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From vjapa...@apache.org
Subject svn commit: r1554701 [1/2] - in /ctakes/branches/ytex: ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ ctakes-ytex-uima/ ctakes-ytex-uima/conceptGraph/ ctakes-ytex-uima/desc/a...
Date Wed, 01 Jan 2014 23:39:31 GMT
Author: vjapache
Date: Wed Jan  1 23:39:31 2014
New Revision: 1554701

URL: http://svn.apache.org/r1554701
Log:
add unit tests
fix ehcache/hiberante warnings
simplify concept graph path resolution

Removed:
    ctakes/branches/ytex/ctakes-ytex-uima/conceptGraph/
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/YTEXPipelineNoDBConsumer.xml
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/DBCollectionReaderTest.java
Modified:
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example
    ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
    ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml
    ctakes/branches/ytex/ctakes-ytex-uima/pom.xml
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBConsumerTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
    ctakes/branches/ytex/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
    ctakes/branches/ytex/ctakes-ytex/README
    ctakes/branches/ytex/ctakes-ytex/scripts/build-classpath.xml
    ctakes/branches/ytex/ctakes-ytex/scripts/data/hsql/umls/create_view.sql
    ctakes/branches/ytex/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/dao/DBUtil.java
    ctakes/branches/ytex/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDao.java
    ctakes/branches/ytex/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/dao/ConceptDaoImpl.java
    ctakes/branches/ytex/ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/ConceptSimilarityServiceImpl.java
    ctakes/branches/ytex/ctakes-ytex/src/test/java/org/apache/ctakes/ytex/ConceptDaoTest.java

Modified: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-datasource.xml Wed Jan  1 23:39:31 2014
@@ -38,7 +38,8 @@ http://www.springframework.org/schema/ao
 				<prop key="hibernate.jdbc.batch_size">${hibernate.jdbc.batch_size}</prop>
 				<prop key="hibernate.order_inserts">${hibernate.order_inserts}</prop>
 				<prop key="hibernate.order_updates">${hibernate.order_updates}</prop>
-				<prop key="hibernate.cache.provider_configuration_file_resource_path">/org/apache/ctakes/ytex/kernel/ehcache.xml</prop>
+				<prop key="net.sf.ehcache.configurationResourceName">org/apache/ctakes/ytex/kernel/ehcache.xml</prop>
+				<prop key="hibernate.cache.provider_configuration_file_resource_path">org/apache/ctakes/ytex/kernel/ehcache.xml</prop>
 				<!-- <prop key="hibernate.connection.isolation">1</prop> -->
 			</props>
 		</property>

Modified: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/beans-kernel-sim.xml Wed Jan  1 23:39:31 2014
@@ -6,12 +6,19 @@
 http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
 http://www.springframework.org/schema/tx http://www.springframework.org/schema/tx/spring-tx-2.5.xsd
 http://www.springframework.org/schema/aop http://www.springframework.org/schema/aop/spring-aop-2.5.xsd">
-	<bean id="conceptSimilarityService" class="org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl"
+	<bean id="conceptSimilarityService"
+		class="org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl"
 		init-method="init">
 		<property name="transactionManager" ref="transactionManager" />
 		<property name="conceptDao" ref="conceptDao" />
 		<property name="classifierEvaluationDao" ref="classifierEvaluationDao" />
 		<property name="cacheManager" ref="cacheManager" />
+		<property name="lcsCache">
+			<bean class="net.sf.ehcache.Cache" factory-bean="cacheManager"
+				factory-method="getCache">
+				<constructor-arg value="lcsCache" />
+			</bean>
+		</property>
 		<property name="pageRankService" ref="pageRankService" />
 		<property name="corpusName" value="${ytex.corpusName}" />
 		<property name="conceptGraphName" value="${ytex.conceptGraphName}" />
@@ -28,21 +35,25 @@ http://www.springframework.org/schema/ao
 		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
 		<property name="cacheManager" ref="cacheManager" />
 	</bean>
-	<bean id="abstractSemanticSimKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel"
+	<bean id="abstractSemanticSimKernel"
+		class="org.apache.ctakes.ytex.kernel.evaluator.SemanticSimKernel"
 		abstract="true">
 		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
 		<property name="cacheManager" ref="cacheManager" />
 	</bean>
-	<bean id="mainSuiSemanticTypeKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
+	<bean id="mainSuiSemanticTypeKernel"
+		class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
 		init-method="init">
 		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
 	</bean>
-	<bean id="tuiSemanticTypeKernel" class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
+	<bean id="tuiSemanticTypeKernel"
+		class="org.apache.ctakes.ytex.kernel.evaluator.SemanticTypeKernel"
 		init-method="init">
 		<property name="mode" value="TUI" />
 		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
 	</bean>
-	<bean id="wordSenseDisambiguator" class="org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl">
+	<bean id="wordSenseDisambiguator"
+		class="org.apache.ctakes.ytex.kernel.wsd.WordSenseDisambiguatorImpl">
 		<property name="conceptSimilarityService" ref="conceptSimilarityService" />
 	</bean>
 </beans>
\ No newline at end of file

Modified: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/kernel/ehcache.xml Wed Jan  1 23:39:31 2014
@@ -1,1065 +1,17 @@
 <?xml version="1.0" encoding="UTF-8"?>
 
-<!--
-CacheManager Configuration
-==========================
-An ehcache.xml corresponds to a single CacheManager.
-
-See instructions below or the ehcache schema (ehcache.xsd) on how to configure.
-
-System property tokens can be specified in this file which are replaced when the configuration
-is loaded. For example multicastGroupPort=${multicastGroupPort} can be replaced with the
-System property either from an environment variable or a system property specified with a
-command line switch such as -DmulticastGroupPort=4446. Another example, useful for Terracotta
-server based deployments is <terracottaConfig url="${serverAndPort}"/ and specify a command line
-switch of -Dserver36:9510
-
-The attributes of <ehcache> are:
-* name - an optional name for the CacheManager.  The name is optional and primarily used
-for documentation or to distinguish Terracotta clustered cache state.  With Terracotta
-clustered caches, a combination of CacheManager name and cache name uniquely identify a
-particular cache store in the Terracotta clustered memory.
-* updateCheck - an optional boolean flag specifying whether this CacheManager should check
-for new versions of Ehcache over the Internet.  If not specified, updateCheck="true".
-* dynamicConfig - an optional setting that can be used to disable dynamic configuration of caches
-associated with this CacheManager.  By default this is set to true - i.e. dynamic configuration
-is enabled.  Dynamically configurable caches can have their TTI, TTL and maximum disk and
-in-memory capacity changed at runtime through the cache's configuration object.
-* monitoring - an optional setting that determines whether the CacheManager should
-automatically register the SampledCacheMBean with the system MBean server.
-
-Currently, this monitoring is only useful when using Terracotta clustering and using the
-Terracotta Developer Console. With the "autodetect" value, the presence of Terracotta clustering
-will be detected and monitoring, via the Developer Console, will be enabled. Other allowed values
-are "on" and "off".  The default is "autodetect". This setting does not perform any function when
-used with JMX monitors.
--->
-<ehcache xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:noNamespaceSchemaLocation="ehcache.xsd"
-         name="org.apache.ctakes.ytex.kernel"
-         updateCheck="false" monitoring="autodetect"
-         dynamicConfig="true">
-
-    <!--
-    DiskStore configuration
-    =======================
-
-    The diskStore element is optional. To turn off disk store path creation, comment out the diskStore
-    element below.
-
-    Configure it if you have overflowToDisk or diskPersistent enabled for any cache.
-
-    If it is not configured, and a cache is created which requires a disk store, a warning will be
-     issued and java.io.tmpdir will automatically be used.
-
-    diskStore has only one attribute - "path". It is the path to the directory where
-    .data and .index files will be created.
-
-    If the path is one of the following Java System Property it is replaced by its value in the
-    running VM. For backward compatibility these should be specified without being enclosed in the ${token}
-    replacement syntax.
-
-    The following properties are translated:
-    * user.home - User's home directory
-    * user.dir - User's current working directory
-    * java.io.tmpdir - Default temp file path
-    * ehcache.disk.store.dir - A system property you would normally specify on the command line
-      e.g. java -Dehcache.disk.store.dir=/u01/myapp/diskdir ...
