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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:55:00 UTC
[11/26] 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/utils/CallTimingFilter.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java b/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java
deleted file mode 100644
index aead6fa..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/CallTimingFilter.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/**
- *
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.String.format;
-import static java.lang.System.nanoTime;
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.io.IOException;
-
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.apache.commons.logging.Log;
-
-/**
- * Logs the time it takes to service HTTP calls into Taverna Server.
- * <p>
- * This class is currently not used.
- *
- * @author Donal Fellows
- */
-public class CallTimingFilter implements Filter {
- private Log log;
- private String name;
-
- @Override
- public void init(FilterConfig filterConfig) throws ServletException {
- log = getLog("Taverna.Server.Performance");
- name = filterConfig.getInitParameter("name");
- }
-
- @Override
- public void doFilter(ServletRequest request, ServletResponse response,
- FilterChain chain) throws IOException, ServletException {
- if (request instanceof HttpServletRequest)
- doFilter((HttpServletRequest) request,
- (HttpServletResponse) response, chain);
- else
- chain.doFilter(request, response);
- }
-
- public void doFilter(HttpServletRequest request,
- HttpServletResponse response, FilterChain chain)
- throws IOException, ServletException {
- long start = nanoTime();
- chain.doFilter(request, response);
- long elapsedTime = nanoTime() - start;
- log.info(format("%s call to %s %s took %.3fms", name,
- request.getMethod(), request.getRequestURI(),
- elapsedTime / 1000000.0));
- }
-
- @Override
- public void destroy() {
- log = null;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java b/server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java
deleted file mode 100644
index 54b0420..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/CapabilityLister.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package org.taverna.server.master.utils;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.Properties;
-
-import javax.annotation.PostConstruct;
-
-import org.taverna.server.master.common.Capability;
-
-/**
- * Utility for listing the capabilities supported by this Taverna Server
- * installation.
- *
- * @author Donal Fellows
- */
-public class CapabilityLister {
- public static final String CAPABILITY_RESOURCE_FILE = "/capabilities.properties";
- private Properties properties = new Properties();
-
- @PostConstruct
- void loadCapabilities() throws IOException {
- try (InputStream is = getClass().getResourceAsStream(
- CAPABILITY_RESOURCE_FILE)) {
- if (is != null)
- properties.load(is);
- }
- }
-
- public List<Capability> getCapabilities() {
- List<Capability> caps = new ArrayList<>();
- for (Entry<Object, Object> entry : properties.entrySet()) {
- Capability c = new Capability();
- c.capability = URI.create(entry.getKey().toString());
- c.version = entry.getValue().toString();
- caps.add(c);
- }
- return caps;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java b/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
deleted file mode 100644
index c27502f..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/CertificateChainFetcher.java
+++ /dev/null
@@ -1,199 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.util.Arrays.asList;
-import static java.util.Collections.unmodifiableList;
-
-import java.io.IOException;
-import java.net.URI;
-import java.security.GeneralSecurityException;
-import java.security.KeyManagementException;
-import java.security.KeyStore;
-import java.security.KeyStoreException;
-import java.security.NoSuchAlgorithmException;
-import java.security.cert.CertificateException;
-import java.security.cert.X509Certificate;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.net.ssl.SSLContext;
-import javax.net.ssl.SSLException;
-import javax.net.ssl.SSLSocket;
-import javax.net.ssl.SSLSocketFactory;
-import javax.net.ssl.TrustManager;
-import javax.net.ssl.TrustManagerFactory;
-import javax.net.ssl.X509TrustManager;
-import javax.xml.ws.Holder;
-
-/**
- * Obtains the certificate chain for an arbitrary SSL service. Maintains a
- * cache.
- *
- * @author Donal Fellows
- */
-public class CertificateChainFetcher {
- public String getProtocol() {
- return protocol;
- }
-
- public void setProtocol(String protocol) {
- this.protocol = protocol;
- }
-
- public String getKeystoreType() {
- return keystoreType;
- }
-
- public void setKeystoreType(String keystoreType) {
- this.keystoreType = keystoreType;
- }
-
- public String getAlgorithm() {
- return algorithm;
- }
-
- public void setAlgorithm(String algorithm) {
- this.algorithm = algorithm;
- }
-
- public int getTimeout() {
- return timeout;
- }
-
- public void setTimeout(int timeout) {
- this.timeout = timeout;
- }
-
- public void setSecure(boolean secure) {
- this.secure = secure;
- }
-
- private boolean secure = true;
- private String protocol = "TLS";
- private String keystoreType = KeyStore.getDefaultType();
- private String algorithm = TrustManagerFactory.getDefaultAlgorithm();
- private int timeout = 10000;
-
- /**
- * Get the certificate chain for a service.
- *
- * @param host
- * The host (name or IP address) to contact the service on.
- * @param port
- * The port to contact the service on.
- * @return The certificate chain, or <tt>null</tt> if no credentials are
- * available.
- * @throws NoSuchAlgorithmException
- * If the trust manager cannot be set up because of algorithm
- * problems.
- * @throws KeyStoreException
- * If the trust manager cannot be set up because of problems
- * with the keystore type.
- * @throws CertificateException
- * If a bad certificate is present in the default keystore;
- * <i>should be impossible</i>.
- * @throws IOException
- * If problems happen when trying to contact the service.
- * @throws KeyManagementException
- * If the SSL context can't have its special context manager
- * installed.
- */
- private X509Certificate[] getCertificateChainForService(String host,
- int port) throws NoSuchAlgorithmException, KeyStoreException,
- CertificateException, IOException, KeyManagementException {
- KeyStore ks = KeyStore.getInstance(keystoreType);
- SSLContext context = SSLContext.getInstance(protocol);
- TrustManagerFactory tmf = TrustManagerFactory.getInstance(algorithm);
- ks.load(null, null);
- tmf.init(ks);
- final Holder<X509Certificate[]> chain = new Holder<>();
- final X509TrustManager defaultTrustManager = (X509TrustManager) tmf
- .getTrustManagers()[0];
- context.init(null, new TrustManager[] { new X509TrustManager() {
- @Override
- public void checkClientTrusted(X509Certificate[] clientChain,
- String authType) throws CertificateException {
- throw new UnsupportedOperationException();
- }
-
- @Override
- public void checkServerTrusted(X509Certificate[] serverChain,
- String authType) throws CertificateException {
- chain.value = serverChain;
- defaultTrustManager.checkServerTrusted(serverChain, authType);
- }
-
- @Override
- public X509Certificate[] getAcceptedIssuers() {
- throw new UnsupportedOperationException();
- }
- } }, null);
- SSLSocketFactory factory = context.getSocketFactory();
- try (SSLSocket socket = (SSLSocket) factory.createSocket(host, port)) {
- socket.setSoTimeout(timeout);
- socket.startHandshake();
- } catch (SSLException e) {
- // Ignore
- }
- return chain.value;
- }
-
- private Map<URI, List<X509Certificate>> cache = new HashMap<>();
-
- /**
- * Gets the certificate chain for a service identified by URI.
- *
- * @param uri
- * The URI of the (secure) service to identify.
- * @return The certificate chain. Will be <tt>null</tt> if the service is
- * not secure.
