UIMA References

The imports section allows this descriptor to import types from other type system descriptors. The import syntax is described in Section 2.2, “Imports”. A type system may import any number of other type systems and then define additional types which refer to imported types. Circular imports are allowed.

The types element contains zero or more typeDescription elements. Each typeDescription has the form:

<typeDescription>
  <name>[TypeName]</name>
  <description>[String]</description>
  <supertypeName>[TypeName]</supertypeName>
  <features>
    ...
  </features>
</typeDescription>

The name element contains the name of the type. A [TypeName] is a dot-separated list of names, where each name consists of a letter followed by any number of letters, digits, or underscores. TypeNames are case sensitive. Letter and digit are as defined by Java; therefore, any Unicode letter or digit may be used (subject to the character encoding defined by the descriptor file's XML header). The name following the final dot is considered to be the “short name” of the type; the preceding portion is the namespace (analogous to the package.class syntax used in Java). Namespaces beginning with uima are reserved and should not be used. Examples of valid type names are:

These would all be considered distinct types since they have different namespaces. Best practice here is to follow the normal Java naming conventions of having namespaces be all lowercase, with the short type names having an initial capital, but this is not mandated, so ABC.mYtyPE is an allowed type name. While type names without namespaces (e.g. TokenAnnotation alone) are allowed, but discouraged because naming conflicts can then result when combining annotators that use different type systems.

The description element contains a textual description of the type. The supertypeName element contains the name of the type from which it inherits (this can be set to the name of another user-defined type, or it may be set to any built-in type which may be subclassed, such as uima.tcas.Annotation for a new annotation type or uima.cas.TOP for a new type that is not an annotation). All three of these elements are required.

The features element of a typeDescription is required only if the type we are specifying introduces new features. If the features element is present, it contains zero or more featureDescription elements, each of which has the form:

<featureDescription>
  <name>[Name]</name>
  <description>[String]</description>
  <rangeTypeName>[Name]</rangeTypeName>
  <elementType>[Name]</elementType>
  <multipleReferencesAllowed>true|false</multipleReferencesAllowed>
</featureDescription>

A feature's name follows the same rules as a type short name – a letter followed by any number of letters, digits, or underscores. Feature names are case sensitive.

The feature's rangeTypeName specifies the type of value that the feature can take. This may be the name of any type defined in your type system, or one of the predefined types. All of the predefined types have names that are prefixed with uima.cas or uima.tcas, for example:

uima.cas.TOP 
uima.cas.String
uima.cas.Long 
uima.cas.FSArray
uima.cas.StringList
uima.tcas.Annotation.

For a complete list of predefined types, see the CAS API documentation.

The elementType of a feature is optional, and applies only when the rangeTypeName is uima.cas.FSArray or uima.cas.FSList The elementType specifies what type of value can be assigned as an element of the array or list. This must be the name of a non-primitive type. If omitted, it defaults to uima.cas.TOP, meaning that any FeatureStructure can be assigned as an element the array or list. Note: depending on the CAS Interface that you use in your code, this constraint may or may not be enforced.

The multipleReferencesAllowed feature is optional, and applies only when the rangeTypeName is an array or list type (it applies to arrays and lists of primitive as well as non-primitive types). Setting this to false (the default) indicates that this feature has exclusive ownership of the array or list, so changes to the array or list are localized. Setting this to true indicates that the array or list may be shared, so changes to it may affect other objects in the CAS. Note: there is currently no guarantee that the framework will enforce this restriction. However, this setting may affect how the CAS is serialized.

There is one other special type that you can declare – a subset of the String type that specifies a restricted set of allowed values. This is useful for features that can have only certain String values, such as parts of speech. Here is an example of how to declare such a type:

<typeDescription>
  <name>PartOfSpeech</name>
  <description>A part of speech.</description>
  <supertypeName>uima.cas.String</supertypeName>
  <allowedValues>
    <value>
      <string>NN</string>
      <description>Noun, singular or mass.</description>
    </value>
    <value>
      <string>NNS</string>
      <description>Noun, plural.</description>
    </value>
    <value>
      <string>VB</string>
      <description>Verb, base form.</description>
    </value></programlisting>
    ...
  </allowedValues>
</typeDescription>

Aggregate Analysis Engines do not contain an annotator, but instead contain one or more component (also called delegate) analysis engines.

Aggregate Analysis Engine Descriptors maintain most of the same structure as Primitive Analysis Engine Descriptors. The differences are:

<delegateAnalysisEngineSpecifiers>

  <delegateAnalysisEngine key="[String]">
    <analysisEngineDescription>...</analysisEngineDescription> |
    <import .../> 
  </delegateAnalysisEngine>

  <delegateAnalysisEngine key="[String]">
    ...
  </delegateAnalysisEngine>

  ...

</delegateAnalysisEngineSpecifiers>

<flowController key="[String]">
    <flowControllerDescription>...</flowControllerDescription> |
    <import .../>
  </flowController>

<flowConstraints>
  <fixedFlow>
    <node>[String]</node>
    <node>[String]</node>
    ...
  </fixedFlow>
</flowConstraints>

<flowConstraints>
  <capabilityLanguageFlow>
    <node>[String]</node>
    <node>[String]</node>
    ...
  </capabilityLanguageFlow>
</flowConstraints>

<overrides>

  <parameter>
    [delegateAnalysisEngineKey]/[parameterName]
  </parameter>

  <parameter>
    [delegateAnalysisEngineKey]/[parameterName]
  </parameter>
  ...

</overrides>

<configurationParameter>
  <name>AggregateParam</name>
  <type>String</type>
  <overrides>
    <parameter>annotator1/param1</parameter>
    <parameter>annotator2/param2</parameter>
  </overrides>
</configurationParameter>

<resourceManagerConfiguration>

  <externalResources>
    <externalResource>
      <name>ExampleResource</name>
      <fileResourceSpecifier>
        <fileUrl>file:MyResourceFile.dat</fileUrl>
      </fileResourceSpecifier>
    </externalResource>
  </externalResources>  

  <externalResourceBindings>
    <externalResourceBinding>
      <key>annotator1/myResource</key>
      <resourceName>ExampleResource</resourceName>
    </externalResourceBinding>
    <externalResourceBinding>
      <key>annotator2/someResource</key>
      <resourceName>ExampleResource</resourceName>
    </externalResourceBinding>
  </externalResourceBindings>

</resourceManagerConfiguration>

<sofaMappings>
  <sofaMapping>
    <componentKey>[keyName]</componentKey>
    <componentSofaName>[sofaName]</componentSofaName>
    <aggregateSofaName>[sofaName]</aggregateSofaName>
  </sofaMapping>
  ...
</sofaMappings>

The basic structure of a Collection Reader descriptor is as follows:

<?xml version="1.0" ?> 
<collectionReaderDescription
    xmlns="http://uima.apache.org/resourceSpecifier">

  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
  <implementationName>[ClassName]</implementationName> 

  <processingResourceMetaData>
    ...
  </processingResourceMetaData>

  <externalResourceDependencies>
   ...
  </externalResourceDependencies>

  <resourceManagerConfiguration>

   ...