-
-    Subdirectories can be specified below the property e.g. java.io.tmpdir/one
-
-    -->
-    <diskStore path="java.io.tmpdir"/>
-    
-    <!-- 
-    TransactionManagerLookup configuration
-    ======================================
-    This class is used by ehcache to lookup the JTA TransactionManager use in the application
-    using an XA enabled ehcache. If no class is specified then DefaultTransactionManagerLookup
-    will find the TransactionManager in the following order
-
-     *GenericJNDI (i.e. jboss, where the property jndiName controls the name of the
-                    TransactionManager object to look up)
-     *Bitronix
-     *Atomikos
-    
-    You can provide you own lookup class that implements the
-    net.sf.ehcache.transaction.manager.TransactionManagerLookup interface. 
-
-    <transactionManagerLookup class="net.sf.ehcache.transaction.manager.DefaultTransactionManagerLookup"
-                              properties="jndiName=java:/TransactionManager" propertySeparator=";"/>
-    -->
- 
-
-    <!--
-    CacheManagerEventListener
-    =========================
-    Specifies a CacheManagerEventListenerFactory which is notified when Caches are added
-    or removed from the CacheManager.
-
-    The attributes of CacheManagerEventListenerFactory are:
-    * class - a fully qualified factory class name
-    * properties - comma separated properties having meaning only to the factory.
-
-    Sets the fully qualified class name to be registered as the CacheManager event listener.
-
-    The events include:
-    * adding a Cache
-    * removing a Cache
-
-    Callbacks to listener methods are synchronous and unsynchronized. It is the responsibility
-    of the implementer to safely handle the potential performance and thread safety issues
-    depending on what their listener is doing.
-
-    If no class is specified, no listener is created. There is no default.
-    -->
-    <cacheManagerEventListenerFactory class="" properties=""/>
-
-
-    <!--
-    CacheManagerPeerProvider
-    ========================
-    (For distributed operation)
-
-    Specifies a CacheManagerPeerProviderFactory which will be used to create a
-    CacheManagerPeerProvider, which discovers other CacheManagers in the cluster.
-
-    One or more providers can be configured. The first one in the ehcache.xml is the default, which is used
-    for replication and bootstrapping.
-
-    The attributes of cacheManagerPeerProviderFactory are:
-    * class - a fully qualified factory class name
-    * properties - comma separated properties having meaning only to the factory.
-
-    Providers are available for RMI, JGroups and JMS as shown following.
-
-    RMICacheManagerPeerProvider
-    +++++++++++++++++++++++++++
-
-    Ehcache comes with a built-in RMI-based distribution system with two means of discovery of
-    CacheManager peers participating in the cluster:
-    * automatic, using a multicast group. This one automatically discovers peers and detects
-      changes such as peers entering and leaving the group
-    * manual, using manual rmiURL configuration. A hardcoded list of peers is provided at
-      configuration time.
-
-    Configuring Automatic Discovery:
-    Automatic discovery is configured as per the following example:
-    <cacheManagerPeerProviderFactory
-                        class="net.sf.ehcache.distribution.RMICacheManagerPeerProviderFactory"
-                        properties="hostName=fully_qualified_hostname_or_ip,
-                                    peerDiscovery=automatic, multicastGroupAddress=230.0.0.1,
-                                    multicastGroupPort=4446, timeToLive=32"/>
-
-    Valid properties are:
-    * peerDiscovery (mandatory) - specify "automatic"
-    * multicastGroupAddress (mandatory) - specify a valid multicast group address
-    * multicastGroupPort (mandatory) - specify a dedicated port for the multicast heartbeat
-      traffic
-    * timeToLive - specify a value between 0 and 255 which determines how far the packets will
-      propagate.
-
-      By convention, the restrictions are:
-      0   - the same host
-      1   - the same subnet
-      32  - the same site
-      64  - the same region
-      128 - the same continent
-      255 - unrestricted
-
-     * hostName - the hostname or IP of the interface to be used for sending and receiving multicast
-       packets (relevant to multi-homed hosts only)
-
-    Configuring Manual Discovery:
-    Manual discovery requires a unique configuration per host. It is contains a list of rmiURLs for
-    the peers, other than itself. So, if we have server1, server2 and server3 the configuration will
-    be:
-
-    In server1's configuration:
-    <cacheManagerPeerProviderFactory class=
-                          "net.sf.ehcache.distribution.RMICacheManagerPeerProviderFactory"
-                          properties="peerDiscovery=manual,
-                          rmiUrls=//server2:40000/sampleCache1|//server3:40000/sampleCache1
-                          | //server2:40000/sampleCache2|//server3:40000/sampleCache2"
-                          propertySeparator="," />
-
-    In server2's configuration:
-    <cacheManagerPeerProviderFactory class=
-                          "net.sf.ehcache.distribution.RMICacheManagerPeerProviderFactory"
-                          properties="peerDiscovery=manual,
-                          rmiUrls=//server1:40000/sampleCache1|//server3:40000/sampleCache1
-                          | //server1:40000/sampleCache2|//server3:40000/sampleCache2"
-                          propertySeparator="," />
-
-    In server3's configuration:
-    <cacheManagerPeerProviderFactory class=
-                          "net.sf.ehcache.distribution.RMICacheManagerPeerProviderFactory"
-                          properties="peerDiscovery=manual,
-                          rmiUrls=//server1:40000/sampleCache1|//server2:40000/sampleCache1
-                          | //server1:40000/sampleCache2|//server2:40000/sampleCache2"
-                          propertySeparator="," />
-
-
-    Valid properties are:
-    * peerDiscovery (mandatory) - specify "manual"
-    * rmiUrls (mandatory) - specify a pipe separated list of rmiUrls, in the form
-                            //hostname:port
-    * hostname (optional) - the hostname is the hostname of the remote CacheManager peer. The port is the listening
-      port of the RMICacheManagerPeerListener of the remote CacheManager peer.
-
-    JGroupsCacheManagerPeerProvider
-    +++++++++++++++++++++++++++++++
-    <cacheManagerPeerProviderFactory
-         class="net.sf.ehcache.distribution.jgroups.JGroupsCacheManagerPeerProviderFactory"
-         properties="channel=ehcache^connect=UDP(mcast_addr=231.12.21.132;mcast_port=45566;ip_ttl=32;
-         mcast_send_buf_size=150000;mcast_recv_buf_size=80000):
-         PING(timeout=2000;num_initial_members=6):
-         MERGE2(min_interval=5000;max_interval=10000):
-         FD_SOCK:VERIFY_SUSPECT(timeout=1500):
-         pbcast.NAKACK(gc_lag=10;retransmit_timeout=3000):
-         UNICAST(timeout=5000):
-         pbcast.STABLE(desired_avg_gossip=20000):
-         FRAG:
-         pbcast.GMS(join_timeout=5000;join_retry_timeout=2000;shun=false;print_local_addr=false)"
-         propertySeparator="^"
-     />
-     JGroups configuration is done by providing a connect string using connect= as in the above example which uses
-     multicast, or since version 1.4, a file= to specify the location of a JGroups configuration file.
-
-     If neither a connect or file property is specified, the default JGroups JChannel will be used.
-
-     Multiple JGroups clusters may be run on the same network by specifying a different CacheManager name. The name
-     is used as the cluster name.
-
-     Since version 1.4 you can specify a channelName to avoid conflicts.
-
-
-    JMSCacheManagerPeerProviderFactory
-    ++++++++++++++++++++++++++++++++++
-    <cacheManagerPeerProviderFactory
-            class="net.sf.ehcache.distribution.jms.JMSCacheManagerPeerProviderFactory"
-            properties="..."
-            propertySeparator=","
-            />
-
-    The JMS PeerProviderFactory uses JNDI to maintain message queue independence. Refer to the manual for full configuration
-    examples using ActiveMQ and Open Message Queue.
-
-    Valid properties are:
-    * initialContextFactoryName (mandatory) - the name of the factory used to create the message queue initial context.
-    * providerURL (mandatory) - the JNDI configuration information for the service provider to use.
-    * topicConnectionFactoryBindingName (mandatory) - the JNDI binding name for the TopicConnectionFactory
-    * topicBindingName (mandatory) - the JNDI binding name for the topic name
-    * getQueueBindingName (mandatory only if using jmsCacheLoader) - the JNDI binding name for the queue name
-    * securityPrincipalName - the JNDI java.naming.security.principal
-    * securityCredentials - the JNDI java.naming.security.credentials
-    * urlPkgPrefixes - the JNDI java.naming.factory.url.pkgs
-    * userName - the user name to use when creating the TopicConnection to the Message Queue
-    * password - the password to use when creating the TopicConnection to the Message Queue
-    * acknowledgementMode - the JMS Acknowledgement mode for both publisher and subscriber. The available choices are
-                            AUTO_ACKNOWLEDGE, DUPS_OK_ACKNOWLEDGE and SESSION_TRANSACTED. The default is AUTO_ACKNOWLEDGE.