- * @throws IOException
- * If the service is unreachable or other connection problems
- * occur.
- * @throws GeneralSecurityException
- * If any of a number of security-related problems occur, such
- * as an inability to match detailed security protocols.
- */
- public List<X509Certificate> getTrustsForURI(URI uri) throws IOException,
- GeneralSecurityException {
- if (!secure)
- return null;
- synchronized (this) {
- if (!cache.containsKey(uri)) {
- int port = uri.getPort();
- if (port == -1)
- switch (uri.getScheme()) {
- case "http":
- port = 80;
- break;
- case "https":
- port = 443;
- break;
- default:
- return null;
- }
- X509Certificate[] chain = getCertificateChainForService(
- uri.getHost(), port);
- if (chain != null)
- cache.put(uri, unmodifiableList(asList(chain)));
- else
- cache.put(uri, null);
- }
- return cache.get(uri);
- }
- }
-
- /**
- * Flushes the cache.
- */
- public void flushCache() {
- synchronized (this) {
- cache.clear();
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java b/server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java
deleted file mode 100644
index 884ff94..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/Contextualizer.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import javax.servlet.ServletContext;
-import javax.ws.rs.core.UriInfo;
-
-import org.springframework.web.context.ServletContextAware;
-import org.taverna.server.master.common.version.Version;
-
-/**
- * Convert a string (URL, etc) to a version that is contextualized to the
- * web-application.
- *
- * @author Donal Fellows
- */
-public class Contextualizer implements ServletContextAware {
- static final String ROOT_PLACEHOLDER = "%{WEBAPPROOT}";
- static final String VERSION_PLACEHOLDER = "%{VERSION}";
- static final String BASE_PLACEHOLDER = "%{BASEURL}";
-
- /**
- * Apply the contextualization operation. This consists of replacing the
- * string <tt>{@value #ROOT_PLACEHOLDER}</tt> with the real root of the webapp.
- *
- * @param input
- * the string to contextualize
- * @return the contextualized string
- */
- public String contextualize(String input) {
- // Hack to work around bizarre CXF bug
- String path = context.getRealPath("/").replace("%2D", "-");
- return input.replace(ROOT_PLACEHOLDER, path).replace(
- VERSION_PLACEHOLDER, Version.JAVA);
- }
-
- /**
- * Apply the contextualization operation. This consists of replacing the
- * string <tt>{@value #ROOT_PLACEHOLDER}</tt> with the real root of the
- * webapp.
- *
- * @param ui
- * Where to get information about the URL used to access the
- * webapp.
- * @param input
- * the string to contextualize
- * @return the contextualized string
- */
- public String contextualize(UriInfo ui, String input) {
- // Hack to work around bizarre CXF bug
- String baseuri = ui.getBaseUri().toString().replace("%2D", "-");
- if (baseuri.endsWith("/"))
- baseuri = baseuri.substring(0, baseuri.length() - 1);
- return contextualize(input).replace(BASE_PLACEHOLDER, baseuri);
- }
-
- private ServletContext context;
-
- @Override
- public void setServletContext(ServletContext servletContext) {
- context = servletContext;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java b/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
deleted file mode 100644
index f8b39e3..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/DerbyUtils.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package org.taverna.server.master.utils;
-
-import java.io.EOFException;
-import java.io.IOException;
-import java.io.Writer;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * Utility class, used to make Derby less broken.
- *
- * @see <a
- * href="http://stackoverflow.com/questions/1004327/getting-rid-of-derby-log">
- * Getting rid of derby.log </a>
- * @see <a
- * href="http://stackoverflow.com/questions/3339736/set-system-property-with-spring-configuration-file">
- * Set system property with Spring configuration file </a>
- */
-public class DerbyUtils {
- /**
- * A writer that channels things on to the log.
- */
- public static final Writer TO_LOG = new DBLog();
- // Hack
- public static final Writer DEV_NULL = TO_LOG;
-}
-
-class DBLog extends Writer {
- private Log log = LogFactory.getLog("Taverna.Server.Database");
- private StringBuilder sb = new StringBuilder();
- private boolean closed = false;
-
- @Override
- public void write(char[] cbuf, int off, int len) throws IOException {
- if (closed)
- throw new EOFException();
- if (!log.isInfoEnabled())
- return;
- sb.append(cbuf, off, len);
- while (!closed) {
- int idx = sb.indexOf("\n"), realIdx = idx;
- if (idx < 0)
- break;
- char ch;
- while (idx > 0 && ((ch = sb.charAt(idx - 1)) == '\r' || ch == ' ' || ch == '\t'))
- idx--;
- if (idx > 0)
- log.info(sb.substring(0, idx));
- sb.delete(0, realIdx + 1);
- }
- }
-
- @Override
- public void flush() throws IOException {
- if (sb.length() > 0) {
- log.info(sb.toString());
- sb = new StringBuilder();
- }
- }
-
- @Override
- public void close() throws IOException {
- flush();
- closed = true;
- sb = null;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java
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diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java b/server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java
deleted file mode 100644
index 19299e2..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/FilenameUtils.java
+++ /dev/null
@@ -1,268 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import java.util.List;
-
-import javax.ws.rs.core.PathSegment;
-
-import org.taverna.server.master.common.DirEntryReference;
-import org.taverna.server.master.exceptions.FilesystemAccessException;
-import org.taverna.server.master.exceptions.NoDirectoryEntryException;
-import org.taverna.server.master.interfaces.Directory;
-import org.taverna.server.master.interfaces.DirectoryEntry;
-import org.taverna.server.master.interfaces.File;
-import org.taverna.server.master.interfaces.TavernaRun;
-
-/**
- * Utility functions for getting entries from directories.
- *
- * @author Donal Fellows
- */
-public class FilenameUtils {
- private static final String TYPE_ERROR = "trying to take subdirectory of file";
- private static final String NO_FILE = "no such directory entry";
- private static final String NOT_A_FILE = "not a file";
- private static final String NOT_A_DIR = "not a directory";
-
- /**
- * Get a named directory entry from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param name
- * The name of the directory entry to look up.
- * @return The directory entry whose name is equal to the last part of the
- * path; an empty path will retrieve the working directory handle
- * itself.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable.
- */
- public DirectoryEntry getDirEntry(TavernaRun run, String name)
- throws FilesystemAccessException, NoDirectoryEntryException {
- Directory dir = run.getWorkingDirectory();
- if (name == null || name.isEmpty())
- return dir;
- DirectoryEntry found = dir;
- boolean mustBeLast = false;
-
- // Must be nested loops; avoids problems with %-encoded "/" chars
- for (String bit : name.split("/")) {
- if (mustBeLast)
- throw new FilesystemAccessException(TYPE_ERROR);
- found = getEntryFromDir(bit, dir);
- dir = null;
- if (found instanceof Directory) {
- dir = (Directory) found;
- mustBeLast = false;
- } else
- mustBeLast = true;
- }
- return found;
- }
-
- /**
- * Get a named directory entry from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param d
- * The path segments describing what to look up.
- * @return The directory entry whose name is equal to the last part of the
- * path; an empty path will retrieve the working directory handle
- * itself.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable.
