
+ <li><a href="#t-global">Global Settings</a></li>
+ <li><a href="#t-users">Users</a></li>
+ <li><a href="#t-workflows">Workflows</a></li>
+ <li><a href="#t-usage">Usage Records</a></li>
+ <li><a href="#t-worker">Local Worker Configuration</a></li>
+</ul>
+
+<div id="t-global">
+<label title="The number of invocations of the main interface webapp that have been done. Be aware that one service call can result in many invocations due to resource resolution." for="invokationCount">Invocation Count:</label>
+<span title="The number of invocations of the main interface webapp that have been done. Be aware that one service call can result in many invocations due to resource resolution." id="invokationCount">0</span>
+<br>
+<label title="The number of runs that currently exist." for="runCount">Run Count:</label>
+<span title="The number of runs that currently exist." id="runCount">0</span>
+<br>
+<label title="The number of runs that are currently operating." for="operatingCount">Operating Run Count:</label>
+<span title="The number of runs that are currently operating." id="operatingCount">0</span>
+<br>
+<label title="Whether workflow runs should create provenance traces by default. Users can explicitly override this." for="generateProvenance">Generate Provenance by Default</label>
+<input type="checkbox" id="generateProvenance" />
+<br>
+<label title="The time it took for the back-end engine to start up, in seconds. Should usually be short." for="startupTime">Back-End Startup Time (seconds):</label>
+<span title="The time it took for the back-end engine to start up, in seconds. Should usually be short." id="startupTime">0</span>
+<br>
+<label title="The exit code from the last time the back-end was shut down. Blank if the back end has never been shut down while the current webapp instance is running (i.e., since the last boot of the container)." for="lastExitCode">Back-End Last Exit Code:</label>
+<span title="The exit code from the last time the back-end was shut down. Blank if the back end has never been shut down while the current webapp instance is running (i.e., since the last boot of the container)." id="lastExitCode"></span>
+<p>
+<label title="Whether new workflow runs should be created. Disabling this does not prevent existing runs from executing." for="allowNew">Allow New Runs</label>
+<input type="checkbox" id="allowNew" />
+<label title="Whether to record the workflows being run by users. Very noisy due to length of workflow documents, occasionally useful." for="logWorkflows">Log Executed Workflows</label>
+<input type="checkbox" id="logWorkflows" />
+<label title="Whether to record exceptions generated by users in the code (as well as converting them to faults and error responses). Useful for debugging, but noisy." for="logFaults">Log User Exceptions</label>
+<input type="checkbox" id="logFaults" />
+<p>
+<label title="The maximum number of workflow runs that can exist at once, in any state." for="runLimit">Maximum Simultaneous Existing Workflow Runs</label>
+<input title="The maximum number of workflow runs that can exist at once, in any state." id="runLimit" size="3" />
+<br>
+<label title="The maximum number of workflow runs that can be executing at once." for="operatingLimit">Maximum Simultaneous Executing Workflow Runs</label>
+<input title="The maximum number of workflow runs that can be executing at once." id="operatingLimit" size="3" />
+<br>
+<label title="How long to allow a workflow to execute for by default (clients can change this), in minutes." for="defaultLifetime">Default Run Lifetime (minutes)</label>
+<input title="How long to allow a workflow to execute for by default (clients can change this), in minutes." id="defaultLifetime" size="7" />
+</div><!-- t-global -->
+
+<div id="t-users">
+<table id="userList">
+ <tr><th>Username<th>System Username</tr>
+</table>
+<h3>Add a user</h3>
+<table border=1>
+ <tr>
+ <td><label title="The user name to create." for="newUsername">Username</label>
+ <td><input title="The user name to create." size=12 id="newUsername" />
+ </tr>
+ <tr>
+ <td><label title="The password to use for the user." for="newPassword">Password</label>
+ <td><input title="The password to use for the user." size=12 id="newPassword" type="password"/>
+ </tr>
+ <tr>
+ <td><label title="The system account to run the user's workflows in; leave blank for the default." for="newSysID">System ID</label>
+ <td><input title="The system account to run the user's workflows in; leave blank for the default." size=12 id="newSysID" />
+ </tr>
+ <tr><td colspan=2>
+ <label title="Whether to allow this user to log in at all." for="newEnabled">Enabled</label>
+ <input type="checkbox" id="newEnabled" />
+ <label title="Whether the user has administrative privileges (can see all workflow runs, can access the administration page)." for="newAdmin">Admin</label>
+ <input type="checkbox" id="newAdmin" />
+ </td></tr>
+ <tr><td colspan=2>
+ <button id="makeNewUser">Create a new user</button>
+ </td></tr>
+</table>
+</div><!-- t-users -->
+
+<div id="t-workflows">
+<label title="Workflow URIs to limit execution to." for="workflows">Workflow URIs (one per line)</label>
+<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="emptyWorkflows">Empty URIs list</button>
+</div>
+
+<div id="t-usage">
+Download <a href="#" id="ur">usage records</a> (warning: may be slow!)