-    <cacheManagerPeerProviderFactory
-            class="net.sf.ehcache.distribution.RMICacheManagerPeerProviderFactory"
-            properties="peerDiscovery=automatic,
-                        multicastGroupAddress=230.0.0.1,
-                        multicastGroupPort=4446, timeToLive=1"
-            propertySeparator=","
-            />
-    -->
-
-
-    <!--
-    CacheManagerPeerListener
-    ========================
-    (Enable for distributed operation)
-
-    Specifies a CacheManagerPeerListenerFactory which will be used to create a
-    CacheManagerPeerListener, which listens for messages from cache replicators participating in the cluster.
-
-    The attributes of cacheManagerPeerListenerFactory are:
-    class - a fully qualified factory class name
-    properties - comma separated properties having meaning only to the factory.
-
-    Ehcache comes with a built-in RMI-based distribution system. The listener component is
-    RMICacheManagerPeerListener which is configured using
-    RMICacheManagerPeerListenerFactory. It is configured as per the following example:
-
-    <cacheManagerPeerListenerFactory
-        class="net.sf.ehcache.distribution.RMICacheManagerPeerListenerFactory"
-        properties="hostName=fully_qualified_hostname_or_ip,
-                    port=40001,
-                    remoteObjectPort=40002,
-                    socketTimeoutMillis=120000"
-                    propertySeparator="," />
-
-    All properties are optional. They are:
-    * hostName - the hostName of the host the listener is running on. Specify
-      where the host is multihomed and you want to control the interface over which cluster
-      messages are received. Defaults to the host name of the default interface if not
-      specified.
-    * port - the port the RMI Registry listener listens on. This defaults to a free port if not specified.
-    * remoteObjectPort - the port number on which the remote objects bound in the registry receive calls.
-                         This defaults to a free port if not specified.
-    * socketTimeoutMillis - the number of ms client sockets will stay open when sending
-      messages to the listener. This should be long enough for the slowest message.
-      If not specified it defaults to 120000ms.
-
-    <cacheManagerPeerListenerFactory
-            class="net.sf.ehcache.distribution.RMICacheManagerPeerListenerFactory"/>
-    -->
-
-    <!--
-    TerracottaConfig
-    ========================
-    (Enable for Terracotta clustered operation)
-
-    Note: You need to install and run one or more Terracotta servers to use Terracotta clustering.
-    See http://www.terracotta.org/web/display/orgsite/Download.
-
-    Specifies a TerracottaConfig which will be used to configure the Terracotta
-    runtime for this CacheManager.
-
-    Configuration can be specified in two main ways: by reference to a source of
-    configuration or by use of an embedded Terracotta configuration file.
-
-    To specify a reference to a source (or sources) of configuration, use the url
-    attribute.  The url attribute must contain a comma-separated list of:
-    * path to Terracotta configuration file (usually named tc-config.xml)
-    * URL to Terracotta configuration file
-    * <server host>:<port> of running Terracotta Server instance
-
-    Simplest example for pointing to a Terracotta server on this machine:
-    <terracottaConfig url="localhost:9510"/>
-    
-    This element has one attribute "rejoin" which can take values of either "true" or "false"
-    <terracottaConfig rejoin="true" url="localhost:9510" />
-    By default, this attribute is true.
-    If rejoin is true, all Terracotta Clustered caches have to be configured with nonstop.
-    Without rejoin, if the Terracotta Server is restarted the client cannot connect back to the
-    server. When enabled, this will enable the client to connect to the new cluster without the 
-    need to restart the node.
-
-    Example using a path to Terracotta configuration file:
-    <terracottaConfig url="/app/config/tc-config.xml"/>
-
-    Example using a URL to a Terracotta configuration file:
-    <terracottaConfig url="http://internal/ehcache/app/tc-config.xml"/>
-
-    Example using multiple Terracotta server instance URLs (for fault tolerance):
-    <terracottaConfig url="host1:9510,host2:9510,host3:9510"/>
-
-    To embed a Terracotta configuration file within the ehcache configuration, simply
-    place a normal Terracotta XML config within the <terracottaConfig> element.
-
-    Example:
-    <terracottaConfig>
-        <tc-config>
-            <servers>
-                <server host="server1" name="s1"/>
-                <server host="server2" name="s2"/>
-            </servers>
-            <clients>
-                <logs>app/logs-%i</logs>
-            </clients>
-        </tc-config>
-    </terracottaConfig>
-
-    For more information on the Terracotta configuration, see the Terracotta documentation.
-    -->
-
-    <!--
-    Cache configuration
-    ===================
-
-    The following attributes are required.
-
-    name:
-    Sets the name of the cache. This is used to identify the cache. It must be unique.
-
-    maxElementsInMemory:
-    Sets the maximum number of objects that will be created in memory.  0 = no limit.
-    In practice no limit means Integer.MAX_SIZE (2147483647) unless the cache is distributed
-    with a Terracotta server in which case it is limited by resources.
-
-    maxElementsOnDisk:
-    Sets the maximum number of objects that will be maintained in the DiskStore
-    The default value is zero, meaning unlimited.
-
-    eternal:
-    Sets whether elements are eternal. If eternal,  timeouts are ignored and the
-    element is never expired.
-
-    overflowToDisk:
-    Sets whether elements can overflow to disk when the memory store
-    has reached the maxInMemory limit.
-
-    The following attributes and elements are optional.
-
-    overflowToOffHeap:
-    (boolean) This feature is available only in enterprise versions of Ehcache.
-    When set to true, enables the cache to utilize off-heap memory
-    storage to improve performance. Off-heap memory is not subject to Java
-    GC. The default value is false.
-
-    maxMemoryOffHeap:
-    (string) This feature is available only in enterprise versions of Ehcache.
-    Sets the amount of off-heap memory available to the cache.
-    This attribute's values are given as <number>k|K|m|M|g|G|t|T for
-    kilobytes (k|K), megabytes (m|M), gigabytes (g|G), or terabytes
-    (t|T). For example, maxMemoryOffHeap="2g" allots 2 gigabytes to
-    off-heap memory.
-
-    This setting is in effect only if overflowToOffHeap is true.
-
-    Note that it is recommended to set maxElementsInMemory to at least 100 elements
-    when using an off-heap store, otherwise performance will be seriously degraded,
-    and a warning will be logged.
-
-    The minimum amount that can be allocated is 128MB. There is no maximum.
-
-    timeToIdleSeconds:
-    Sets the time to idle for an element before it expires.
-    i.e. The maximum amount of time between accesses before an element expires
-    Is only used if the element is not eternal.
-    Optional attribute. A value of 0 means that an Element can idle for infinity.
-    The default value is 0.
-
-    timeToLiveSeconds:
-    Sets the time to live for an element before it expires.
-    i.e. The maximum time between creation time and when an element expires.
-    Is only used if the element is not eternal.
-    Optional attribute. A value of 0 means that and Element can live for infinity.
-    The default value is 0.
-
-    diskPersistent:
-    Whether the disk store persists between restarts of the Virtual Machine.
-    The default value is false.
-
-    diskExpiryThreadIntervalSeconds:
-    The number of seconds between runs of the disk expiry thread. The default value
-    is 120 seconds.
-
-    diskSpoolBufferSizeMB:
-    This is the size to allocate the DiskStore for a spool buffer. Writes are made
-    to this area and then asynchronously written to disk. The default size is 30MB.
-    Each spool buffer is used only by its cache. If you get OutOfMemory errors consider
-    lowering this value. To improve DiskStore performance consider increasing it. Trace level
-    logging in the DiskStore will show if put back ups are occurring.
-
-    clearOnFlush:
-    whether the MemoryStore should be cleared when flush() is called on the cache.
-    By default, this is true i.e. the MemoryStore is cleared.
-
-    statistics:
-    Whether to collect statistics. Note that this should be turned on if you are using
-    the Ehcache Monitor. By default statistics is turned off to favour raw performance.