  </resourceManagerConfiguration>

</collectionReaderDescription>

The frameworkImplementation element must always be set to the value org.apache.uima.java.

The implementationName element contains the fully-qualified class name of the Collection Reader implementation. This must name a class that implements the CollectionReader interface.

The processingResourceMetaData element contains essentially the same information as a Primitive Analysis Engine Descriptor's' analysisEngineMetaData element:

<processingResourceMetaData>

  <name> [String] </name>
  <description>[String]</description>
  <version>[String]</version>
  <vendor>[String]</vendor>

  <configurationParameters>
     ...
  </configurationParameters>

  <configurationParameterSettings>
    ...
  </configurationParameterSettings> 

  <typeSystemDescription>
   ...
  </typeSystemDescription> 

  <typePriorities>
   ...
  </typePriorities> 

  <fsIndexes>
   ...
  </fsIndexes>

  <capabilities>
   ...
  </capabilities> 

</processingResourceMetaData>

The contents of these elements are the same as that described in Section 2.4.1.2, “Analysis Engine MetaData”, with the exception that the capabilities section should not declare any inputs (because the Collection Reader is always the first component to receive the CAS).

The externalResourceDependencies and resourceManagerConfiguration elements are exactly the same as in the Primitive Analysis Engine Descriptors (see Section 2.4.1.10, “External Resource Dependencies” and Section 2.4.1.11, “Resource Manager Configuration”.

The basic structure of a CAS Initializer Descriptor is as follows:

<?xml version="1.0" encoding="UTF-8" ?> 
<casInitializerDescription
    xmlns="http://uima.apache.org/resourceSpecifier">

  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
  <implementationName>[ClassName] </implementationName>

  <processingResourceMetaData>
    ...
  </processingResourceMetaData>

  <externalResourceDependencies>
    ...
  </externalResourceDependencies>

  <resourceManagerConfiguration>
    ...
  </resourceManagerConfiguration>

</casInitializerDescription>

The frameworkImplementation element must always be set to the value org.apache.uima.java.

The implementationName element contains the fully-qualified class name of the CAS Initializer implementation. This must name a class that implements the CasInitializer interface.

The processingResourceMetaData element contains essentially the same information as a Primitive Analysis Engine Descriptor's' analysisEngineMetaData element, as described in Section 2.4.1.2, “Analysis Engine MetaData”, with the exception of some changes to the capabilities section. A CAS Initializer's capabilities element looks like this:

<capabilities>
  <capability>
    <outputs>
      <type allAnnotatorFeatures="true|false">[String]</type>
      <type>[TypeName]</type>
      ...
      <feature>[TypeName]:[Name]</feature>
      ...
    </outputs>

    <outputSofas>
      <sofaName>[name]</sofaName>
      ...
    </outputSofas>

    <mimeTypesSupported>
      <mimeType>[MIME Type]</mimeType>
      ...
    </mimeTypesSupported>
  </capability>

  <capability>
    ...
  </capability>
  ...
</capabilities>

The differences between a CAS Initializer's capabilities declaration and an Analysis Engine's capabilities declaration are that the CAS Initializer does not declare any input CAS types and features or input Sofas (because it is always the first to operate on a CAS), it doesn't have a language specifier, and that the CAS Initializer may declare a set of MIME types that it supports for its input documents. Examples include: text/plain, text/html, and application/pdf. For a list of MIME types see http://www.iana.org/assignments/media-types/. This information is currently only for users' information, the framework does not use it for anything. This may change in future versions.

The externalResourceDependencies and resourceManagerConfiguration elements are exactly the same as in the Primitive Analysis Engine Descriptors (see Section 2.4.1.10, “External Resource Dependencies” and Section 2.4.1.11, “Resource Manager Configuration”).

The basic structure of a CAS Consumer Descriptor is as follows:

<?xml version="1.0" encoding="UTF-8" ?> 
<casConsumerDescription 
    xmlns="http://uima.apache.org/resourceSpecifier">

  <frameworkImplementation>org.apache.uima.java</frameworkImplementation> 

  <implementationName>[ClassName]</implementationName> 

  <processingResourceMetaData>
    ...
  </processingResourceMetaData>

  <externalResourceDependencies>
    ...
  </externalResourceDependencies>

  <resourceManagerConfiguration>
    ...
  </resourceManagerConfiguration>
</casConsumerDescription>

The frameworkImplementation element currently must have the value org.apache.uima.java, or org.apache.uima.cpp.

The next subelement, <annotatorImplementationName> is how the UIMA framework determines which annotator class to use. This should contain a fully-qualified Java class name for Java implementations, or the name of a .dll or .so file for C++ implementations.

The frameworkImplementation element must always be set to the value org.apache.uima.java.

The implementationName element must contain the fully-qualified class name of the CAS Consumer implementation, or the name of a .dll or .so file for C++ implementations. For Java, the named class must implement the CasConsumer interface.

The processingResourceMetaData element contains essentially the same information as a Primitive Analysis Engine Descriptor's analysisEngineMetaData element, described in Section 2.4.1.2, “Analysis Engine MetaData”, except that the CAS Consumer Descriptor's capabilities element should not declare outputs or outputSofas (since CAS Consumers do not modify the CAS).

The externalResourceDependencies and resourceManagerConfiguration elements are exactly the same as in Primitive Analysis Engine Descriptors (see Section 2.4.1.10, “External Resource Dependencies” and Section 2.4.1.11, “Resource Manager Configuration”.

The CPM will abort if the Collection Reader throws a large number of consecutive exceptions (default = 100). This default can by changed by using the Java initialization parameter -DMaxCRErrorThreshold xxx.

The CAS Processors that make up the Processing Pipeline and the CAS Consumer pipeline are specified with the <casProcessor> entity, which appears within the <casProcessors> entity. It may appear multiple times, once for each CAS Processor specified for this CPE.

The order of the <casProcessor> entities with the <casProcessors> section specifies the order in which the CAS Processors will run. Although CAS Consumers are usually put at the end of the pipeline, they need not be. Also, Aggregate Analysis Engines may include CAS Consumers.