+<p>
+<label title="The name of a file to write usage records to. Note that this file will end up containing many XML documents concatenated together; it is up to you to split them up as necessary. Each record is only written as it is generated; this does not produce historic data." for="usageRecordDumpFile">Usage Record Dump File</label>
+<input title="The name of a file to write usage records to. Note that this file will end up containing many XML documents concatenated together; it is up to you to split them up as necessary. Each record is only written as it is generated; this does not produce historic data." id="usageRecordDumpFile" size="50" />
+</div><!-- t-usage -->
+
+<div id="t-worker">
+ <div id="a-worker">
+
+ <h3><a href="#">Subprocess Implementation Control</a></h3>
+ <div>
+ <table>
+ <tr>
+ <td> <label title="The full path of the Java executable to use. Normally set correct by default." for="javaBinary">Java Executable (for subprocesses):</label> </td>
+ <td> <input title="The full path of the Java executable to use. Normally set correct by default." id="javaBinary" size="80" /> </td>
+ </tr>
+ <tr>
+ <td> <label title="The full path of the secure subprocess fork engine to use. Normally set correct by default." for="serverForkerJar">Subprocess Factory JAR:</label> </td>
+ <td> <input title="The full path of the secure subprocess fork engine to use. Normally set correct by default." id="serverForkerJar" size="80" /> </td>
+ </tr>
+ <tr>
+ <td> <label title="The full path of a file containing the credentials to use with sudo. Leave blank to use a password-less connection (see documentation for how to configure)." for="runasPasswordFile">File with password for sudo:</label> </td>
+ <td> <input title="The full path of a file containing the credentials to use with sudo. Leave blank to use a password-less connection (see documentation for how to configure)." id="runasPasswordFile" size="80" /> </td>
+ </tr>
+ <tr>
+ <td> <label title="The full path of the user filesystem access and workflow initiation engine to use. Normally set correct by default." for="serverWorkerJar">User Filesystem Access JAR:</label> </td>
+ <td> <input title="The full path of the user filesystem access and workflow initiation engine to use. Normally set correct by default." id="serverWorkerJar" size="80" /> </td>
+ </tr>
+ <tr>
+ <td> <label title="The full path of the workflow engine executable. Normally set correctly by default." for="executeWorkflowScript">Workflow Engine Executable:</label> </td>
+ <td> <input title="The full path of the workflow engine executable. Normally set correctly by default." id="executeWorkflowScript" size="80" /> </td>
+ </tr>
+ </table>
+ </div>
+
+ <h3><a href="#">Worker Registration Control</a></h3>
+ <div>
+ <label title="The machine hosting the RMI registry. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" for="registryHost">Registry Host</label>
+ <input title="The machine hosting the RMI registry. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" id="registryHost" size="20" />
+ <label title="The port number the RMI registry. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" for="registryPort">Port</label>
+ <input title="The port number the RMI registry. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" id="registryPort" size="5" />
+ <br>
+ <label title="The full path of the RMI registry implementation JAR file. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" for="registryJar">RMI Registry JAR</label>
+ <input title="The full path of the RMI registry implementation JAR file. WARNING: changing this will probably break your configuration! Contact the myGrid team for help before adjusting!" id="registryJar" size="80" />
+ <br>
+ <label title="The time to wait (in seconds) for the back-end processes to boot and register themselves with the RMI registry. Busy machines may need a longer value here." for="registrationWaitSeconds">Time to wait for registration (seconds)</label>
+ <input title="The time to wait (in seconds) for the back-end processes to boot and register themselves with the RMI registry. Busy machines may need a longer value here." id="registrationWaitSeconds" size="5" />