-    To enable set statistics="true"
-
-    memoryStoreEvictionPolicy:
-    Policy would be enforced upon reaching the maxElementsInMemory limit. Default
-    policy is Least Recently Used (specified as LRU). Other policies available -
-    First In First Out (specified as FIFO) and Less Frequently Used
-    (specified as LFU)
-
-    copyOnRead:
-    Whether an Element is copied when being read from a cache.
-    By default this is false.
-
-    copyOnWrite:
-    Whether an Element is copied when being added to the cache.
-    By default this is false.
-
-    Cache elements can also contain sub elements which take the same format of a factory class
-    and properties. Defined sub-elements are:
-
-    * cacheEventListenerFactory - Enables registration of listeners for cache events, such as
-      put, remove, update, and expire.
-
-    * bootstrapCacheLoaderFactory - Specifies a BootstrapCacheLoader, which is called by a
-      cache on initialisation to prepopulate itself.
-
-    * cacheExtensionFactory - Specifies a CacheExtension, a generic mechanism to tie a class
-      which holds a reference to a cache to the cache lifecycle.
-
-    * cacheExceptionHandlerFactory - Specifies a CacheExceptionHandler, which is called when
-      cache exceptions occur.
-
-    * cacheLoaderFactory - Specifies a CacheLoader, which can be used both asynchronously and
-      synchronously to load objects into a cache. More than one cacheLoaderFactory element
-      can be added, in which case the loaders form a chain which are executed in order. If a
-      loader returns null, the next in chain is called.
-
-    * copyStrategy - Specifies a fully qualified class which implements
-      net.sf.ehcache.store.compound.CopyStrategy. This strategy will be used for copyOnRead
-      and copyOnWrite in place of the default which is serialization.
-
-
-    Cache Event Listeners
-    +++++++++++++++++++++
-
-    All cacheEventListenerFactory elements can take an optional property listenFor that describes
-    which events will be delivered in a clustered environment.  The listenFor attribute has the
-    following allowed values:
-
-    * all - the default is to deliver all local and remote events
-    * local - deliver only events originating in the current node
-    * remote - deliver only events originating in other nodes
-
-    Example of setting up a logging listener for local cache events:
-
-    <cacheEventListenerFactory class="my.company.log.CacheLogger"
-        listenFor="local" />
-
-
-    RMI Cache Replication
-    +++++++++++++++++++++
-
-    Each cache that will be distributed needs to set a cache event listener which replicates
-    messages to the other CacheManager peers. For the built-in RMI implementation this is done
-    by adding a cacheEventListenerFactory element of type RMICacheReplicatorFactory to each
-    distributed cache's configuration as per the following example:
-
-    <cacheEventListenerFactory class="net.sf.ehcache.distribution.RMICacheReplicatorFactory"
-         properties="replicateAsynchronously=true,
-         replicatePuts=true,
-         replicatePutsViaCopy=false,
-         replicateUpdates=true,
-         replicateUpdatesViaCopy=true,
-         replicateRemovals=true
-         asynchronousReplicationIntervalMillis=<number of milliseconds"
-         propertySeparator="," />
-
-    The RMICacheReplicatorFactory recognises the following properties:
-
-    * replicatePuts=true|false - whether new elements placed in a cache are
-      replicated to others. Defaults to true.
-
-    * replicatePutsViaCopy=true|false - whether the new elements are
-      copied to other caches (true), or whether a remove message is sent. Defaults to true.
-
-    * replicateUpdates=true|false - whether new elements which override an
-      element already existing with the same key are replicated. Defaults to true.
-
-    * replicateRemovals=true - whether element removals are replicated. Defaults to true.
-
-    * replicateAsynchronously=true | false - whether replications are
-      asynchronous (true) or synchronous (false). Defaults to true.
-
-    * replicateUpdatesViaCopy=true | false - whether the new elements are
-      copied to other caches (true), or whether a remove message is sent. Defaults to true.
-
-    * asynchronousReplicationIntervalMillis=<number of milliseconds> - The asynchronous
-      replicator runs at a set interval of milliseconds. The default is 1000. The minimum
-      is 10. This property is only applicable if replicateAsynchronously=true
-
-
-    JGroups Replication
-    +++++++++++++++++++
-
-    For the Jgroups replication this is done with:
-    <cacheEventListenerFactory class="net.sf.ehcache.distribution.jgroups.JGroupsCacheReplicatorFactory"
-                            properties="replicateAsynchronously=true, replicatePuts=true,
-               replicateUpdates=true, replicateUpdatesViaCopy=false,
-               replicateRemovals=true,asynchronousReplicationIntervalMillis=1000"/>
-    This listener supports the same properties as the RMICacheReplicationFactory.
-
-
-    JMS Replication
-    +++++++++++++++
-
-    For JMS-based replication this is done with:
-    <cacheEventListenerFactory
-          class="net.sf.ehcache.distribution.jms.JMSCacheReplicatorFactory"
-          properties="replicateAsynchronously=true,
-                       replicatePuts=true,
-                       replicateUpdates=true,
-                       replicateUpdatesViaCopy=true,
-                       replicateRemovals=true,
-                       asynchronousReplicationIntervalMillis=1000"
-           propertySeparator=","/>
-
-    This listener supports the same properties as the RMICacheReplicationFactory.
-
-    Cluster Bootstrapping
-    +++++++++++++++++++++
-
-    Bootstrapping a cluster may use a different mechanism to replication. e.g you can mix
-    JMS replication with bootstrap via RMI - just make sure you have the cacheManagerPeerProviderFactory
-    and cacheManagerPeerListenerFactory configured.
-
-    There are two bootstrapping mechanisms: RMI and JGroups.
-
-    RMI Bootstrap
-
-    The RMIBootstrapCacheLoader bootstraps caches in clusters where RMICacheReplicators are
-    used. It is configured as per the following example:
-
-    <bootstrapCacheLoaderFactory
-        class="net.sf.ehcache.distribution.RMIBootstrapCacheLoaderFactory"
-        properties="bootstrapAsynchronously=true, maximumChunkSizeBytes=5000000"
-        propertySeparator="," />
-
-    The RMIBootstrapCacheLoaderFactory recognises the following optional properties:
-
-    * bootstrapAsynchronously=true|false - whether the bootstrap happens in the background
-      after the cache has started. If false, bootstrapping must complete before the cache is
-      made available. The default value is true.
-
-    * maximumChunkSizeBytes=<integer> - Caches can potentially be very large, larger than the
-      memory limits of the VM. This property allows the bootstraper to fetched elements in
-      chunks. The default chunk size is 5000000 (5MB).
-
-    JGroups Bootstrap
-
-    Here is an example of bootstrap configuration using JGroups boostrap:
-
-    <bootstrapCacheLoaderFactory class="net.sf.ehcache.distribution.jgroups.JGroupsBootstrapCacheLoaderFactory"
-                                    properties="bootstrapAsynchronously=true"/>
-
-    The configuration properties are the same as for RMI above. Note that JGroups bootstrap only supports
-    asynchronous bootstrap mode.
-
-
-    Cache Exception Handling
-    ++++++++++++++++++++++++
-
-    By default, most cache operations will propagate a runtime CacheException on failure. An
-    interceptor, using a dynamic proxy, may be configured so that a CacheExceptionHandler can
-    be configured to intercept Exceptions. Errors are not intercepted.
-
-    It is configured as per the following example:
-
-      <cacheExceptionHandlerFactory class="com.example.ExampleExceptionHandlerFactory"
-                                      properties="logLevel=FINE"/>
-
-    Caches with ExceptionHandling configured are not of type Cache, but are of type Ehcache only,
-    and are not available using CacheManager.getCache(), but using CacheManager.getEhcache().
-
-
-    Cache Loader
-    ++++++++++++
-
-    A default CacheLoader may be set which loads objects into the cache through asynchronous and
-    synchronous methods on Cache. This is different to the bootstrap cache loader, which is used
-    only in distributed caching.
-
-    It is configured as per the following example:
-
-        <cacheLoaderFactory class="com.example.ExampleCacheLoaderFactory"
-                                      properties="type=int,startCounter=10"/>
-
-    Transactions
-    ++++++++++++
-
-    To enable an ehcache as transactions, set the transactionalMode
-
-    transactionalMode="xa" - high performance JTA/XA implementation
-    transactionalMode="xa_strict" - canonically correct JTA/XA implementation
-    transactionMode="local" - high performance local transactions involving caches only
-    transactionalMode="off" - the default, no transactions
-
-    If set, all cache operations will need to be done through transactions.