- */
- public DirectoryEntry getDirEntry(TavernaRun run, List<PathSegment> d)
- throws FilesystemAccessException, NoDirectoryEntryException {
- Directory dir = run.getWorkingDirectory();
- if (d == null || d.isEmpty())
- return dir;
- DirectoryEntry found = dir;
- boolean mustBeLast = false;
-
- // Must be nested loops; avoids problems with %-encoded "/" chars
- for (PathSegment segment : d)
- for (String bit : segment.getPath().split("/")) {
- if (mustBeLast)
- throw new FilesystemAccessException(TYPE_ERROR);
- found = getEntryFromDir(bit, dir);
- dir = null;
- if (found instanceof Directory) {
- dir = (Directory) found;
- mustBeLast = false;
- } else
- mustBeLast = true;
- }
- return found;
- }
-
- /**
- * Get a named directory entry from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param d
- * The directory reference describing what to look up.
- * @return The directory entry whose name is equal to the last part of the
- * path in the directory reference; an empty path will retrieve the
- * working directory handle itself.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- */
- public DirectoryEntry getDirEntry(TavernaRun run, DirEntryReference d)
- throws FilesystemAccessException, NoDirectoryEntryException {
- Directory dir = run.getWorkingDirectory();
- if (d == null || d.path == null || d.path.isEmpty())
- return dir;
- DirectoryEntry found = dir;
- boolean mustBeLast = false;
-
- for (String bit : d.path.split("/")) {
- if (mustBeLast)
- throw new FilesystemAccessException(TYPE_ERROR);
- found = getEntryFromDir(bit, dir);
- dir = null;
- if (found instanceof Directory) {
- dir = (Directory) found;
- mustBeLast = false;
- } else
- mustBeLast = true;
- }
- return found;
- }
-
- /**
- * Get a named directory entry from a directory.
- *
- * @param name
- * The name of the entry; must be "<tt>/</tt>"-free.
- * @param dir
- * The directory to look in.
- * @return The directory entry whose name is equal to the given name.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable.
- */
- private DirectoryEntry getEntryFromDir(String name, Directory dir)
- throws FilesystemAccessException, NoDirectoryEntryException {
- if (dir == null)
- throw new FilesystemAccessException(NO_FILE);
- for (DirectoryEntry entry : dir.getContents())
- if (entry.getName().equals(name))
- return entry;
- throw new NoDirectoryEntryException(NO_FILE);
- }
-
- /**
- * Get a named directory from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param d
- * The directory reference describing what to look up.
- * @return The directory whose name is equal to the last part of the path in
- * the directory reference; an empty path will retrieve the working
- * directory handle itself.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable, or if the
- * name doesn't refer to a directory.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- */
- public Directory getDirectory(TavernaRun run, DirEntryReference d)
- throws FilesystemAccessException, NoDirectoryEntryException {
- DirectoryEntry dirEntry = getDirEntry(run, d);
- if (dirEntry instanceof Directory)
- return (Directory) dirEntry;
- throw new FilesystemAccessException(NOT_A_DIR);
- }
-
- /**
- * Get a named directory from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param name
- * The name of the directory to look up.
- * @return The directory.
- * @throws FilesystemAccessException
- * If the directory isn't specified or isn't readable, or if the
- * name doesn't refer to a directory.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- */
- public Directory getDirectory(TavernaRun run, String name)
- throws FilesystemAccessException, NoDirectoryEntryException {
- DirectoryEntry dirEntry = getDirEntry(run, name);
- if (dirEntry instanceof Directory)
- return (Directory) dirEntry;
- throw new FilesystemAccessException(NOT_A_DIR);
- }
-
- /**
- * Get a named file from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param d
- * The directory reference describing what to look up.
- * @return The file whose name is equal to the last part of the path in the
- * directory reference; an empty path will retrieve the working
- * directory handle itself.
- * @throws FilesystemAccessException
- * If the file isn't specified or isn't readable, or if the name
- * doesn't refer to a file.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- */
- public File getFile(TavernaRun run, DirEntryReference d)
- throws FilesystemAccessException, NoDirectoryEntryException {
- DirectoryEntry dirEntry = getDirEntry(run, d);
- if (dirEntry instanceof File)
- return (File) dirEntry;
- throw new FilesystemAccessException(NOT_A_FILE);
- }
-
- /**
- * Get a named file from a workflow run.
- *
- * @param run
- * The run whose working directory is to be used as the root of
- * the search.
- * @param name
- * The name of the file to look up.
- * @return The file whose name is equal to the last part of the path in the
- * directory reference; an empty path will retrieve the working
- * directory handle itself.
- * @throws FilesystemAccessException
- * If the file isn't specified or isn't readable, or if the name
- * doesn't refer to a file.
- * @throws NoDirectoryEntryException
- * If there is no such entry.
- */
- public File getFile(TavernaRun run, String name)
- throws FilesystemAccessException, NoDirectoryEntryException {
- DirectoryEntry dirEntry = getDirEntry(run, name);
- if (dirEntry instanceof File)
- return (File) dirEntry;
- throw new FilesystemAccessException(NOT_A_FILE);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java b/server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java
deleted file mode 100644
index ff52e81..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/FlushThreadLocalCacheInterceptor.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package org.taverna.server.master.utils;
-
-import org.apache.cxf.jaxrs.provider.ProviderFactory;
-import org.apache.cxf.message.Message;
-import org.apache.cxf.phase.AbstractPhaseInterceptor;
-import org.apache.cxf.phase.Phase;
-
-public class FlushThreadLocalCacheInterceptor extends
- AbstractPhaseInterceptor<Message> {
- public FlushThreadLocalCacheInterceptor() {
- super(Phase.USER_LOGICAL_ENDING);
- }
-
- @Override
- public void handleMessage(Message message) {
- ProviderFactory.getInstance(message).clearThreadLocalProxies();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java b/server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java
deleted file mode 100644
index 55a260b..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/InvocationCounter.java
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright (C) 2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.annotation.ElementType.METHOD;
-import static java.lang.annotation.RetentionPolicy.RUNTIME;
-
-import java.lang.annotation.Documented;
-import java.lang.annotation.Retention;
-import java.lang.annotation.Target;
-
-import org.aspectj.lang.annotation.Aspect;
-import org.aspectj.lang.annotation.Before;
-
-/**
- * This class is responsible for counting all invocations of publicly-exposed
- * methods of the webapp. It's connected to the webapp primarily through an
- * AspectJ-style pointcut.
- *
- * @author Donal Fellows
- */
-@Aspect
-public class InvocationCounter {
- private int count;
-
- @Before("@annotation(org.taverna.server.master.utils.InvocationCounter.CallCounted)")
- public synchronized void count() {
- count++;
- }
-
- public synchronized int getCount() {
- return count;
- }
-
- /**
- * Mark methods that should be counted by the invocation counter.
- *
- * @author Donal Fellows
- */
- @Retention(RUNTIME)
- @Documented
- @Target(METHOD)
- public static @interface CallCounted {
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java b/server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java
deleted file mode 100644
index 252e316..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/JCECheck.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright (C) 2012 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.Integer.MAX_VALUE;
-import static javax.crypto.Cipher.getMaxAllowedKeyLength;
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.security.GeneralSecurityException;
-import java.security.NoSuchAlgorithmException;
-
-import javax.annotation.PostConstruct;
-
-import org.apache.commons.logging.Log;
-
-/**
- * Trivial bean that checks for whether the JCE policy files that allow
- * unlimited strength security are present, and warns in the log if not.