The overall format of the <casProcessor> entity is:

<casProcessor deployment="local|remote|integrated" name="[String]" >
    <descriptor>
      <import ...> | <include .../>
    </descriptor>
    <configurationParameterSettings>...</configurationParameterSettings>
    <sofaNameMappings>...</sofaNameMappings>
    <runInSeparateProcess>...</runInSeparateProcess>
    <deploymentParameters>...</deploymentParameters>
    <filter/>
    <errorHandling>...</errorHandling>
    <checkpoint batch="Number"/>
</casProcessor>

The <casProcessor> element has two mandatory attributes, deployment and name. The mandatory name attribute specifies a unique string identifying the CAS Processor.

The mandatory deployment attribute specifies the CAS Processor deployment mode. Currently, three deployment options are supported:

A number of elements may appear within the <casProcessor> element.

<configurationParameterSettings>
  <nameValuePair>
    <name>CivilianTitles</name>
    <value>
      <array>
        <string>Mr.</string>
        <string>Ms.</string>
        <string>Mrs.</string>
        <string>Dr.</string>
      </array>  
    </value>
  </nameValuePair>
  ...
</configurationParameterSettings>

<sofaNameMappings>
  <sofaNameMapping cpeSofaName="a_CPE_name"
                   componentSofaName="a_component_Name"/>
  ...
</sofaNameMappings>

<runInSeparateProcess>
    <exec dir="[String]" executable="[String]">
        <env key="[String]" value ="[String]"/>
        ...
        <arg>[String]</arg>
        ...
    </exec>
</runInSeparateProcess>

<env key="CLASSPATH" value="C:Javalib"/>

<runInSeparateProcess>
    <exec executable="java">
        <arg>-DVNS_HOST=localhost</arg> 
        <arg>-DVNS_PORT=9099</arg>
        <arg>org.apache.uima.reference_impl.analysis_engine.service.
vinci.VinciAnalysisEngineService_impl</arg> 
        <arg>C:uimadescdeployCasProcessor.xml</arg>
    </exec>
<runInSeparateProcess>

java -DVNS_HOST=localhost -DVNS_PORT=9099 
  org.apache.uima.reference_impl.analysis_engine.service.vinci.\\
              VinciAnalysisEngineService_impl 
  C:uimadescdeployCasProcessor.xml

<arg>${descriptor}</arg>

<deploymentParameters>
    <parameter name="[String]" value="..." type="string|integer" /> 
    ...
</deploymentParameters>

<deploymentParameters>
  <parameter name="service-access" value="exclusive" type="string"/> 
</deploymentParameters>

<errorHandling>
  <maxConsecutiveRestarts action="continue|disable|terminate"
                           value="[Number]"/>
  <errorRateThreshold action="continue|disable|terminate" value="[Rate]"/>
  <timeout max="[Number]"/>
</errorHandling>

<errorRateThreshold value="3/1000" action="disable"/>

<checkpoint batch="1000">

The type system specifies what kind of data you will be able to manipulate in your annotators. The type system defines two kinds of entities, types and features. Types are arranged in a single inheritance tree and define the kinds of entities (objects) you can manipulate in the CAS. Features optionally specify slots or fields within a type. The correspondence to Java is to equate a CAS Type to a Java Class, and the CAS Features to fields within the type. A critical difference is that CAS types have no methods; they are just data structures with named slots (features). These features can have as values primitive things like integers, floating point numbers, and strings, and they also can hold references to other instances of objects in the CAS. We call instances of the data structures declared by the type system “feature structures” (not to be confused with “features”). Feature structures are similar to the many variants of record structures found in computer science.^[6]

Each CAS Type defines a supertype; it is a subtype of that supertype. This means that any features that the supertype defines are features of the subtype; in other words, it inherits its supertype's features. Only single inheritance is supported; a type's feature set is the union of all of the features in its supertype hierarchy. There is a built-in type called uima.cas.TOP; this is the top, root node of the inheritance tree. It defines no features.

The values that can be stored in features are either built-in primitive values or references to other feature structures. The primitive values are boolean, byte, short (16 bit integers), integer (32 bit), long (64 bit), float (32 bit), double (64 bit floats) and strings; the official names of these are uima.cas.Boolean, uima.cas.Byte, uima.cas.Short, uima.cas.Integer, uima.cas.Long, uima.cas.Float , uima.cas.Double and uima.cas.String . The strings are Java strings, and characters are Java characters. Technically, this means that characters are UTF-16 code points, which is not quite the same as a Unicode character. This distinction should make no difference for almost all applications. The CAS also defines other basic built-in types for arrays of these, plus arrays of references to other objects, called uima.cas.IntegerArray , uima.cas.FloatArray, uima.cas.StringArray, uima.cas.FSArray, etc.

The CAS also defines a built-in type called uima.tcas.Annotation which inherits from uima.cas.AnnotationBase which in turn inherits from uima.cas.TOP. There are two features defined by this type, called begin and end, both of which are integer valued.

Creating and accessing data in the CAS requires knowledge about the types and features defined in the type system. The idea is similar to other data access APIs, such as the XML DOM or SAX APIs, or database access APIs such as JDBC. Contrary to those APIs, however, the CAS does not use the names of type system entities directly in the APIs. Rather, you use the type system to access type and feature entities by name, then use these entities in the data manipulation APIs. This can be compared to the Java reflection APIs: the type system is comparable to the Java class loader, and the type and feature objects to the java.lang.Class and java.lang.reflect.Field classes.

Why does it have to be this complicated? You wouldn't normally use reflection to create a Java object, either. As mentioned earlier, the JCas provides the more straightforward method to manipulate CAS data. The CAS access methods described here need only be used for generic types of applications that need to be able to handle any kind of data (e.g., generic tooling) or when the JCas may not be used for other reasons. The generic kinds of applications are exactly the ones where you would use the reflection API in Java as well.

Each view of a CAS provides a set of indexes for that view. Instances of feature structures can be added to a view's indexes. These indexes provide the only way for other annotators to locate existing data in the CAS. The only way for an annotator to use data that another annotator has created is by using an index (or the method getAllIndexedFS of the object FSIndexRepository) to retrieve feature structures the first annotator created. If you want the data you create to be visible to other annotators, you must explicitly call methods which add it to the indexes — you must index it.

Indexes are named and are associated with a CAS Type; they are used to index instances of that CAS type (including instances of that type's subtypes). If you are using multiple views (see Chapter 6, Multiple CAS Views of an Artifact in UIMA Tutorial and Developers' Guides), each view contains a separate instantiation of all of the indexes. To access an index, you minimally need to know its name. A CAS view provides an index repository which you can query for indexes for that view. Once you have a handle to an index, you can get information about the feature structures in the index, the size of the index, as well as an iterator over the feature structures.