-
-    Cache Writer
-    ++++++++++++
-
-    A CacheWriter maybe be set to write to an underlying resource. Only one CacheWriter can be
-    been to a cache.
-
-    It is configured as per the following example for write-through:
-
-        <cacheWriter writeMode="write-through" notifyListenersOnException="true">
-            <cacheWriterFactory class="net.sf.ehcache.writer.TestCacheWriterFactory"
-                                properties="type=int,startCounter=10"/>
-        </cacheWriter>
-
-    And it is configured as per the following example for write-behind:
-
-        <cacheWriter writeMode="write-behind" minWriteDelay="1" maxWriteDelay="5"
-                     rateLimitPerSecond="5" writeCoalescing="true" writeBatching="true" writeBatchSize="1"
-                     retryAttempts="2" retryAttemptDelaySeconds="1">
-            <cacheWriterFactory class="net.sf.ehcache.writer.TestCacheWriterFactory"
-                                properties="type=int,startCounter=10"/>
-        </cacheWriter>
-
-    The cacheWriter element has the following attributes:
-    * writeMode: the write mode, write-through or write-behind
-
-    These attributes only apply to write-through mode:
-    * notifyListenersOnException: Sets whether to notify listeners when an exception occurs on a writer operation.
-
-    These attributes only apply to write-behind mode:
-    * minWriteDelay: Set the minimum number of seconds to wait before writing behind. If set to a value greater than 0,
-      it permits operations to build up in the queue. This is different from the maximum write delay in that by waiting
-      a minimum amount of time, work is always being built up. If the minimum write delay is set to zero and the
-      CacheWriter performs its work very quickly, the overhead of processing the write behind queue items becomes very
-      noticeable in a cluster since all the operations might be done for individual items instead of for a collection
-      of them.
-    * maxWriteDelay: Set the maximum number of seconds to wait before writing behind. If set to a value greater than 0,
-      it permits operations to build up in the queue to enable effective coalescing and batching optimisations.
-    * writeBatching: Sets whether to batch write operations. If set to true, writeAll and deleteAll will be called on
-      the CacheWriter rather than write and delete being called for each key. Resources such as databases can perform
-      more efficiently if updates are batched, thus reducing load.
-    * writeBatchSize: Sets the number of operations to include in each batch when writeBatching is enabled. If there are
-      less entries in the write-behind queue than the batch size, the queue length size is used.
-    * rateLimitPerSecond: Sets the maximum number of write operations to allow per second when writeBatching is enabled.
-    * writeCoalescing: Sets whether to use write coalescing. If set to true and multiple operations on the same key are
-      present in the write-behind queue, only the latest write is done, as the others are redundant.
-    * retryAttempts: Sets the number of times the operation is retried in the CacheWriter, this happens after the
-      original operation.
-    * retryAttemptDelaySeconds: Sets the number of seconds to wait before retrying an failed operation.
-
-    Cache Extension
-    +++++++++++++++
-
-    CacheExtensions are a general purpose mechanism to allow generic extensions to a Cache.
-    CacheExtensions are tied into the Cache lifecycle.
-
-    CacheExtensions are created using the CacheExtensionFactory which has a
-    <code>createCacheCacheExtension()</code> method which takes as a parameter a
-    Cache and properties. It can thus call back into any public method on Cache, including, of
-    course, the load methods.
-
-    Extensions are added as per the following example:
-
-         <cacheExtensionFactory class="com.example.FileWatchingCacheRefresherExtensionFactory"
-                             properties="refreshIntervalMillis=18000, loaderTimeout=3000,
-                                         flushPeriod=whatever, someOtherProperty=someValue ..."/>
-
-    Cache Decorator Factory
-    +++++++++++++++++++++++
-
-    Cache decorators can be configured directly in ehcache.xml. The decorators will be created and added to the CacheManager.
-    It accepts the name of a concrete class that extends net.sf.ehcache.constructs.CacheDecoratorFactory
-    The properties will be parsed according to the delimiter (default is comma ',') and passed to the concrete factory's
-    <code>createDecoratedEhcache(Ehcache cache, Properties properties)</code> method along with the reference to the owning cache.
-
-    It is configured as per the following example:
-
-        <cacheDecoratorFactory
-			class="net.sf.ehcache.constructs.nonstop.NonStopCacheDecoratorFactory"
-			properties="name=localReadsCacheDecorator, timeoutBehavior=localReads ..." />
-
-    Terracotta Clustering
-    +++++++++++++++++++++
-
-    Cache elements can also contain information about whether the cache can be clustered with Terracotta.
-    The <terracotta> sub-element has the following sub-elements:
-    
-    * Nonstop: Nonstop caches can be configured for Terracotta clustered caches. Sample:
-    	<cache name="terracottaClusteredCache">
-    		<terracotta>
-    			<nonstop enabled="true" immediateTimeout="true" timeoutMillis="15000">
-    				<timeoutBehavior type="exception" />
-    		</terracotta>
-    	</cache>
-    	All attributes and the sub-element "timeoutBehavior" are optional. Nonstop is enabled by default for 
-    	Terracotta Clustered Caches. Please refer to Nonstop documentation on how to use nonstop.
-    	
-    The <terracotta> sub-element has the following attributes:
-
-    * clustered=true|false - indicates whether this cache should be clustered with Terracotta. By
-      default, if the <terracotta> element is included, clustered=true.
-
-    * valueMode=serialization|identity - indicates whether this cache should be clustered with
-      serialized copies of the values or using Terracotta identity mode.  By default, values will
-      be cached in serialization mode which is similar to other replicated Ehcache modes.  The identity
-      mode is only available in certain Terracotta deployment scenarios and will maintain actual object
-      identity of the keys and values across the cluster.  In this case, all users of a value retrieved from
-      the cache are using the same clustered value and must provide appropriate locking for any changes
-      made to the value (or objects referred to by the value).
-      
-    * copyOnRead=true|false - indicates whether cache values are deserialized on every read or if the
-      materialized cache value can be re-used between get() calls. This setting is useful if a cache
-      is being shared by callers with disparate classloaders or to prevent local drift if keys/values
-      are mutated locally w/o putting back to the cache. NOTE: This setting is only relevant for caches
-      with valueMode=serialization
-
-    * coherent=strict|non-strict|off - Indicates whether this cache should have coherent reads and writes 
-      with guaranteed consistency across the cluster. By default, its value is "non-strict".
-      The old values "true" and "false" are deprecated and should not be used. Config using the old values
-      will be translated to the new values with "true" translating to "strict" and "false" translating to 
-      "off".   If this attribute is set to false (or "incoherent" mode), values from the cache are read without
-      locking, possibly yielding stale data. Writes to a cache in incoherent mode are batched and applied 
-      without acquiring cluster-wide locks, possibly creating inconsistent values across cluster. 
-      Incoherent mode is a performance optimization with weaker concurrency guarantees and should generally be used
-      for bulk-loading caches, for loading a read-only cache, or where the application that can tolerate reading 
-      stale data. This setting overrides coherentReads, which is deprecated.
-
-    * synchronousWrites=true|false - When set to true, clustered caches use
-      Terracotta SYNCHRONOUS WRITE locks. Asynchronous writes (synchronousWrites="false") maximize performance by 
-      allowing clients to proceed without waiting for a "transaction received" acknowledgement from the server. 
-      Synchronous writes (synchronousWrites="true")  maximize data safety by requiring that a client receive server 
-      acknowledgement of a transaction before that client can proceed. If coherence mode is disabled using 
-      configuration (coherent="false") or through the coherence API, only asynchronous writes can occur 
-      (synchronousWrites="true" is ignored). By default this value is false (i.e. clustered caches use normal
-       Terracotta WRITE locks).
-    
-    * storageStrategy=classic|DCV2 - Can be used to configure how the key/values of the cache are stored. The key/values
-      can be stored locally in the vm or stored in the Terracotta Server Array. "classic" value for the attribute stores 
-      the key/values in the local vm and using "DCV2" stores it in the Terracotta Server Array. This attribute is 
-      optional and default value is "classic"
-      
-    * concurrency - A non-negative integer that can be used to specify the number of segments that will be used by the map 
-      underneath the Terracotta Store. Its optional and has default value of 0, which means will use default values based
-      on the internal Map being used underneath the store. This value cannot be changed programmatically once cache is initialized.