- *
- * @author Donal Fellows
- */
-public class JCECheck {
- /**
- * Write a message to the log that says whether an unlimited strength
- * {@linkplain #Cipher cipher} is present. This is the official proxy for
- * whether the unlimited strength JCE policy files have been installed; if
- * absent, the message is logged as a warning, otherwise it is just
- * informational.
- */
- @PostConstruct
- public void checkForUnlimitedJCE() {
- Log log = getLog("Taverna.Server.Utils");
-
- try {
- if (getMaxAllowedKeyLength("AES") < MAX_VALUE)
- log.warn("maximum key length very short; unlimited "
- + "strength JCE policy files maybe missing");
- else
- log.info("unlimited strength JCE policy in place");
- } catch (GeneralSecurityException e) {
- log.warn("problem computing key length limits!", e);
- }
- }
-
- /**
- * @return Whether the unlimited strength JCE policy files are present (or
- * rather whether an unlimited strength {@linkplain #Cipher cipher}
- * is permitted).
- */
- public boolean isUnlimitedStrength() {
- try {
- return getMaxAllowedKeyLength("AES") == MAX_VALUE;
- } catch (NoSuchAlgorithmException e) {
- return false;
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java b/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
deleted file mode 100644
index ba9ec81..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/JDOSupport.java
+++ /dev/null
@@ -1,270 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.annotation.ElementType.METHOD;
-import static java.lang.annotation.RetentionPolicy.RUNTIME;
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.lang.annotation.Documented;
-import java.lang.annotation.Retention;
-import java.lang.annotation.Target;
-import java.util.WeakHashMap;
-
-import javax.annotation.Nonnull;
-import javax.annotation.Nullable;
-import javax.annotation.PreDestroy;
-import javax.jdo.JDOException;
-import javax.jdo.PersistenceManager;
-import javax.jdo.PersistenceManagerFactory;
-import javax.jdo.Query;
-import javax.jdo.Transaction;
-
-import org.apache.commons.logging.Log;
-import org.aspectj.lang.ProceedingJoinPoint;
-import org.aspectj.lang.annotation.Around;
-import org.aspectj.lang.annotation.Aspect;
-import org.springframework.beans.factory.annotation.Required;
-
-/**
- * Simple support class that wraps up and provides access to the correct parts
- * of JDO.
- *
- * @author Donal Fellows
- *
- * @param <T> The context class that the subclass will be working with.
- */
-public abstract class JDOSupport<T> {
- private Class<T> contextClass;
- private PersistenceManagerBuilder pmb;
-
- /**
- * Instantiate this class, supplying it a handle to the class that will be
- * used to provide context for queries and accesses.
- *
- * @param contextClass
- * Must match the type parameter to the class itself.
- */
- protected JDOSupport(@Nonnull Class<T> contextClass) {
- this.contextClass = contextClass;
- }
-
- /**
- * @param persistenceManagerBuilder
- * The JDO engine to use for managing persistence.
- */
- @Required
- public void setPersistenceManagerBuilder(
- PersistenceManagerBuilder persistenceManagerBuilder) {
- pmb = persistenceManagerBuilder;
- }
-
- private PersistenceManager pm() {
- if (isPersistent())
- return pmb.getPersistenceManager();
- return null;
- }
-
- /**
- * Has this class actually been configured with a persistence manager by
- * Spring?
- *
- * @return Whether there is a persistence manager installed.
- */
- protected boolean isPersistent() {
- return pmb != null;
- }
-
- /**
- * Get an instance of a query in JDOQL.
- *
- * @param filter
- * The filter part of the query.
- * @return The query, which should be executed to retrieve the results.
- */
- @Nonnull
- protected Query query(@Nonnull String filter) {
- return pm().newQuery(contextClass, filter);
- }
-
- /**
- * Get an instance of a named query attached to the context class (as an
- * annotation).
- *
- * @param name
- * The name of the query.
- * @return The query, which should be executed to retrieve the results.
- * @see javax.jdo.annotations.Query
- */
- @Nonnull
- protected Query namedQuery(@Nonnull String name) {
- return pm().newNamedQuery(contextClass, name);
- }
-
- /**
- * Make an instance of the context class persist in the database. It's
- * identity must not already exist.
- *
- * @param value
- * The instance to persist.
- * @return The persistence-coupled instance.
- */
- @Nullable
- protected T persist(@Nullable T value) {
- if (value == null)
- return null;
- return pm().makePersistent(value);
- }
-
- /**
- * Make a non-persistent (i.e., will hold its value past the end of the
- * transaction) copy of a persistence-coupled instance of the context class.
- *
- * @param value
- * The value to decouple.
- * @return The non-persistent copy.
- */
- @Nullable
- protected T detach(@Nullable T value) {
- if (value == null)
- return null;
- return pm().detachCopy(value);
- }
-
- /**
- * Look up an instance of the context class by its identity.
- *
- * @param id
- * The identity of the object.
- * @return The instance, which is persistence-coupled.
- */
- @Nullable
- protected T getById(Object id) {
- try {
- return pm().getObjectById(contextClass, id);
- } catch (Exception e) {
- return null;
- }
- }
-
- /**
- * Delete a persistence-coupled instance of the context class.
- *
- * @param value
- * The value to delete.
- */
- protected void delete(@Nullable T value) {
- if (value != null)
- pm().deletePersistent(value);
- }
-
- /**
- * Manages integration of JDO transactions with Spring.
- *
- * @author Donal Fellows
- */
- @Aspect
- public static class TransactionAspect {
- private Object lock = new Object();
- private Log log = getLog("Taverna.Server.Utils");
- private volatile int txid;
-
- @Around(value = "@annotation(org.taverna.server.master.utils.JDOSupport.WithinSingleTransaction) && target(support)", argNames = "support")
- Object applyTransaction(ProceedingJoinPoint pjp, JDOSupport<?> support)
- throws Throwable {
- synchronized (lock) {
- PersistenceManager pm = support.pm();
- int id = ++txid;
- Transaction tx = (pm == null) ? null : pm.currentTransaction();
- if (tx != null && tx.isActive())
- tx = null;
- if (tx != null) {
- if (log.isDebugEnabled())
- log.debug("starting transaction #" + id);
- tx.begin();
- }
- try {
- Object result = pjp.proceed();
- if (tx != null) {
- tx.commit();
- if (log.isDebugEnabled())
- log.debug("committed transaction #" + id);
- }
- tx = null;
- return result;
- } catch (Throwable t) {
- try {
- if (tx != null) {
- tx.rollback();
- if (log.isDebugEnabled())
- log.debug("rolled back transaction #" + id);
- }
- } catch (JDOException e) {
- log.warn("rollback failed unexpectedly", e);
- }
- throw t;
- }
- }
- }
- }
-
- /**
- * Mark a method (of a subclass of {@link JDOSupport}) as having a
- * transaction wrapped around it. The transactions are managed correctly in
- * the multi-threaded case.