Indexes are defined in the XML descriptor metadata for the application. Each CAS View has its own, separate instantiation of indexes based on these definitions, kept in the view's index repository. When you obtain an index, it is always from a particular CAS view. When you index an item, it is always added to all indexes where it belongs, within just one repository. You can specify different repositories (associated with different CAS views) to use; a given Feature Structure instance may be indexed in more than one CAS View.

Iterators allow you to enumerate the feature structures in an index. FS iterators provide two kinds of APIs: the regular Java iterator API, and a specific FS iterator API where the usual Java iterator APIs (hasNext() and next()) are replaced by isValid(), moveToNext() (which does not return an element) and get(). Which API style you use is up to you, but we do not recommend mixing the styles as the results are sometimes unexpected. If you just want to iterate over an index from start to finish, either style is equally appropriate. If you also use moveTo(FeatureStructure fs) and moveToPrevious(), it is better to use the special FS iterator style.

Indexes are created by specifying them in the annotator's or aggregate's resource descriptor. An index specification includes its name, the CAS type being indexed, the kind of index it is, and an (optional) ordering relation on the feature structures to be indexed. At startup time, all index specifications are combined; duplicate definitions (having the same name) are allowed only if their definitions are the same.

Feature structure instances need to be explicitly added to the index repository by a method call. Feature structures that are not indexed will not be visible to other annotators, (unless they are located via being referenced by some other feature of another feature structure, which is indexed, or through a chain of these).

The framework defines an unnamed bag index which indexes all types. The only access provided for this index is the getAllIndexedFs(type) method on the index repository, which returns an iterator over all indexed instances of the specified type (including its subtypes) for that CAS View.

The framework defines one standard, built-in annotation index, called AnnotationIndex, which indexes the uima.tcas.Annotation type: all feature structures of type uima.tcas.Annotation or its subtypes are automatically indexed with this built-in index.

The ordering relation used by this index is to first order by the value of the “begin” features (in ascending order) and then by the value of the “end” feature (in descending order). This ordering insures that longer annotations starting at the same spot come before shorter ones. For Subjects of Analysis other than Text, this may not be an appropriate index.

Here is a code fragment that, given a CAS Type System, will print a list of all types.

// Get all type names from the type system
// and print them to stdout.
private void listTypes1(TypeSystem ts) {
  // Get an iterator over types
  Iterator typeIterator = ts.getTypeIterator();
  Type t;
  System.out.println("Types in the type system:");
  while (typeIterator.hasNext()) {
    // Retrieve a type...
    t = (Type) typeIterator.next();
    // ...and print its name.
    System.out.println(t.getName());
  }
  System.out.println();
}

This method is passed the type system as a parameter. From the type system, we can get an iterator over all known types. If you run this against a CAS created with no additional user-defined types, we should see something like this on the console:

Types in the type system: 
uima.cas.Boolean 
uima.cas.Byte
uima.cas.Short 
uima.cas.Integer 
uima.cas.Long 
uima.cas.ArrayBase 
...
        

If the type system had user-defined types these would show up too. Note that some of these types are not directly creatable – they are types used by the framework in the type hierarchy (e.g. uima.cas.ArrayBase).

CAS type names include a name-space prefix. The components of a type name are separated by the dot (.). A type name component must start with a Unicode letter, followed by an arbitrary sequence of letters, digits and the underscore (_). By convention, the last component of a type name starts with an uppercase letter, the rest start with a lowercase letter.

Listing the type names is mildly useful, but it would be even better if we could see the inheritance relation between the types. The following code prints the inheritance tree in indented format.

private static final int INDENT = 2;
private void listTypes2(TypeSystem ts) {
  // Get the root of the inheritance tree.
  Type top = ts.getTopType();
  // Recursively print the tree.
  printInheritanceTree(ts, top, 0);
}

private void printInheritanceTree(TypeSystem ts, Type type, int level) {
  indent(level); // Print indentation.
  System.out.println(type.getName());
  // Get a vector of the immediate subtypes.
  Vector subTypes =
    ts.getDirectlySubsumedTypes(type);
  ++level; // Increase the indentation level.
  for (int i = 0; i < subTypes.size(); i++) {
    // Print the subtypes.
    printInheritanceTree(ts, (Type) subTypes.get(i), level);
  }
}
  
// A simple, inefficient indenter
private void indent(int level) {
  int spaces = level * INDENT;
  for (int i = 0; i < spaces; i++) {
    System.out.print(" ");
  }
}

This example shows that you can traverse the type hierarchy by starting at the top with TypeSystem.getTopType and by retrieving subtypes with TypeSystem.getDirectlySubsumedTypes().

The Javadocs also have APIs that allow you to access the features, as well as what the allowed value type is for that feature. Here is sample code which prints out all the features of all the types, together with the allowed value types (the feature “range”). Each feature has a “domain” which is the type where it is defined, as well as a “range”.

private void listFeatures2(TypeSystem ts) {
  Iterator featureIterator = ts.getFeatures();
  Feature f;
  System.out.println("Features in the type system:");
  while (featureIterator.hasNext()) {
    f = (Feature) featureIterator.next();
    System.out.println(
      f.getShortName() + ": " +
      f.getDomain() + " -> " + f.getRange());
  }
  System.out.println();
}

We can ask a feature object for its domain (the type it is defined on) and its range (the type of the value of the feature). The terminology derives from the fact that features can be viewed as functions on subspaces of the object space.

Assume a type system declaration that defines two types: Entity and Person. Entity has no features defined within it but inherits from uima.tcas.Annotation – so it has the begin and end features. Person is, in turn, a subtype of Entity, and adds firstName and lastName features. CAS type systems are declaratively specified using XML; the format of this XML is described in Section 2.3, “Type System Descriptors”.

<!-- Type System Definition -->
<typeSystemDescription>
  <types>
    <typeDescription>
      <name>com.xyz.proj.Entity</name>
      <description />
      <supertypeName>uima.tcas.Annotation</supertypeName>
    </typeDescription>
    <typeDescription>
      <name>Person</name>
      <description />
      <supertypeName>com.xyz.proj.Entity </supertypeName>
      <features>
        <featureDescription>
          <name>firstName</name>
          <description />
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
        <featureDescription>
          <name>lastName</name>
          <description />
          <rangeTypeName>uima.cas.String</rangeTypeName>
        </featureDescription>
      </features>
    </typeDescription>
  </types>
</typeSystemDescription>

To be able to access types and features, we need to know their names. The CAS interface defines constants that hold the names of built-in feature names, such as, e.g., CAS.TYPE_NAME_INTEGER. It is good programming practice to create such constants for the types and features you define, for your own use as well as for others who will be using your annotators.