-
-   The <terracotta> sub-element also has a nonstop sub-element to allow configuration of non stop or graceful degradation behaviour.
-   It has the following attributes:
-
-   enabled="true" - defaults to true.
-
-   timeoutMillis - An SLA setting, so that if the cache operation takes longer than the allowed ms, it will timeout.
-
-   immediateTimeout="true|false" - What to do on receipt of a ClusterOffline event indicating that communications with the active Terracotta
-    server are interrupted.
-
-   timeoutBehavior="noop|exception|localReads" - What to do when a timeout has occurred.
-
-
-    Simplest example to indicate clustering:
-        <terracotta/>
-
-    To indicate the cache should not be clustered (or remove the <terracotta> element altogether):
-        <terracotta clustered="false"/>
-
-    To indicate the cache should be clustered using identity mode:
-        <terracotta clustered="true" valueMode="identity"/>
-        
-    To indicate the cache should be clustered using incoherent mode for bulk load:
-        <terracotta clustered="true" coherent="false"/>
-    
-    To indicate the cache should be clustered using synchronous-write locking level:
-        <terracotta clustered="true" synchronousWrites="true"/>
-        
-    To indicate the key/values should be stored in the Terracotta Server Array:
-        <terracotta clustered="true" storageStrategy="DCV2"/>
-        
-    -->
-
-    <!--
-    Mandatory Default Cache configuration. These settings will be applied to caches
-    created programmatically using CacheManager.add(String cacheName).
-
-    The defaultCache has an implicit name "default" which is a reserved cache name.
-    -->
-    <defaultCache
-            maxElementsInMemory="10000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />
-
-    <cache name="normCache"
-            maxElementsInMemory="100000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />
-    <cache name="conceptSimCache"
-            maxElementsInMemory="100000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />
-    <cache name="linSimCache"
-            maxElementsInMemory="100000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />
-    <cache name="lchSimCache"
-            maxElementsInMemory="100000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />
-    <cache name="lcsCache"
-            maxElementsInMemory="100000"
-            eternal="false"
-            timeToIdleSeconds="120"
-            timeToLiveSeconds="120"
-            overflowToDisk="false"
-            memoryStoreEvictionPolicy="LRU"
-            />    
-    <!--
-    Sample caches. Following are some example caches. Remove these before use.
-    -->
-
-    <!--
-    Sample cache named sampleCache1
-    This cache contains a maximum in memory of 10000 elements, and will expire
-    an element if it is idle for more than 5 minutes and lives for more than
-    10 minutes.
-
-    If there are more than 10000 elements it will overflow to the
-    disk cache, which in this configuration will go to wherever java.io.tmp is
-    defined on your system. On a standard Linux system this will be /tmp"
-    <cache name="sampleCache1"
-           maxElementsInMemory="10000"
-           maxElementsOnDisk="1000"
-           eternal="false"
-           overflowToDisk="true"
-           diskSpoolBufferSizeMB="20"
-           timeToIdleSeconds="300"
-           timeToLiveSeconds="600"
-           memoryStoreEvictionPolicy="LFU"
-           transactionalMode="off"
-            />
-    -->
-
-
-    <!--
-    Sample cache named sampleCache2
-    This cache has a maximum of 1000 elements in memory. There is no overflow to disk, so 1000
-    is also the maximum cache size. Note that when a cache is eternal, timeToLive and
-    timeToIdle are not used and do not need to be specified.
-    <cache name="sampleCache2"
-           maxElementsInMemory="1000"
-           eternal="true"
-           overflowToDisk="false"
-           memoryStoreEvictionPolicy="FIFO"
-            />
-    -->
-
-
-    <!--
-    Sample cache named sampleCache3. This cache overflows to disk. The disk store is
-    persistent between cache and VM restarts. The disk expiry thread interval is set to 10
-    minutes, overriding the default of 2 minutes.
-    <cache name="sampleCache3"
-           maxElementsInMemory="500"
-           eternal="false"
-           overflowToDisk="true"
-           timeToIdleSeconds="300"
-           timeToLiveSeconds="600"
-           diskPersistent="true"
-           diskExpiryThreadIntervalSeconds="1"
-           memoryStoreEvictionPolicy="LFU"
-            />
-    -->
-
-    <!--
-    Sample distributed cache named sampleReplicatedCache1.
-    This cache replicates using defaults.
-    It also bootstraps from the cluster, using default properties.
-    <cache name="sampleReplicatedCache1"
-           maxElementsInMemory="10"
-           eternal="false"
-           timeToIdleSeconds="100"
-           timeToLiveSeconds="100"
-           overflowToDisk="false">
-
-        <cacheEventListenerFactory
-                class="net.sf.ehcache.distribution.RMICacheReplicatorFactory"/>
-        <bootstrapCacheLoaderFactory
-                class="net.sf.ehcache.distribution.RMIBootstrapCacheLoaderFactory"/>
-    </cache>
-    -->
-
-
-    <!--
-    Sample distributed cache named sampleReplicatedCache2.
-    This cache replicates using specific properties.
-    It only replicates updates and does so synchronously via copy
-    <cache name="sampleRepicatedCache2"
-           maxElementsInMemory="10"
-           eternal="false"
-           timeToIdleSeconds="100"
-           timeToLiveSeconds="100"
-           overflowToDisk="false">
-        <cacheEventListenerFactory
-                class="net.sf.ehcache.distribution.RMICacheReplicatorFactory"
-                properties="replicateAsynchronously=false, replicatePuts=false,
-                            replicatePutsViaCopy=false, replicateUpdates=true,
-                            replicateUpdatesViaCopy=true, replicateRemovals=false"/>
-    </cache>
-    -->
-
-    <!--
-    Sample distributed cache named sampleReplicatedCache3.
-    This cache replicates using defaults except that the asynchronous replication
-    interval is set to 200ms.
-    This one includes / and # which were illegal in ehcache 1.5.
-    <cache name="sampleReplicatedCache3"
-           maxElementsInMemory="10"
-           eternal="false"
-           timeToIdleSeconds="100"
-           timeToLiveSeconds="100"
-           overflowToDisk="true">
-        <cacheEventListenerFactory
-                class="net.sf.ehcache.distribution.RMICacheReplicatorFactory"
-                properties="asynchronousReplicationIntervalMillis=200"/>
-    </cache>
-    -->
-
-    <!--
-    Sample Terracotta clustered cache named sampleTerracottaCache.
-    This cache uses Terracotta to cluster the contents of the cache.
-    -->
-    <!--
-    <cache name="sampleTerracottaCache"
-           maxElementsInMemory="1000"
-           eternal="false"
-           timeToIdleSeconds="3600"
-           timeToLiveSeconds="1800"
-           overflowToDisk="false">
-        <terracotta/>
-    </cache>
-    -->
-
-    <!--
-      Sample xa enabled cache named xaCache
-    <cache name="xaCache"
-           maxElementsInMemory="500"
-           eternal="false"
-           timeToIdleSeconds="300"
-           timeToLiveSeconds="600"
-           overflowToDisk="false"
-           diskPersistent="false"
-           diskExpiryThreadIntervalSeconds="1"
-           transactionalMode="xa_strict">
-	</cache>
-    -->
-
-    <!--
-      Sample copy on both read and write cache named copyCache
-      using the default (explicitly configured here as an example) ReadWriteSerializationCopyStrategy
-      class could be any implementation of net.sf.ehcache.store.compound.CopyStrategy
-    <cache name="copyCache"
-           maxElementsInMemory="500"
-           eternal="false"
-           timeToIdleSeconds="300"
-           timeToLiveSeconds="600"
-           overflowToDisk="false"
-           diskPersistent="false"
-           diskExpiryThreadIntervalSeconds="1"
-           copyOnRead="true"
-           copyOnWrite="true">
-        <copyStrategy class="net.sf.ehcache.store.compound.ReadWriteSerializationCopyStrategy" />
-	</cache>
-    -->
-    <!--
-      Sample, for Enterprise Ehcache only, demonstrating a tiered cache with in-memory, off-heap and disk stores. In this example the in-memory (on-heap) store is limited to 10,000 items ... which for example for 1k items would use 10MB of memory, the off-heap store is limited to 4GB and the disk store is unlimited in size.