+ <br>
+ <label title="How long to wait (in milliseconds) between probes to the registry to detect the registration of a back-end process." for="registrationPollMillis">Time to wait between polling to
+ detect registration (milliseconds)</label>
+ <input title="How long to wait (in milliseconds) between probes to the registry to detect the registration of a back-end process." id="registrationPollMillis" size="5" />
+ </div>
+
+ <h3><a href="#">System User/Factory ID Mapping</a></h3>
+ <div>
+ <table title="The mapping of system user IDs to factory identifiers (used in the RMI registry). Note that this is read-only." id="factoryProcessMapping" border="1">
+ </table>
+ </div>
+
+ <h3><a href="#">Extra Workflow Engine Configuration</a></h3>
+ <div>
+ <h4>System Properties</h4>
+ <table id="extraArguments-prop">
+ <tr><td></td><td><button title="Add a system property to pass to the back-end engine." id="extra-prop-add">Add System Property</button></td></tr>
+ </table>
+ <h4>Environment Variables</h4>
+ <table id="extraArguments-env">
+ <tr><td></td><td><button title="Add an environment variable to pass to the back-end engine." id="extra-env-add">Add Environment Variable</button></td></tr>
+ </table>
+ <h4>Java Runtime Configuration</h4>
+ <table id="extraArguments-runtime">
+ <tr><td></td><td><button title="Add a Java runtime parameter (e.g., Xmx=400m to set the memory usage limit to 400MB) to pass to the back-end engine. Note the lack of a leading '-' character!" id="extra-run-add">Add Runtime Configuration</button></td></tr>
+ </table>
+ </div>
+
+ </div><!-- a-worker -->
+</div><!-- t-worker -->
+
+</div>
+
+<hr>
+<address>Donal Fellows / University of Manchester</address>
+
+<!-- DIALOG BOXES -->
+<div id="dialog-confirm" title="Delete user?" style="display: none">
+ <p>
+ <span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span>
+ This user will be permanently deleted from the system. Are you sure?
+ </p>
+</div>
+
+<div id="dialog-password" title="Change password?" style="display: none">
+ <p>
+ <span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span>
+ This will permanently change the user's password. Make sure you wish
+ to do this.
+ </p>
+ <p>
+ <input title="New password" id="change-password" type="password" size="12" />
+ <br>
+ Please repeat it to be sure...
+ <br>
+ <input title="New password (again)" id="change-password2" type="password" size="12" />
+ </p>
+</div>
+
+<div id="dialog-environment" title="Set environment variable?" style="display: none">
+ <p>
+ <span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span>
+ Set an environment variable to be passed to the workflow engine.
+ </p>
+ <p>
+ <input title="Environment variable name" id="env-key" size="15" /> =
+ <input title="Environment variable value" id="env-value" size="20" />
+ </p>
+</div>
+
+<div id="dialog-runtime" title="Set runtime configuration?" style="display: none">
+ <p>
+ <span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span>
+ Set a runtime parameter (e.g., -Xmx400m for a 400MB memory limit) for the Java runtime.
+ </p>
+ <p>
+ <input title="Java runtime configuration parameter" id="runtime-value" size="20" />
+ </p>
+</div>
+
+<div id="dialog-property" title="Set runtime property?" style="display: none">
+ <p>
+ <span class="ui-icon ui-icon-alert" style="float:left; margin:0 7px 20px 0;"></span>
+ Set a configuration property for the Java runtime.
+ </p>
+ <p>
+ <input title="System property name" id="prop-key" size="15" /> =
+ <input title="System property value" id="prop-value" size="20" />
+ </p>
+</div>
+
+</body>
+</html>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/resources/capabilities.properties
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/resources/capabilities.properties b/taverna-server-webapp/src/main/resources/capabilities.properties
new file mode 100644
index 0000000..2b4844f
--- /dev/null
+++ b/taverna-server-webapp/src/main/resources/capabilities.properties
@@ -0,0 +1,38 @@
+# This is currently a hand-curated list. This sucks!