- *
- * @author Donal Fellows
- */
- @Target(METHOD)
- @Retention(RUNTIME)
- @Documented
- public @interface WithinSingleTransaction {
- }
-
- /**
- * Manages {@linkplain PersistenceManager persistence managers} in a way
- * that doesn't cause problems when the web application is unloaded.
- *
- * @author Donal Fellows
- */
- public static class PersistenceManagerBuilder {
- private PersistenceManagerFactory pmf;
- private WeakHashMap<Thread, PersistenceManager> cache = new WeakHashMap<>();
-
- /**
- * @param persistenceManagerFactory
- * The JDO engine to use for managing persistence.
- */
- @Required
- public void setPersistenceManagerFactory(
- PersistenceManagerFactory persistenceManagerFactory) {
- pmf = persistenceManagerFactory;
- }
-
- @Nonnull
- public PersistenceManager getPersistenceManager() {
- if (cache == null)
- return pmf.getPersistenceManager();
- Thread t = Thread.currentThread();
- PersistenceManager pm = cache.get(t);
- if (pm == null && pmf != null) {
- pm = pmf.getPersistenceManager();
- cache.put(t, pm);
- }
- return pm;
- }
-
- @PreDestroy
- void clearThreadCache() {
- WeakHashMap<Thread, PersistenceManager> cache = this.cache;
- this.cache = null;
- for (PersistenceManager pm : cache.values())
- if (pm != null)
- pm.close();
- cache.clear();
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java b/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
deleted file mode 100644
index a8aa937..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/LoggingDerbyAdapter.java
+++ /dev/null
@@ -1,138 +0,0 @@
-package org.taverna.server.master.utils;
-
-import static java.lang.System.currentTimeMillis;
-import static java.lang.Thread.sleep;
-import static org.apache.commons.logging.LogFactory.getLog;
-
-import java.sql.DatabaseMetaData;
-import java.util.Properties;
-
-import org.apache.commons.logging.Log;
-import org.datanucleus.store.rdbms.adapter.DerbyAdapter;
-import org.datanucleus.store.rdbms.identifier.IdentifierFactory;
-import org.datanucleus.store.rdbms.key.CandidateKey;
-import org.datanucleus.store.rdbms.key.ForeignKey;
-import org.datanucleus.store.rdbms.key.Index;
-import org.datanucleus.store.rdbms.key.PrimaryKey;
-import org.datanucleus.store.rdbms.sql.SQLTable;
-import org.datanucleus.store.rdbms.table.Column;
-import org.datanucleus.store.rdbms.table.Table;
-import org.datanucleus.store.rdbms.table.TableImpl;
-import org.datanucleus.store.rdbms.table.ViewImpl;
-
-/**
- * Evil hack to allow logging of the DDL spat out to Derby.
- *
- * @author Donal Fellows
- */
-public class LoggingDerbyAdapter extends DerbyAdapter {
- Log log = getLog("Taverna.Server.SQL");
-
- private StringBuilder ddl = new StringBuilder();
- private volatile long timeout;
- private Thread timer;
-
- private synchronized void logDDL() {
- if (ddl.length() > 0) {
- log.info("Data definition language:\n" + ddl);
- ddl.setLength(0);
- }
- timer = null;
- }
-
- private synchronized void doLog(String item) {
- ddl.append(item);
- if (!item.endsWith("\n"))
- ddl.append('\n');
- timeout = currentTimeMillis() + 5000;
- if (timer == null)
- timer = new OneShotThread("DDL logger timeout", new Runnable() {
- @Override
- public void run() {
- try {
- while (timeout > currentTimeMillis())
- sleep(1000);
- } catch (InterruptedException e) {
- // Ignore
- }
- logDDL();
- }
- });
- }
-
- /**
- * Creates an Apache Derby adapter based on the given metadata which logs
- * the DDL it creates.
- */
- public LoggingDerbyAdapter(DatabaseMetaData metadata) {
- super(metadata);
- }
-
- @Override
- public String getCreateTableStatement(TableImpl table, Column[] columns,
- Properties props, IdentifierFactory factory) {
- String statement = super.getCreateTableStatement(table, columns, props,
- factory);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getCreateIndexStatement(Index index, IdentifierFactory factory) {
- String statement = super.getCreateIndexStatement(index, factory);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getAddCandidateKeyStatement(CandidateKey ck,
- IdentifierFactory factory) {
- String statement = super.getAddCandidateKeyStatement(ck, factory);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getAddPrimaryKeyStatement(PrimaryKey pk,
- IdentifierFactory factory) {
- String statement = super.getAddPrimaryKeyStatement(pk, factory);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getAddColumnStatement(Table table, Column col) {
- String statement = super.getAddColumnStatement(table, col);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getAddForeignKeyStatement(ForeignKey fk,
- IdentifierFactory factory) {
- String statement = super.getAddForeignKeyStatement(fk, factory);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getDeleteTableStatement(SQLTable tbl) {
- String statement = super.getDeleteTableStatement(tbl);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getDropTableStatement(Table table) {
- String statement = super.getDropTableStatement(table);
- doLog(statement);
- return statement;
- }
-
- @Override
- public String getDropViewStatement(ViewImpl view) {
- String statement = super.getDropViewStatement(view);
- doLog(statement);
- return statement;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java b/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java
deleted file mode 100644
index 68b813d..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/OneShotThread.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package org.taverna.server.master.utils;
-
-public class OneShotThread extends Thread {
- public OneShotThread(String name, Runnable target) {
- super(target, name);
- setContextClassLoader(null);
- setDaemon(true);
- start();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java b/server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java
deleted file mode 100644
index a892b52..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/RestUtils.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import javax.ws.rs.OPTIONS;
-import javax.ws.rs.core.Response;
-
-/**
- * Utilities that make it easier to write REST services.
- *
- * @author Donal Fellows
- */
-public class RestUtils {
- /**
- * Generate a response to an HTTP OPTIONS request.
- *
- * @param methods
- * The state-changing methods supported, if any.
- * @return the required response
- * @see OPTIONS
- */
- public static Response opt(String... methods) {
- StringBuilder sb = new StringBuilder("GET,");
- for (String m : methods)
- sb.append(m).append(",");
- sb.append("HEAD,OPTIONS");
- return Response.ok().header("Allow", sb.toString()).entity("").build();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java b/server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java
deleted file mode 100644
index 0b2d4ea..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/RuntimeExceptionWrapper.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import org.aspectj.lang.annotation.AfterThrowing;
-import org.aspectj.lang.annotation.Aspect;
-import org.taverna.server.master.exceptions.GeneralFailureException;
-
-/**
- * Aspect used to convert {@linkplain RuntimeException runtime exceptions} into
- * a form that can be nicely conveyed to the outside world as HTTP errors.
- *
- * @author Donal Fellows
- */
-@Aspect
-public class RuntimeExceptionWrapper {
- /**
- * Map an unexpected exception to one that can be correctly reported as a
- * problem.
- *
- * @param exn
- * The runtime exception being trapped.
- * @throws GeneralFailureException
- * The known exception type that it is mapped to.
- */
- @AfterThrowing(pointcut = "execution(* org.taverna.server.master.rest..*(..)) && !bean(*Provider.*)", throwing = "exn")
- public void wrapRuntimeException(RuntimeException exn)
- throws GeneralFailureException {
- // Exclude security-related exceptions
- if (exn.getClass().getName().startsWith("org.springframework.security."))