-    <cache name="tieredCache"
-           maxElementsInMemory="10000"
-           eternal="false"
-           timeToLiveSeconds="600"
-           overflowToOffHeap="true"
-           maxMemoryOffHeap="4g"
-           overflowToDisk="true"
-           diskPersistent="false"
-           diskExpiryThreadIntervalSeconds="1"
-     </cache>
---> 
+<ehcache name="org.apache.ctakes.ytex.kernel" updateCheck="false"
+	monitoring="autodetect" dynamicConfig="true">
+	<diskStore path="java.io.tmpdir" />
+	<defaultCache maxElementsInMemory="10000" eternal="false"
+		timeToIdleSeconds="120" timeToLiveSeconds="120"
+		diskExpiryThreadIntervalSeconds="120" memoryStoreEvictionPolicy="LRU" />
+	<cache name="org.hibernate.cache.internal.StandardQueryCache"
+		maxElementsInMemory="100" eternal="false" timeToLiveSeconds="120" />
+	<cache name="org.hibernate.cache.spi.UpdateTimestampsCache"
+		maxElementsInMemory="10000" eternal="true" />
+	<cache name="lcsCache" maxElementsInMemory="10000" eternal="false" />
+	<cache name="normCache" maxElementsInMemory="10000" eternal="false" />
+	<cacheManagerEventListenerFactory
+		class="" properties="" />
 </ehcache>

Modified: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mssql.example Wed Jan  1 23:39:31 2014
@@ -21,7 +21,6 @@ db.password=
 db.type=mssql
 db.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver
 db.initStatements=
-ytex.beanRefContext=classpath*:beanRefContext.xml
 hibernate.dialect=org.hibernate.dialect.SQLServerDialect
 
 # transaction isolation level

Modified: ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example (original)
+++ ctakes/branches/ytex/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/ytex.properties.mysql.example Wed Jan  1 23:39:31 2014
@@ -17,7 +17,6 @@ db.url=jdbc:mysql://localhost:3306/ytex?
 db.type=mysql
 db.driver=com.mysql.jdbc.Driver
 db.initStatements=
-ytex.beanRefContext=classpath*:beanRefContext.xml
 hibernate.dialect=org.hibernate.dialect.MySQLMyISAMDialect
 
 # transaction isolation level

Modified: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml (original)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml Wed Jan  1 23:39:31 2014
@@ -1,209 +1,253 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    Licensed to the Apache Software Foundation (ASF) under one
-    or more contributor license agreements.  See the NOTICE file
-    distributed with this work for additional information
-    regarding copyright ownership.  The ASF licenses this file
-    to you under the Apache License, Version 2.0 (the
-    "License"); you may not use this file except in compliance
-    with the License.  You may obtain a copy of the License at
-
-      http://www.apache.org/licenses/LICENSE-2.0
-
-    Unless required by applicable law or agreed to in writing,
-    software distributed under the License is distributed on an
-    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-    KIND, either express or implied.  See the License for the
-    specific language governing permissions and limitations
-    under the License.
--->
+<!-- Licensed to the Apache Software Foundation (ASF) under one or more contributor 
+	license agreements. See the NOTICE file distributed with this work for additional 
+	information regarding copyright ownership. The ASF licenses this file to 
+	you under the Apache License, Version 2.0 (the "License"); you may not use 
+	this file except in compliance with the License. You may obtain a copy of 
+	the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required 
+	by applicable law or agreed to in writing, software distributed under the 
+	License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS 
+	OF ANY KIND, either express or implied. See the License for the specific 
+	language governing permissions and limitations under the License. -->
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
-  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
-  <analysisEngineMetaData>
-  	<description>
-  	Identical to ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml with the following changes:
-  	substitute ytex SegmentRegexAnnotator for SimpleSegmentAnnotator;
-  	substitute ytex SentenceDetectorAnnotator for SentenceDetectorAnnotator; 
-  	substitute ytex DictionaryLookupAnnotator for DictionaryLookupAnnotatorUMLS
-  	</description>
-  </analysisEngineMetaData>
-  <primitive>false</primitive>
-  <delegateAnalysisEngineSpecifiers>
-    <delegateAnalysisEngine key="Chunker">
-      <import location="../../../ctakes-chunker/desc/Chunker.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="TokenizerAnnotator">
-      <import location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
-      <import location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
-      <import location="./DictionaryLookupAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="StatusAnnotator">
-      <import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="NegationAnnotator">
-      <import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="SentenceDetectorAnnotator">
-      <import location="./SentenceDetectorAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="LookupWindowAnnotator">
-      <import location="../../../ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
-      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
-      <import location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="SegmentRegexAnnotator">
-      <import location="SegmentRegexAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="POSTagger">
-      <import location="../../../ctakes-pos-tagger/desc/POSTagger.xml"/>
-    </delegateAnalysisEngine>
-	<!-- 
-	<delegateAnalysisEngine key="ClearPOSTagger">
-	<import location="../../../ctakes-pos-tagger/desc/ClearNLPPOSTagger.xml"/>
-	</delegateAnalysisEngine>
-	 -->    
-    <delegateAnalysisEngine key="LvgAnnotator">
-      <import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="AssertionAnnotator">
-      <import location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
-    </delegateAnalysisEngine>
-    <delegateAnalysisEngine key="DependencyParser">
-      <import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml"/>
-    </delegateAnalysisEngine>
-<delegateAnalysisEngine key="SemanticRoleLabeler">
-<import location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPSemanticRoleLabelerAE.xml"/>
-</delegateAnalysisEngine>    
-  </delegateAnalysisEngineSpecifiers>
-  <analysisEngineMetaData>
-    <name>AggregatePlaintextUMLSProcessor</name>
-    <description>Runs the complete pipeline for annotating clinical documents in plain text format using the built in UMLS (SNOMEDCT and RxNORM) dictionaries.  This uses the dictionary lookup/desc/DictionaryLookupAnnotatorUMLS.xml
-and requires an UMLS license.  Please update DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and password.
-</description>
-    <version/>
-    <vendor/>
-    <configurationParameters searchStrategy="language_fallback">
-      <configurationParameter>
-        <name>ChunkCreatorClass</name>
-        <type>String</type>
-        <multiValued>false</multiValued>
-        <mandatory>true</mandatory>
-        <overrides>
-          <parameter>Chunker/ChunkCreatorClass</parameter>
-        </overrides>
-      </configurationParameter>
-    </configurationParameters>
-    <configurationParameterSettings>
-      <nameValuePair>
-        <name>ChunkCreatorClass</name>
-        <value>
-          <string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator</string>
-        </value>
-      </nameValuePair>
-    </configurationParameterSettings>
-    <flowConstraints>
-      <fixedFlow>
-        <node>SegmentRegexAnnotator</node>
-        <node>SentenceDetectorAnnotator</node>
-        <node>TokenizerAnnotator</node>
-        <node>LvgAnnotator</node>
-        <node>ContextDependentTokenizerAnnotator</node>
-        <node>POSTagger</node>
-		<!-- <node>ClearPOSTagger</node>  -->        
-        <node>Chunker</node>
-        <node>AdjustNounPhraseToIncludeFollowingNP</node>
-        <node>AdjustNounPhraseToIncludeFollowingPPNP</node>
-        <node>LookupWindowAnnotator</node>
-        <node>DictionaryLookupAnnotatorDB</node>
-        <!-- 
-        <node>DependencyParser</node>
-		<node>SemanticRoleLabeler</node>        
-        <node>AssertionAnnotator</node>
-        	<node>StatusAnnotator</node>
-        	<node>NegationAnnotator</node>
-	        <node>ExtractionPrepAnnotator</node>
-         -->
-      </fixedFlow>
-    </flowConstraints>
-    <typePriorities>
-      <name>Ordering</name>
-      <description>For subiterator</description>
-      <version>1.0</version>
-      <priorityList>
-        <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
-        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
-        <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
-      </priorityList>
-      <priorityList>
-        <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
-        <type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
-      </priorityList>
-    </typePriorities>
-    <fsIndexCollection/>
-    <capabilities>
-      <capability>
-        <inputs/>
-        <outputs>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID</type>
-          <type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
-          <type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
-          <type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP</type>
-          <type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP</type>        
-        </outputs>
-        <languagesSupported/>
-      </capability>
-    </capabilities>
-    <operationalProperties>
-      <modifiesCas>true</modifiesCas>
-      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
-      <outputsNewCASes>false</outputsNewCASes>
-    </operationalProperties>
-  </analysisEngineMetaData>
-  <resourceManagerConfiguration/>
+	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+	<analysisEngineMetaData>
+		<description>
+			Identical to
+			ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