/** Entity type name constant. */
public static final String ENTITY_TYPE_NAME = "com.xyz.proj.Entity";
  
/** Person type name constant. */
public static final String PERSON_TYPE_NAME = "com. xyz.proj.Person";

/** First name feature name constant. */
public static final String FIRST_NAME_FEAT_NAME = "firstName";

/** Last name feature name constant. */
public static final String LAST_NAME_FEAT_NAME = "lastName";

Next we define type and feature member variables; these will hold the values of the type and feature objects needed by the CAS APIs, to be assigned during typeSystemInit().

// Type system object variables
private Type entityType;
private Type personType;
private Feature firstNameFeature;
private Feature lastNameFeature;
private Type stringType;

The type system does not throw an exception if we ask for something that is not known, it simply returns null; therefore the code checks for this and throws a proper exception. We require all these types and features to be defined for the annotator to work. One might imagine situations where certain computations are predicated on some type or feature being defined in the type system, but that is not the case here.

// Get a type object corresponding to a name.
// If it doesn't exist, throw an exception.
private Type initType(String typeName)
  throws AnnotatorInitializationException {
  Type type = ts.getType(typeName);
  if (type == null) {
    throw new AnnotatorInitializationException(
      AnnotatorInitializationException.TYPE_NOT_FOUND,
      new Object[] { this.getClass().getName(), typeName });
  }
  return type;
}

// We add similar code for retrieving feature objects.
// Get a feature object from a name and a type object.
// If it doesn't exist, throw an exception.
private Feature initFeature(String featName, Type type)
  throws AnnotatorInitializationException {
  Feature feat = type.getFeatureByBaseName(featName);
  if (feat == null) {
    throw new AnnotatorInitializationException(
      AnnotatorInitializationException.FEATURE_NOT_FOUND,
      new Object[] { this.getClass().getName(), featName });
  }
  return feat;
}

Using these two functions, code for initializing the type system described above would be:

public void typeSystemInit(TypeSystem aTypeSystem)
    throws AnalysisEngineProcessException {
  this.typeSystem = aTypeSystem;
  // Set type system member variables.
  this.entityType = initType(ENTITY_TYPE_NAME);
  this.personType = initType(PERSON_TYPE_NAME);
  this.firstNameFeature =
    initFeature(FIRST_NAME_FEAT_NAME, personType);
  this.lastNameFeature =
    initFeature(LAST_NAME_FEAT_NAME, personType);
  this.stringType = initType(CAS.TYPE_NAME_STRING);
}

Note that we initialize the string type by using a type name constant from the CAS.

An unnamed built-in bag index exists which holds all feature structures which are indexed. The only access to this index is the method getAllIndexedFs(Type) which returns an iterator over all indexed Feature Structures.

The CAS also contains a built-in index for the type uima.tcas.Annotation, which sorts annotations in the order in which they appear in the document. Annotations are sorted first by increasing begin position. Ties are then broken by decreasing end position (so that longer annotations come first). Annotations that match in both their begin and end features are sorted using the Type Priority (see Section 2.4.1.6, “Type Priority Definition” )

Feature Structures are added to the indexes by calling the FSIndexRepository.addFS(FeatureStructure) method or the equivalent convenience method CAS.addFsToIndexes(FeatureStructure). This adds the Feature Structure to all indexes that are defined for the type of that FeatureStructure (or any of its supertypes). Note that you should not add a Feature Structure to the indexes until you have set values for all of the features that may be used as sort keys in an index.

Iterators are objects of class org.apache.uima.cas.FSIterator. This class extends java.util.Iterator and implements the normal Java iterator methods, plus additional ones that allow moving both forwards and backwards.

The built-in index over the uima.tcas.Annotation type named “AnnotationIndex” has additional capabilities. To use them, you first get a reference to this built-in index using either the getAnnotationIndex method on a CAS View object, or by asking the FSIndexRepository object for an index having the particular name “AnnotationIndex”, for example:

AnnotationIndex idx = aCAS.getAnnotationIndex(); 
// or you can iterate over a specific subtype of Annotation:        
AnnotationIndex idx = aCAS.getAnnotationIndex(aType); 

This object can be used to produce several additional kinds of iterators. It can produce unambiguous iterators; these skip over elements until it finds one where the start position of the next annotation is equal to or greater than the end position of the previously returned annotation.

It can also produce several kinds of subiterators; these are iterators whose annotations fall within the span of another annotation. This kind of iterator can also have the unambiguous property, if desired. It also can be “strict” or not; strict means that the returned annotation lies completely within the span of the controlling annotation. Non-strict only implies that the beginning of the returned annotation falls within the span of the controlling annotation.

There is also a method which produces an AnnotationTree object, which contains nodes representing the results of doing a strict, unambiguous subiterator over the span of some controlling annotation. For more details, please refer to the Javadocs for the org.apache.uima.cas.text package.

There is a set of API calls that build constraint objects. These objects can be used directly to test if a particular feature structure matches (satisfies) the constraint, or they can be passed to the createFilteredIterator method to create an iterator that skips over instances which fail to satisfy the constraint.

It is possible to specify a feature value located by following a chain of references starting from the feature structure being tested. Here's a scenario to explore this concept. Let's suppose you have the following type system (namespaces are omitted for clarity):

If you want to filter Token instances, such that only those tokens get through which are proper names of class 3 (for example), you would need a test that started with a Token instance, followed its PartOfSpeech reference to another instance (the ProperName instance) and then tested the Class feature of that instance for a value equal to 3.

To support this, the filtering approach has components that specify tests, and components that specify “paths”. The tests that can be done include testing references to type instances to see if they are instances of some type or its subtypes; this is done with a FSTypeConstraint constraint. Other tests check for equality or, for numeric values, ranges.

Each test may be combined with a path – to get to the value to test. Tests that start from a feature structure instance can be combined with and and or connectors. The Javadocs for these are in the package org.apache.uima.cas in the classes that end in Constraint, plus the classes ConstraintFactory, FeaturePath and CAS. Here's an example; assume the variable cas holds a reference to a CAS instance.

// Start by getting the constraint factory from the CAS.
ConstraintFactory cf = cas.getConstraintFactory();

// To specify a path to an item to test, you start by
// creating an empty path.
FeaturePath path = cas.createFeaturePath();

// Add POS feature to path, creating one-element path.
path.addFeature(posFeat);

// You can extend the chain arbitrarily by adding additional
// features.

// Create a new type constraint.  

// Type constraints will check that structures
// they match against have a type at least as specific
// as the type specified in the constraint.
FSTypeConstraint nounConstraint = cf.createTypeConstraint();

// Set the type (by default it is TOP).
// This succeeds if the type being tested by this constraint
// is nounType or a subtype of nounType.
nounConstraint.add(nounType);

// Embed the noun constraint under the pos path.
// This means, associate the test with the path, so it tests the
// proper value.