- return;
- throw new GeneralFailureException(exn);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java b/server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java
deleted file mode 100644
index 9bbcc2f..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/UsernamePrincipal.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import java.io.Serializable;
-import java.security.Principal;
-
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.userdetails.UserDetails;
-
-/**
- * A simple serializable principal that just records the name.
- *
- * @author Donal Fellows
- */
-public class UsernamePrincipal implements Principal, Serializable {
- private static final long serialVersionUID = 2703493248562435L;
- public UsernamePrincipal(String username) {
- this.name = username;
- }
-
- public UsernamePrincipal(Principal other) {
- this.name = other.getName();
- }
-
- public UsernamePrincipal(Authentication auth) {
- this(auth.getPrincipal());
- }
-
- public UsernamePrincipal(Object principal) {
- if (principal instanceof Principal)
- this.name = ((Principal) principal).getName();
- else if (principal instanceof String)
- this.name = (String) principal;
- else if (principal instanceof UserDetails)
- this.name = ((UserDetails) principal).getUsername();
- else
- this.name = principal.toString();
- }
-
- private String name;
-
- @Override
- public String getName() {
- return name;
- }
-
- @Override
- public String toString() {
- return "Principal<" + name + ">";
- }
-
- @Override
- public boolean equals(Object o) {
- if (o instanceof Principal) {
- Principal p = (Principal) o;
- return name.equals(p.getName());
- }
- return false;
- }
-
- @Override
- public int hashCode() {
- return name.hashCode();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/WSDLHeadOptionsInterceptor.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/WSDLHeadOptionsInterceptor.java b/server-webapp/src/main/java/org/taverna/server/master/utils/WSDLHeadOptionsInterceptor.java
deleted file mode 100644
index 96cdc6d..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/WSDLHeadOptionsInterceptor.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.taverna.server.master.utils;
-
-import static org.apache.commons.logging.LogFactory.getLog;
-import static org.apache.cxf.common.util.UrlUtils.parseQueryString;
-import static org.apache.cxf.message.Message.HTTP_REQUEST_METHOD;
-import static org.apache.cxf.message.Message.QUERY_STRING;
-import static org.apache.cxf.message.Message.REQUEST_URL;
-import static org.apache.cxf.phase.Phase.READ;
-
-import java.util.Map;
-
-import org.apache.commons.logging.Log;
-import org.apache.cxf.binding.soap.interceptor.EndpointSelectionInterceptor;
-import org.apache.cxf.interceptor.Fault;
-import org.apache.cxf.message.Message;
-import org.apache.cxf.phase.AbstractPhaseInterceptor;
-
-
-/**
- * Thunk for TAVSERV-293.
- *
- * @author Donal Fellows (based on work by Daniel Hagen)
- */
-public class WSDLHeadOptionsInterceptor extends
- AbstractPhaseInterceptor<Message> {
- public static final Log log = getLog("Taverna.Server.Utils");
-
- public WSDLHeadOptionsInterceptor() {
- super(READ);
- getAfter().add(EndpointSelectionInterceptor.class.getName());
- }
-
- @Override
- public void handleMessage(Message message) throws Fault {
- String method = (String) message.get(HTTP_REQUEST_METHOD);
- String query = (String) message.get(QUERY_STRING);
-
- if (("HEAD".equals(method) || "OPTIONS".equals(method))
- && query != null && !query.trim().isEmpty()
- && isRecognizedQuery(query)) {
- log.debug("adjusting message request method " + method + " for "
- + message.get(REQUEST_URL) + " to GET");
- message.put(HTTP_REQUEST_METHOD, "GET");
- }
- }
-
- /*
- * Stolen from http://permalink.gmane.org/gmane.comp.apache.cxf.user/20037
- * which is itself in turn stolen from
- * org.apache.cxf.frontend.WSDLGetInterceptor.isRecognizedQuery
- */
- /**
- * Is this a query for WSDL or XSD relating to it?
- *
- * @param query
- * The query string to check
- * @return If the query is one to handle.
- * @see org.apache.cxf.frontend.WSDLGetInterceptor#isRecognizedQuery(Map,String,String,org.apache.cxf.service.model.EndpointInfo)
- * WSDLGetInterceptor
- */
- private boolean isRecognizedQuery(String query) {
- Map<String, String> map = parseQueryString(query);
- return map.containsKey("wsdl") || map.containsKey("xsd");
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java b/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
deleted file mode 100644
index 03fc749..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/WebappAwareDataSource.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static java.lang.Thread.currentThread;
-import static java.sql.DriverManager.deregisterDriver;
-import static java.sql.DriverManager.getDrivers;
-import static org.taverna.server.master.utils.Contextualizer.ROOT_PLACEHOLDER;
-
-import java.io.PrintWriter;
-import java.sql.Connection;
-import java.sql.Driver;
-import java.sql.DriverManager;
-import java.sql.SQLException;
-import java.util.Enumeration;
-
-import javax.annotation.PreDestroy;
-
-import org.apache.commons.dbcp.BasicDataSource;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.springframework.beans.factory.annotation.Required;
-
-/**
- * Add some awareness of the context so that we can locate databases internally
- * to the webapp.
- *
- * @author Donal Fellows
- */
-public class WebappAwareDataSource extends BasicDataSource {
- Log log = LogFactory.getLog("Taverna.Server.Utils");
- private transient boolean init;
- private Contextualizer ctxt;
- private String shutdownUrl;
-
- @Required
- public void setContextualizer(Contextualizer ctxt) {
- this.ctxt = ctxt;
- }
-
- /**
- * A JDBC connection URL to use on shutting down the database. If not set,
- * do nothing special.
- *
- * @param url
- */
- public void setShutdownUrl(String url) {
- shutdownUrl = url;
- }
-
- private void doInit() {
- synchronized (this) {
- if (!init) {
- setDriverClassLoader(currentThread().getContextClassLoader());
- String url = getUrl();
- if (url.contains(ROOT_PLACEHOLDER)) {
- String newurl = ctxt.contextualize(url);
- setUrl(newurl);
- log.info("mapped " + url + " to " + newurl);
- } else {
- log.info("did not find " + ROOT_PLACEHOLDER + " in " + url);
- }
- init = true;
- }
- }
- }
-
- // -=-=-=-=-=-=-=-=-=-=- HOOKS -=-=-=-=-=-=-=-=-=-=-
-
- @Override
- public Connection getConnection() throws SQLException {
- doInit();
- return super.getConnection();
- }
-
- @Override
- public void setLogWriter(PrintWriter pw) throws SQLException {
- doInit();
- super.setLogWriter(pw);
- }
-
- @Override
- public void setLoginTimeout(int num) throws SQLException {
- doInit();
- super.setLoginTimeout(num);
- }
-
- @Override
- public PrintWriter getLogWriter() throws SQLException {
- doInit();
- return super.getLogWriter();
- }
-
- @Override
- public int getLoginTimeout() throws SQLException {
- doInit();
- return super.getLoginTimeout();
- }
-
- @PreDestroy
- void realClose() {
- try {
- close();
- } catch (SQLException e) {
- log.warn("problem shutting down DB connection", e);
- }
- try {
- if (shutdownUrl != null)
- DriverManager.getConnection(ctxt.contextualize(shutdownUrl));
- } catch (SQLException e) {
- // Expected; ignore it
- }
- log = null;
- dropDriver();
- }
-
- private void dropDriver() {
- Enumeration<Driver> drivers = getDrivers();
- while (drivers.hasMoreElements()) {
- Driver d = drivers.nextElement();
- if (d.getClass().getClassLoader() == getDriverClassLoader()
- && d.getClass().getName().equals(getDriverClassName())) {
- try {
- deregisterDriver(d);
- } catch (SQLException e) {
- }
- break;
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/utils/X500Utils.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/X500Utils.java b/server-webapp/src/main/java/org/taverna/server/master/utils/X500Utils.java
deleted file mode 100644
index da4cff0..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/X500Utils.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.utils;
-
-import static javax.security.auth.x500.X500Principal.RFC2253;
-
-import java.math.BigInteger;
-import java.security.cert.X509Certificate;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.annotation.PreDestroy;
-import javax.security.auth.x500.X500Principal;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * Support class that factors out some of the messier parts of working with
- * X.500 identities and X.509 certificates.