+			with the following changes:
+			substitute ytex SegmentRegexAnnotator for SimpleSegmentAnnotator;
+			substitute ytex SentenceDetectorAnnotator for SentenceDetectorAnnotator;
+			substitute ytex DictionaryLookupAnnotator for
+			DictionaryLookupAnnotatorUMLS
+			add SenseDisambiguatorAnnotator
+		</description>
+	</analysisEngineMetaData>
+	<primitive>false</primitive>
+	<delegateAnalysisEngineSpecifiers>
+		<delegateAnalysisEngine key="Chunker">
+			<import location="../../../ctakes-chunker/desc/Chunker.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="TokenizerAnnotator">
+			<import
+				location="../../../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="ContextDependentTokenizerAnnotator">
+			<import
+				location="../../../ctakes-context-tokenizer/desc/analysis_engine/ContextDependentTokenizerAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DictionaryLookupAnnotatorDB">
+			<import location="./DictionaryLookupAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="StatusAnnotator">
+			<import location="../../../ctakes-ne-contexts/desc/StatusAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="NegationAnnotator">
+			<import location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SentenceDetectorAnnotator">
+			<import location="./SentenceDetectorAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SenseDisambiguatorAnnotator">
+			<import location="./SenseDisambiguatorAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="LookupWindowAnnotator">
+			<import
+				location="../../../ctakes-clinical-pipeline/desc/analysis_engine/LookupWindowAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingNP">
+			<import
+				location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingNP.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="AdjustNounPhraseToIncludeFollowingPPNP">
+			<import
+				location="../../../ctakes-chunker/desc/AdjustNounPhraseToIncludeFollowingPPNP.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SegmentRegexAnnotator">
+			<import location="SegmentRegexAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="POSTagger">
+			<import location="../../../ctakes-pos-tagger/desc/POSTagger.xml" />
+		</delegateAnalysisEngine>
+		<!-- <delegateAnalysisEngine key="ClearPOSTagger"> <import location="../../../ctakes-pos-tagger/desc/ClearNLPPOSTagger.xml"/> 
+			</delegateAnalysisEngine> -->
+		<delegateAnalysisEngine key="LvgAnnotator">
+			<import location="../../../ctakes-lvg/desc/analysis_engine/LvgAnnotator.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="AssertionAnnotator">
+			<import
+				location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="DependencyParser">
+			<import
+				location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPDependencyParserAE.xml" />
+		</delegateAnalysisEngine>
+		<delegateAnalysisEngine key="SemanticRoleLabeler">
+			<import
+				location="../../../ctakes-dependency-parser/desc/analysis_engine/ClearNLPSemanticRoleLabelerAE.xml" />
+		</delegateAnalysisEngine>
+	</delegateAnalysisEngineSpecifiers>
+	<analysisEngineMetaData>
+		<name>AggregatePlaintextUMLSProcessor</name>
+		<description>Runs the complete pipeline for annotating clinical
+			documents in plain text format using the built in UMLS (SNOMEDCT and
+			RxNORM) dictionaries. This uses the dictionary
+			lookup/desc/DictionaryLookupAnnotatorUMLS.xml
+			and requires an UMLS license. Please update
+			DictionaryLookupAnnotatorUMLS.xml file with your UMLS username and
+			password.
+		</description>
+		<version />
+		<vendor />
+		<configurationParameters searchStrategy="language_fallback">
+			<configurationParameter>
+				<name>ChunkCreatorClass</name>
+				<type>String</type>
+				<multiValued>false</multiValued>
+				<mandatory>true</mandatory>
+				<overrides>
+					<parameter>Chunker/ChunkCreatorClass</parameter>
+				</overrides>
+			</configurationParameter>
+		</configurationParameters>
+		<configurationParameterSettings>
+			<nameValuePair>
+				<name>ChunkCreatorClass</name>
+				<value>
+					<string>org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator
+					</string>
+				</value>
+			</nameValuePair>
+		</configurationParameterSettings>
+		<flowConstraints>
+			<fixedFlow>
+				<node>SegmentRegexAnnotator</node>
+				<node>SentenceDetectorAnnotator</node>
+				<node>TokenizerAnnotator</node>
+				<node>LvgAnnotator</node>
+				<node>ContextDependentTokenizerAnnotator</node>
+				<node>POSTagger</node>
+				<!-- <node>ClearPOSTagger</node> -->
+				<node>Chunker</node>
+				<node>AdjustNounPhraseToIncludeFollowingNP</node>
+				<node>AdjustNounPhraseToIncludeFollowingPPNP</node>
+				<node>LookupWindowAnnotator</node>
+				<node>DictionaryLookupAnnotatorDB</node>
+				<node>SenseDisambiguatorAnnotator</node>
+				<!-- <node>DependencyParser</node> <node>SemanticRoleLabeler</node> <node>AssertionAnnotator</node> 
+					<node>StatusAnnotator</node> <node>NegationAnnotator</node> <node>ExtractionPrepAnnotator</node> -->
+			</fixedFlow>
+		</flowConstraints>
+		<typePriorities>
+			<name>Ordering</name>
+			<description>For subiterator</description>
+			<version>1.0</version>
+			<priorityList>
+				<type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+				<type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+				<type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+			</priorityList>
+			<priorityList>
+				<type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+				<type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+				</type>
+			</priorityList>
+		</typePriorities>
+		<fsIndexCollection />
+		<capabilities>
+			<capability>
+				<inputs />
+				<outputs>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NewlineToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.WordToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.VP
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.refsem.UmlsConcept
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.UCP
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.TimeAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SymbolToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.Sentence
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspanSegment
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.SBAR
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RomanNumeralAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.RangeAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PunctuationToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Property
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.Properties
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.PersonTitleAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PRT
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.PP
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.OntologyConcept
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.NumToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.MeasurementAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Lemma
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.LST
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.INTJ
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.FractionAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.structured.DocumentID
+					</type>
+					<type allAnnotatorFeatures="true">uima.tcas.DocumentAnnotation</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.DateAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopySrcAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.CopyDestAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.ContractionToken
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.ContextAnnotation
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.Chunk
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.CONJP
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.BaseToken
+					</type>
+					<type allAnnotatorFeatures="true">uima.cas.AnnotationBase</type>
+					<type allAnnotatorFeatures="true">uima.tcas.Annotation</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADVP
+					</type>
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.syntax.ADJP
+					</type>
+				</outputs>
+				<languagesSupported />
+			</capability>
+		</capabilities>
+		<operationalProperties>
+			<modifiesCas>true</modifiesCas>
+			<multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+			<outputsNewCASes>false</outputsNewCASes>
+		</operationalProperties>
+	</analysisEngineMetaData>
+	<resourceManagerConfiguration />
 </analysisEngineDescription>

Modified: ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml
URL: http://svn.apache.org/viewvc/ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml?rev=1554701&r1=1554700&r2=1554701&view=diff
==============================================================================
--- ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml (original)
+++ ctakes/branches/ytex/ctakes-ytex-uima/desc/analysis_engine/SenseDisambiguatorAnnotator.xml Wed Jan  1 23:39:31 2014
@@ -2,7 +2,7 @@
 <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier">
 	<frameworkImplementation>org.apache.uima.java</frameworkImplementation>
 	<primitive>true</primitive>
-	<annotatorImplementationName>ytex.uima.annotators.SenseDisambiguatorAnnotator
+	<annotatorImplementationName>org.apache.ctakes.ytex.uima.annotators.SenseDisambiguatorAnnotator
 	</annotatorImplementationName>
 	<analysisEngineMetaData>
 		<name>SenseDisambiguatorAnnotator</name>
@@ -26,7 +26,7 @@
 		<configurationParameterSettings />
 		<typeSystemDescription>
 			<imports>
-				<import name="ytex.uima.YTEXTypes" />
+				<import name="org.apache.ctakes.ytex.types.TypeSystem" />
 			</imports>
 		</typeSystemDescription>
 		<typePriorities />
@@ -34,7 +34,7 @@
 		<capabilities>
 			<capability>
 				<inputs>
-					<type allAnnotatorFeatures="true">edu.mayo.bmi.uima.core.type.NamedEntity
+					<type allAnnotatorFeatures="true">org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
 					</type>
 				</inputs>
 				<outputs />



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