// The result is a test which will
// match a feature structure that has a posFeat defined
// which has a value which is an instance of a nounType or
// one of its subtypes.
FSMatchConstraint embeddedNoun = cf.embedConstraint(path, nounConstraint);

// Create a type constraint for token (or a subtype of it)
FSTypeConstraint tokenConstraint = cf.createTypeConstraint();

// Set the type.
tokenConstraint.add(tokenType);

// Create the final constraint by conjoining the two constraints.
FSMatchConstraint nounTokenCons = cf.and(nounConstraint, tokenConstraint);

// Create a filtered iterator from some annotation iterator.
FSIterator it = cas.createFilteredIterator(annotIt, nounTokenCons);

The main objects implementing the APIs discussed here are shown in the diagram below. The hierarchy represents that there is a way to get from an upper object to an instance of the lower object, usually by using a method on the upper object; this is not an inheritance hierarchy.

Figure 4.1. CAS Object hierarchy

The main Interface is the CAS interface. This has most of the functionality of the CAS, except for the type system metadata access, and the indexing access. JCas and CAS are alternative representations and API approaches to the CAS; each has a method to get the other. You can mix JCas and CAS APIs in your application as needed. To use the JCas APIs, you have to create the Java classes that correspond to the CAS types, and include them in the Java class path of the application. If you have a CAS object, you can get a JCas object by using the getJCas() method call on the CAS object; likewise, you can get the CAS object from a JCas by using the getCAS() method call on the JCas object. There is also a low level CAS interface that is not part of the official API, and is intended for internal use only – it is not documented here.

The type system metadata APIs are found in the TypeSystem interface. The objects defining each type and feature are defined by the interfaces Type and Feature. The Type interface has methods to see what types subsume other types, to iterate over the types available, and to extract information about the types, including what features it has. The Feature interface has methods that get what type it belongs to, its name, and its range (the kind of values it can hold).

The FSIndexRepository gives you access to methods to get instances of indexes, and also provides access to the iterator over all indexed feature structures: getAllIndexedFs(aType). The FSIndex and AnnotationIndex objects give you methods to create instances of iterators.

Iterators and the CAS methods that create new feature structures return FeatureStructure objects. These objects can be used to set and get the values of defined features within them.

If the type system specification changes, you have to re-run the JCasGen generator. This will produce updated Java for the Class Models that capture the changed specification. If you have previously augmented the source for these Java Class Models, your changes must be merged with the newly (re)generated Java source code for the Class Models. This can be done by hand, or you can run the version of JCasGen that is integrated with Eclipse, and use automatic merging that is done using Eclipse's EMF plug-in. You can obtain Eclipse and the needed EMF plug-in from http://www.eclipse.org/.

If you run the generator version that works without using Eclipse, it will not merge Java source changes you may have previously made; if you want them retained, you'll have to do the merging by hand.

The Java source merging will keep additional constructors, additional fields, and any changes you may have made to the readObject method (see below). Merging will not delete classes in the target corresponding to deleted CAS types, which no longer are in the source – you should delete these by hand.

Any additional constructors that you add must include the JCas argument. The first line of your constructor is required to be

this(jcas);        // run the standard constructor

where jcas is the passed in JCas reference. If the type you're defining extends uima.tcas.Annotation, JCasGen will automatically add a constructor which takes 2 additional parameters – the begin and end Java int values, and set the uima.tcas.Annotation begin and end fields.

Here's an example: If you're defining a type MyType which has a feature parent, you might make an additional constructor which has an additional argument of parent:

MyType(JCas jcas, MyType parent) {
  this(jcas);        // run the standard constructor
  setParent(parent); // set the parent field from the parameter
}

The following modifications, if made in generated items, will be preserved when regenerating.

The public/private etc. flags associated with methods (getters and setters). You can change the default (“public”) if needed.

“final” or “abstract” can be added to the type itself, with the usual semantics.

When running aggregate AEs (Analysis Engines), or a set of AEs in a collection processing engine, the UIMA framework will build a merged type system (Note: this “merge” is merging types, not to be confused with merging Java source code, discussed above). This merged type system has all the types of every component used in the application. In addition, application code can use UIMA Framework APIs to read and merge type descriptions, manually.

In most cases, each type system can have its own Java Class Models generated individually, perhaps at an earlier time, and the resulting class files (or .jar files containing these class files) can be put in the class path to enable JCas.

However, it is possible that there may be multiple definitions of the same CAS type, each of which might have different features defined. In this case, the UIMA framework will create a merged type by accumulating all the defined features for a particular type into that type's type definition. However, the JCas classes for these types are not automatically merged, which can create some issues for JCas users, as discussed in the next section.

When there are multiple definitions of the same CAS type with different features defined, then JCasGen can be re-run on the merged type system, to create one set of JCas Class definitions for the merged types, which can then be shared by all the components. Directions for running JCasGen can be found in Chapter 6, JCasGen User's Guide in UIMA Tools Guide and Reference. This is typically done by the person who is assembling the Aggregate Analysis Engine or Collection Processing Engine. The resulting merged Java Class Model will then contain get and set methods for the complete set of features. These Java classes must then be made available in the class path, replacing the pre-merge versions of the classes.

If hand-modifications were done to the pre-merge versions of the classes, these must be applied to the merged versions, as described in section Section 5.4.1, “Keeping hand-coded augmentations when regenerating”, above. If just one of the pre-merge versions had hand-modifications, the source for this hand-modified version can be put into the file system where the generated output will go, and the -merge option for JCasGen will automatically merge the hand-modifications with the generated code. If both pre-merged versions had hand-modifications, then these modifications must be manually merged.

An alternative to this is packaging the components as individual PEAR files, each with their own version of the JCas generated Classes. The Framework (as of release 2.2) can run PEAR files using the pear file descriptor, and supply each component with its particular version of the JCas generated class.

The recommended approach in UIMA is to build and maintain type systems as separate components, which are imported by Annotators. Using this approach, Type Merging does not occur because the Type System and its JCas classes are centrally managed and shared by the annotators.

If you do choose to create a JCas Annotator that relies on Type Merging (meaning that your annotator redefines a Type that is already in use elsewhere, and adds its own features), this can negatively impact the reusability of your annotator, unless your component is used as a PEAR file.

If not using PEAR file packaging isolation capability, whenever anyone wants to combine your annotator with another annotator that uses a different version of the same Type, they will need to be aware of all of the issues described in the previous section. They will need to have the know-how to re-run JCasGen and appropriately set up their classpath to include the merged Java classes and to not include the pre-merge classes. (To enable this, you should package these classes separately from other .jar files for your annotator, so that they can be more easily excluded.) And, if you have done hand-modifications to your JCas classes, the person assembling your annotator will need to properly merge those changes. These issues significantly complicate the task of combining annotators, and will cause your annotator not to be as easily reusable as other UIMA annotators.