- *
- * @author Donal Fellows
- */
-public class X500Utils {
- private Log log = LogFactory.getLog("Taverna.Server.Utils");
-
- @PreDestroy
- void closeLog() {
- log = null;
- }
-
- private static final char DN_SEPARATOR = ',';
- private static final char DN_ESCAPE = '\\';
- private static final char DN_QUOTE = '"';
-
- /**
- * Parse the DN from the Principal and extract the CN field.
- *
- * @param id
- * The identity to extract the distinguished name from.
- * @param fields
- * The names to look at when finding the field to return. Each
- * should be an upper-cased string.
- * @return The common-name part of the distinguished name, or the literal
- * string "<tt>none</tt>" if there is no CN.
- */
- public String getName(X500Principal id, String... fields) {
- String dn = id.getName(RFC2253);
-
- int i = 0;
- int startIndex = 0;
- boolean ignoreThisChar = false;
- boolean inQuotes = false;
- Map<String, String> tokenized = new HashMap<>();
-
- for (i = 0; i < dn.length(); i++)
- if (ignoreThisChar)
- ignoreThisChar = false;
- else if (dn.charAt(i) == DN_QUOTE)
- inQuotes = !inQuotes;
- else if (inQuotes)
- continue;
- else if (dn.charAt(i) == DN_ESCAPE)
- ignoreThisChar = true;
- else if ((dn.charAt(i) == DN_SEPARATOR) && !ignoreThisChar) {
- storeDNField(tokenized, dn.substring(startIndex, i).trim()
- .split("=", 2));
- startIndex = i + 1;
- }
- if (inQuotes || ignoreThisChar)
- log.warn("was parsing invalid DN format");
- // Add last token - after the last delimiter
- storeDNField(tokenized, dn.substring(startIndex).trim().split("=", 2));
-
- for (String field : fields) {
- String value = tokenized.get(field);
- if (value != null)
- return value;
- }
- return "none";
- }
-
- private void storeDNField(Map<String, String> container, String[] split) {
- if (split == null || split.length != 2)
- return;
- String key = split[0].toUpperCase();
- if (container.containsKey(key))
- log.warn("duplicate field in DN: " + key);
- // LATER: Should the field be de-quoted?
- container.put(key, split[1]);
- }
-
- /**
- * Get the serial number from a certificate as a hex string.
- *
- * @param cert
- * The certificate to extract from.
- * @return A hex string, in upper-case.
- */
- public String getSerial(X509Certificate cert) {
- return new BigInteger(1, cert.getSerialNumber().toByteArray())
- .toString(16).toUpperCase();
- }
-}
\ 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/utils/package-info.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/utils/package-info.java b/server-webapp/src/main/java/org/taverna/server/master/utils/package-info.java
deleted file mode 100644
index 612e61c..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/utils/package-info.java
+++ /dev/null
@@ -1,10 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-/**
- * Miscellaneous utility classes. Includes aspects that might be attached
- * for purposes such as transaction management and invocation tracking.
- */
-package org.taverna.server.master.utils;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/worker/CompletionNotifier.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/worker/CompletionNotifier.java b/server-webapp/src/main/java/org/taverna/server/master/worker/CompletionNotifier.java
deleted file mode 100644
index 10b3830..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/worker/CompletionNotifier.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright (C) 2010-2011 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.worker;
-
-
-/**
- * How to convert a notification about the completion of a job into a message.
- *
- * @author Donal Fellows
- */
-public interface CompletionNotifier {
- /**
- * @return The name of this notifier.
- */
- String getName();
-
- /**
- * Called to get the content of a message that a workflow run has finished.
- *
- * @param name
- * The name of the run.
- * @param run
- * What run are we talking about.
- * @param code
- * What the exit code was.
- * @return The plain-text content of the message.
- */
- String makeCompletionMessage(String name, RemoteRunDelegate run, int code);
-
- /**
- * Called to get the subject of the message to dispatch.
- *
- * @param name
- * The name of the run.
- * @param run
- * What run are we talking about.
- * @param code
- * What the exit code was.
- * @return The plain-text subject of the message.
- */
- String makeMessageSubject(String name, RemoteRunDelegate run, int code);
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/worker/FactoryBean.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/worker/FactoryBean.java b/server-webapp/src/main/java/org/taverna/server/master/worker/FactoryBean.java
deleted file mode 100644
index 5d0f371..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/worker/FactoryBean.java
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * Copyright (C) 2013 The University of Manchester
- *
- * See the file "LICENSE" for license terms.
- */
-package org.taverna.server.master.worker;
-
-import org.taverna.server.master.notification.atom.EventDAO;
-
-/**
- * What the remote run really needs of its factory.
- *
- * @author Donal Fellows
- */
-public interface FactoryBean {
- /**
- * @return Whether a run can actually be started at this time.
- */
- boolean isAllowingRunsToStart();
-
- /**
- * @return a handle to the master Atom event feed (<i>not</i> the per-run
- * feed)
- */
- EventDAO getMasterEventFeed();
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/worker/PasswordIssuer.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/worker/PasswordIssuer.java b/server-webapp/src/main/java/org/taverna/server/master/worker/PasswordIssuer.java
deleted file mode 100644
index d3c5b8a..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/worker/PasswordIssuer.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package org.taverna.server.master.worker;
-
-import java.security.NoSuchAlgorithmException;
-import java.security.SecureRandom;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-/**
- * A simple password issuing bean.