+
+######## --- PLATFORM --- ########
+http\://ns.taverna.org.uk/2013/software/taverna = 2.5
+
+######## --- OUTPUTS/PROVENANCE --- ########
+http\://ns.taverna.org.uk/2013/bundle/run = 1.0
+http\://ns.taverna.org.uk/2013/provenance/prov = 1.0
+
+######## --- ACTIVITIES --- ########
+http\://ns.taverna.org.uk/2010/activity/nested-workflow = 1.5
+http\://ns.taverna.org.uk/2010/activity/apiconsumer = 1.5
+http\://ns.taverna.org.uk/2010/activity/beanshell = 1.5
+http\://ns.taverna.org.uk/2010/activity/localworker = 1.5
+http\://ns.taverna.org.uk/2010/activity/biomart = 1.5
+http\://ns.taverna.org.uk/2010/activity/biomoby/object = 1.5
+http\://ns.taverna.org.uk/2010/activity/biomoby/service = 1.5
+http\://ns.taverna.org.uk/2010/activity/rshell = 1.5
+http\://ns.taverna.org.uk/2010/activity/soaplab = 1.5
+http\://ns.taverna.org.uk/2010/activity/spreadsheet-import = 1.5
+http\://ns.taverna.org.uk/2010/activity/constant = 1.5
+http\://ns.taverna.org.uk/2010/activity/component = 1.5
+http\://ns.taverna.org.uk/2010/activity/wsdl = 1.5
+http\://ns.taverna.org.uk/2010/activity/wsdl/xml-splitter/in = 1.5
+http\://ns.taverna.org.uk/2010/activity/wsdl/xml-splitter/out = 1.5
+http\://ns.taverna.org.uk/2010/activity/tool = 1.5
+http\://ns.taverna.org.uk/2010/activity/rest = 1.5
+http\://ns.taverna.org.uk/2010/activity/xpath = 1.5
+http\://ns.taverna.org.uk/2010/activity/webdav = 1.5
+http\://ns.taverna.org.uk/2010/activity/interaction = 1.5
+
+######## --- DISPATCH LAYERS --- ########
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/ErrorBounce = 1.5
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Failover = 1.5
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Invoke = 1.5
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Loop = 1.5
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Parallelize = 1.5
+http\://ns.taverna.org.uk/2010/scufl2/taverna/dispatchlayer/Retry = 1.5
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/resources/log4j.properties
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/resources/log4j.properties b/taverna-server-webapp/src/main/resources/log4j.properties
new file mode 100644
index 0000000..ea0ea12
--- /dev/null
+++ b/taverna-server-webapp/src/main/resources/log4j.properties
@@ -0,0 +1,39 @@
+log4j.rootLogger=info, R
+log4j.category.DataNucleus.Query=warn
+#log4j.category.DataNucleus.Datastore.Schema=debug
+#log4j.logger.org.springframework.security=DEBUG
+#log4j.category.Taverna=debug
+
+log4j.appender.R=org.apache.log4j.RollingFileAppender
+log4j.appender.R.File=${catalina.home}/logs/tavserv.out
+log4j.appender.R.MaxFileSize=10MB
+log4j.appender.R.MaxBackupIndex=30
+log4j.appender.R.layout=org.apache.log4j.PatternLayout
+log4j.appender.R.layout.ConversionPattern=%d{yyyyMMdd'T'HHmmss.SSS} %-5p %c{1} %C{1} - %m%n
+
+#log4j.category.Taverna=INFO, A1
+#log4j.category.Taverna.Server.LocalWorker.RunDB=INFO
+#log4j.category.Taverna.Server.Webapp=INFO
+#log4j.category.Taverna.Server.LocalWorker.Policy=INFO
+#log4j.category.Taverna.Server.LocalWorker.Security=INFO
+## Swallow Derby's messages
+#log4j.category.Derby=WARN, B2
+## Will you _shut up_, DataNucleus! <hits with rolled-up newspaper>
+#log4j.category.DataNucleus=WARN, B2
+##log4j.category.DataNucleus.SchemaTool=DEBUG
+##log4j.category.DataNucleus.Datastore.Schema=DEBUG
+##log4j.category.DataNucleus.Datastore.Native=DEBUG
+##log4j.logger.org.springframework.security=DEBUG, B2
+#log4j.category.org.springframework=INFO, B2
+#log4j.category.org.apache.cxf=INFO, B2
+#log4j.category.org.apache.cxf.jaxrs.utils.JAXRSUtils=INFO
+#log4j.category.eu.medsea=INFO, B2
+#log4j.category.org.apache.axiom=INFO, B2
+## Appender for Taverna Server components
+#log4j.appender.A1=org.apache.log4j.ConsoleAppender
+#log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+#log4j.appender.A1.layout.ConversionPattern=%d{yyyyMMdd'T'HHmmss.SSS} %-5p %c{1} %C{1} - %m%n
+## Appender for Framework components
+#log4j.appender.B2=org.apache.log4j.ConsoleAppender
+#log4j.appender.B2.layout=org.apache.log4j.PatternLayout
+#log4j.appender.B2.layout.ConversionPattern=%d{yyyyMMdd'T'HHmmss.SSS} %-5p %c{1} - %m%n
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/2c71f9a9/taverna-server-webapp/src/main/resources/security.policy
----------------------------------------------------------------------
diff --git a/taverna-server-webapp/src/main/resources/security.policy b/taverna-server-webapp/src/main/resources/security.policy
new file mode 100644
index 0000000..1ec4166
--- /dev/null
+++ b/taverna-server-webapp/src/main/resources/security.policy
@@ -0,0 +1,3 @@
+grant {
+ permission java.security.AllPermission "*:*";
+};