There is one built-in type, uima.tcas.DocumentAnnotion, to which applications can add additional features. (All other built-in types are "feature-final" and you cannot add additional features to them.) Frequently, additional features are added to uima.tcas.DocumentAnnotion to provide a place to store document-level metadata.

For the same reasons mentioned in the previous section, adding features to DocumentAnnotation is not recommended if you are using JCas. Instead, it is recommended that you define your own type for storing your document-level metadata. You can create an instance of this type and add it to the indexes in the usual way. You can then retrieve this instance using the iterator returned from the methodgetAllIndexedFS(type) on an instance of a JFSIndexRepository object. (As of UIMA v2.1, you do not have to declare a custom index in your descriptor to get this to work).

If you do choose to add features to DocumentAnnotation, there are additional issues to be aware of. The UIMA SDK provides the JCas cover class for the built-in definition of DocumentAnnotation, in the separate jar file uima-document-annotation.jar. If you add additional features to DocumentAnnotation, you must remove this jar file from your classpath, because you will not want to use the default JCas cover class. You will need to re-run JCasGen as described in Section 5.5.2, “JCasGen support for type merging”. JCasGen will generate a new cover class for DocumentAnnotation, which you must place in your classpath in lieu of the version in uima-document-annotation.jar.

Also, this is the reason why the method JCas.getDocumentAnnotationFs() returns type TOP, rather than type DocumentAnnotation. Because the DocumentAnnotation class can be replaced by users, it is not part of uima-core.jar and so the core UIMA framework cannot have any references to it. In your code, you may “cast” the result of JCas.getDocumentAnnotationFs() to type DocumentAnnotation, which must be available on the classpath either via uima-document-annotation.jar or by including a custom version that you have generated using JCasGen.

The new operator creates new instances of JCas types. It takes at least one parameter, the JCas instance in which the type is to be created. For example, if there was a type Meeting defined, you can create a new instance of it using:

Meeting m = new Meeting(jcas);

Other variations of constructors can be added in custom code; the single parameter version is the one automatically generated by JCasGen. For types that are subtypes of Annotation, JCasGen also generates an additional constructor with additional “begin” and “end” arguments.

If the CAS type Meeting had fields location and time, you could get or set these by using getter or setter methods. These methods have names formed by splicing together the word “get” or “set” followed by the field name, with the first letter of the field name capitalized. For instance

getLocation()

The getter forms take no parameters and return the value of the field; the setter forms take one parameter, the value to set into the field, and return void.

There are built-in CAS types for arrays of integers, strings, floats, and feature structures. For fields whose values are these types of arrays, there is an alternate form of getters and setters that take an additional parameter, written as the first parameter, which is the index in the array of an item to get or set.

The only way to access instances (not otherwise referenced from other instances) passed in to your annotator in its JCas is to use an iterator over some index. Indexes in the CAS are specified in the annotator descriptor. Indexes have a name; text annotators have a built-in, standard index over all annotations.

To get an index, first get the JFSIndexRepository from the JCas using the method jcas.getJFSIndexRepository(). Here are the calls to get indexes:

JFSIndexRepository ir = jcas.getJFSIndexRepository();

ir.getIndex(name-of-index) // get the index by its name, a string
ir.getIndex(name-of-index, Foo.type) // filtered by specific type

ir.getAnnotationIndex()      // get AnnotationIndex
ir.getAnnotationIndex(Foo.type)      // filtered by specific type

For convenience, the getAnnotationIndex method is available directly on the JCas object instance; the implementation merely forwards to the associated index repository.

Filtering types have to be a subtype of the type specified for this index in its index specification. They can be written as either Foo.type or if you have an instance of Foo, you can write

fooInstance.jcasType.casType.  

Foo is (of course) an example of the name of the type.

CAS indexes are maintained automatically by the CAS. But you must add any instances of feature structures you want the index to find, to the indexes by using the call:

myInstance.addToIndexes();

Do this after setting all features in the instance which could be used in indexing, for example, in determining the sorting order. After indexing, do not change the values of these particular features because the indexes will not be updated. If you need to change the values, you must first remove the instance from the CAS indexes, change the values, and then add the instance back. To remove an instance from the indexes, use the method:

myInstance.removeFromIndexes();

When writing a Multi-View component, you may need to index instances in multiple CAS views. The methods above use the indexes associated with the current JCas object. There is a variation of the addToIndexes / removeFromIndexes methods which takes one argument: a reference to a JCas object holding the view in which you want to index this instance.

myInstance.addToIndexes(anotherJCas)
myInstance.removeFromIndexes(anotherJCas)

You can also explicitly add instances to other views using the addFsToIndexes method on other JCas (or CAS) objects. For instance, if you had 2 other CAS views (myView1 and myView2), in which you wanted to index myInstance, you could write:

myInstance.addToIndexes(); //addToIndexes used with the new operator
myView1.addFsToIndexes(myInstance); // index myInstance in myView1
myView2.addFsToIndexes(myInstance); // index myInstance in myView2

The rules for determining which index to use with a particular JCas object are designed to behave the way most would think they should; if you need specific behavior, you can always explicitly designate which view the index adding and removing operations should work on.

The rules are: If the instance is a subtype of AnnotationBase, then the view is the view associated with the annotation as specified in the feature holding the view reference in AnnotationBase. Otherwise, if the instance was created using the "new" operator, then the view is the view passed to the instance's constructor. Otherwise, if the instance was created by getting a feature value from some other instance, whose range type is a feature structure, then the view is the same as the referring instance. Otherwise, if the instance was created by any of the Feature Structure Iterator operations over some index, then it is the view associated with the index.

Once you have an index obtained from the JCas, you can get an iterator from the index; here is an example:

FSIndexRepository ir = jcas.getFSIndexRepository();
FSIndex myIndex = ir.getIndex("myIndexName");
FSIterator myIterator = myIndex.iterator();

JFSIndexRepository ir = jcas.getJFSIndexRepository();
FSIndex myIndex = ir.getIndex("myIndexName", Foo.type); // filtered
FSIterator myIterator = myIndex.iterator();

Iterators work like normal Java iterators, but are augmented to support additional capabilities. Iterators are described in the CAS Reference, Section 4.7, “Indexes and Iterators”.

The basic concept of a UIMA application includes assembling engines into a flow. The application made up of these Engines are run within the UIMA Framework, either by the Collection Processing Manager, or by using more basic UIMA Framework APIs.