- *
- * @author Donal Fellows
- */
-public class PasswordIssuer {
- private static final char[] ALPHABET = { 'a', 'b', 'c', 'd', 'e', 'f', 'g',
- 'h', 'i', 'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r', 's', 't',
- 'u', 'v', 'w', 'x', 'y', 'z', 'A', 'B', 'C', 'D', 'E', 'F', 'G',
- 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T',
- 'U', 'V', 'W', 'X', 'Y', 'Z', '1', '2', '3', '4', '5', '6', '7',
- '8', '9', '0', '!', '@', '#', '$', '%', '^', '&', '*', '(', ')',
- ',', '.', '<', '>', '/', '?', ':', ';', '-', '_', '+', '[', ']',
- '{', '}', '`', '~' };
- private Log log = LogFactory.getLog("Taverna.Server.Worker");
- private SecureRandom r;
- private int length;
-
- public PasswordIssuer() {
- r = new SecureRandom();
- log.info("constructing passwords with " + r.getAlgorithm());
- setLength(8);
- }
-
- public PasswordIssuer(String algorithm) throws NoSuchAlgorithmException {
- r = SecureRandom.getInstance(algorithm);
- log.info("constructing passwords with " + r.getAlgorithm());
- setLength(8);
- }
-
- public void setLength(int length) {
- this.length = length;
- log.info("issued password will be " + this.length
- + " symbols chosen from " + ALPHABET.length);
- }
-
- /**
- * Issue a password.
- *
- * @return The new password.
- */
- public String issue() {
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < length; i++)
- sb.append(ALPHABET[r.nextInt(ALPHABET.length)]);
- log.info("issued new password of length " + sb.length());
- return sb.toString();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyImpl.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyImpl.java b/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyImpl.java
deleted file mode 100644
index f5613c7..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyImpl.java
+++ /dev/null
@@ -1,158 +0,0 @@
-/*
- * 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.identity.WorkflowInternalAuthProvider.PREFIX;
-
-import java.net.URI;
-import java.util.List;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.springframework.beans.factory.annotation.Required;
-import org.springframework.security.core.Authentication;
-import org.springframework.security.core.GrantedAuthority;
-import org.springframework.security.core.context.SecurityContextHolder;
-import org.taverna.server.master.common.Roles;
-import org.taverna.server.master.common.Workflow;
-import org.taverna.server.master.exceptions.NoCreateException;
-import org.taverna.server.master.exceptions.NoDestroyException;
-import org.taverna.server.master.exceptions.NoUpdateException;
-import org.taverna.server.master.interfaces.Policy;
-import org.taverna.server.master.interfaces.TavernaRun;
-import org.taverna.server.master.interfaces.TavernaSecurityContext;
-import org.taverna.server.master.utils.UsernamePrincipal;
-
-/**
- * Basic policy implementation that allows any workflow to be instantiated by
- * any user, but which does not permit users to access each others workflow
- * runs. It also imposes a global limit on the number of workflow runs at once.
- *
- * @author Donal Fellows
- */
-class PolicyImpl implements Policy {
- Log log = LogFactory.getLog("Taverna.Server.Worker.Policy");
- private PolicyLimits limits;
- private RunDBSupport runDB;
-
- @Required
- public void setLimits(PolicyLimits limits) {
- this.limits = limits;
- }
-
- @Required
- public void setRunDB(RunDBSupport runDB) {
- this.runDB = runDB;
- }
-
- @Override
- public int getMaxRuns() {
- return limits.getMaxRuns();
- }
-
- @Override
- public Integer getMaxRuns(UsernamePrincipal user) {
- return null;
- }
-
- @Override
- public int getOperatingLimit() {
- return limits.getOperatingLimit();
- }
-
- @Override
- public List<URI> listPermittedWorkflowURIs(UsernamePrincipal user) {
- return limits.getPermittedWorkflowURIs();
- }
-
- private boolean isSelfAccess(String runId) {
- Authentication auth = SecurityContextHolder.getContext()
- .getAuthentication();
- boolean self = false;
- String id = null;
- for (GrantedAuthority a : auth.getAuthorities()) {
- String aa = a.getAuthority();
- if (aa.equals(Roles.SELF)) {
- self = true;
- continue;
- }
- if (!aa.startsWith(PREFIX))
- continue;
- id = aa.substring(PREFIX.length());
- }
- return self && runId.equals(id);
- }
-
- @Override
- public boolean permitAccess(UsernamePrincipal user, TavernaRun run) {
- String username = user.getName();
- TavernaSecurityContext context = run.getSecurityContext();
- if (context.getOwner().getName().equals(username)) {
- if (log.isDebugEnabled())
- log.debug("granted access by " + user.getName() + " to "
- + run.getId());
- return true;
- }
- if (isSelfAccess(run.getId())) {
- if (log.isDebugEnabled())
- log.debug("access by workflow to itself: " + run.getId());
- return true;
- }
- if (log.isDebugEnabled())
- log.debug("considering access by " + user.getName() + " to "
- + run.getId());
- return context.getPermittedReaders().contains(username);
- }
-
- @Override
- public void permitCreate(UsernamePrincipal user, Workflow workflow)
- throws NoCreateException {
- if (user == null)
- throw new NoCreateException(
- "anonymous workflow creation not allowed");
- if (runDB.countRuns() >= getMaxRuns())
- throw new NoCreateException("server load exceeded; please wait");
- }
-
- @Override
- public synchronized void permitDestroy(UsernamePrincipal user, TavernaRun run)
- throws NoDestroyException {
- if (user == null)
- throw new NoDestroyException();
- String username = user.getName();
- TavernaSecurityContext context = run.getSecurityContext();
- if (context.getOwner() == null
- || context.getOwner().getName().equals(username))
- return;
- if (!context.getPermittedDestroyers().contains(username))
- throw new NoDestroyException();
- }
-
- @Override
- public void permitUpdate(UsernamePrincipal user, TavernaRun run)
- throws NoUpdateException {
- if (user == null)
- throw new NoUpdateException(
- "workflow run not owned by you and you're not granted access");
- TavernaSecurityContext context = run.getSecurityContext();
- if (context.getOwner().getName().equals(user.getName()))
- return;
- if (isSelfAccess(run.getId())) {
- if (log.isDebugEnabled())
- log.debug("update access by workflow to itself: " + run.getId());
- return;
- }
- if (!context.getPermittedUpdaters().contains(user.getName()))
- throw new NoUpdateException(
- "workflow run not owned by you and you're not granted access");
- }
-
- @Override
- public void setPermittedWorkflowURIs(UsernamePrincipal user,
- List<URI> permitted) {
- limits.setPermittedWorkflowURIs(permitted);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-server/blob/27cbb9cb/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyLimits.java
----------------------------------------------------------------------
diff --git a/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyLimits.java b/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyLimits.java
deleted file mode 100644
index 8cbc7ea..0000000
--- a/server-webapp/src/main/java/org/taverna/server/master/worker/PolicyLimits.java
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@@ -1,43 +0,0 @@
-/*
- * Copyright (C) 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;
-
-/**
- * The worker policy delegates certain limits to the state model of the
- * particular worker.
- *
- * @author Donal Fellows
- */
-public interface PolicyLimits {
- /**
- * @return the maximum number of extant workflow runs in any state
- */
- int getMaxRuns();
-
- /**
- * @return the maximum number of workflow runs in the
- * {@linkplain Status#Operating operating} state.
- */
- int getOperatingLimit();
-
- /**
- * @return the list of URIs to workflows that may be used to create workflow
- * runs. If empty or <tt>null</tt>, no restriction is present.
- */
- List<URI> getPermittedWorkflowURIs();
-
- /**
- * @param permitted
- * the list of URIs to workflows that may be used to create
- * workflow runs.
- */
- void setPermittedWorkflowURIs(List<URI> permitted);
-}