The UIMA Framework exists within a JVM (Java Virtual Machine). A JVM has the capability to load multiple applications, in a way where each one is isolated from the others, by using a separate class loader for each application. For instance, one set of UIMA Framework Classes could be shared by multiple sets of application - specific classes, even if these application-specific classes had the same names but were different versions.

If you are using the ExtensionClassPaths, the JCas cover classes are loaded under a class loader created by the ResourceManager part of the UIMA Framework. If you reference the same JCas classes outside of any UIMA component, for instance, in top level application code, the JCas classes used by that top level application code also must be in the class path for the application code.

Alternatively, you could do all the JCas processing inside a UIMA component (and do no processing using JCas outside of the UIMA pipeline).

The first step in the PEAR creation process is to create a PEAR structure. The PEAR structure is a structured tree of folders and files, including the following elements:

Figure 6.1. The PEAR Structure

After creating the PEAR structure, the component's descriptor files, code files, resources files, and any other files and folders are copied into the corresponding folders of the PEAR structure. The developer should make sure that the code would work with this layout of files and folders, and that there are no broken links. Although it is strongly discouraged, the optional elements of the PEAR structure can be replaced by other user defined files and folder, if required for the component to work properly.

Currently there are three types of component packages depending on their deployment:

The installation descriptor is an xml file called install.xml under the metadata folder of the PEAR structure. It's also called InsD. The InsD XML file should be created in the UTF-8 file encoding. The InsD should contain the following sections:

The following is a sample “documented template” which describes content of the installation descriptor install.xml:

<? xml version="1.0" encoding="UTF-8"?>
<!-- Installation Descriptor Template -->
<COMPONENT_INSTALLATION_DESCRIPTOR>
  <!-- Specifications of OS names, including version, etc. -->
  <OS>
    <NAME>OS_Name_1</NAME>
    <NAME>OS_Name_2</NAME>
  </OS>
  <!-- Specifications of required standard toolkits -->
  <TOOLKITS>
    <JDK_VERSION>JDK_Version</JDK_VERSION>
  </TOOLKITS>

  <!-- There are 2 types of variables that are used in the InsD:
       a) $main_root , which will be substituted with the real path to the
                 main component root directory after installing the
                 main (submitted) component
       b) $component_id$root, which will be substituted with the real path
          to the root directory of a given delegate component after
          installing the given delegate component -->

  <!-- Specification of submitted component (AE)             -->
  <!-- Note: submitted_component_id is assigned by developer; -->
  <!--       XML descriptor file name is set by developer.    -->
  <!-- Important: ID element should be the first in the       -->
  <!--            SUBMITTED_COMPONENT section.                -->
  <!-- Submitted component may include optional specification -->
  <!-- of Collection Reader that can be used for testing the  -->
  <!-- submitted component.                                   -->
  <!-- Submitted component may include optional specification -->
  <!-- of CAS Consumer that can be used for testing the       -->
  <!-- submitted component.                                   -->

  <SUBMITTED_COMPONENT>
    <ID>submitted_component_id</ID>
    <NAME>Submitted component name</NAME>
    <DESC>$main_root/desc/ComponentDescriptor.xml</DESC>

    <!-- deployment options:                                   -->
    <!-- a) "standard" is deploying AE locally                 -->
    <!-- b) "service"  is deploying AE locally as a service,   -->
    <!--    using specified command (script)                   -->
    <!-- c) "network"  is deploying a pure network AE, which   -->
    <!--    is running somewhere on the network                -->

    <DEPLOYMENT>standard | service | network</DEPLOYMENT>

    <!-- Specifications for "service" deployment option only   -->
    <SERVICE_COMMAND>$main_root/bin/startService.bat</SERVICE_COMMAND>
    <SERVICE_WORKING_DIR>$main_root</SERVICE_WORKING_DIR>
    <SERVICE_COMMAND_ARGS>

      <ARGUMENT>
        <VALUE>1st_parameter_value</VALUE>
        <COMMENTS>1st parameter description</COMMENTS>
      </ARGUMENT>

      <ARGUMENT>
        <VALUE>2nd_parameter_value</VALUE>
        <COMMENTS>2nd parameter description</COMMENTS>
      </ARGUMENT>

    </SERVICE_COMMAND_ARGS>

    <!-- Specifications for "network" deployment option only   -->

    <NETWORK_PARAMETERS>
      <VNS_SPECS VNS_HOST="vns_host_IP" VNS_PORT="vns_port_No" />
    </NETWORK_PARAMETERS>

    <!-- General specifications                                -->

    <COMMENTS>Main component description</COMMENTS>

    <COLLECTION_READER>
      <COLLECTION_ITERATOR_DESC>
        $main_root/desc/CollIterDescriptor.xml
      </COLLECTION_ITERATOR_DESC>

      <CAS_INITIALIZER_DESC>
        $main_root/desc/CASInitializerDescriptor.xml
      </CAS_INITIALIZER_DESC>
    </COLLECTION_READER>

    <CAS_CONSUMER>
      <DESC>$main_root/desc/CASConsumerDescriptor.xml</DESC>
    </CAS_CONSUMER>

  </SUBMITTED_COMPONENT>
  <!-- Specifications of the component installation process -->
  <INSTALLATION>
    <!-- List of delegate components that should be installed together -->
    <!-- with the main submitted component (for aggregate components)  -->
    <!-- Important: ID element should be the first in each             -->

    <!--            DELEGATE_COMPONENT section.                        -->
    <DELEGATE_COMPONENT>
      <ID>first_delegate_component_id</ID>
      <NAME>Name of first required separate component</NAME>
    </DELEGATE_COMPONENT>

    <DELEGATE_COMPONENT>
      <ID>second_delegate_component_id</ID>
      <NAME>Name of second required separate component</NAME>
    </DELEGATE_COMPONENT>

    <!-- Specifications of local path names that should be replaced -->
    <!-- with real path names after the main component as well as   -->
    <!-- all required delegate (library) components are installed.  -->
    <!-- <FILE> and <REPLACE_WITH> values may use the $main_root or -->
    <!-- one of the $component_id$root variables.                   -->
    <!-- Important: ACTION element should be the first in each      -->
    <!--            PROCESS section.                                -->

    <PROCESS>
      <ACTION>find_and_replace_path</ACTION>
      <PARAMETERS>
        <FILE>$main_root/desc/ComponentDescriptor.xml</FILE>
        <FIND_STRING>../resources/dict/</FIND_STRING>
        <REPLACE_WITH>$main_root/resources/dict/</REPLACE_WITH>
        <COMMENTS>Specify actual dictionary location in XML component
          descriptor
        </COMMENTS>
      </PARAMETERS>
    </PROCESS>

    <PROCESS>
      <ACTION>find_and_replace_path</ACTION>
      <PARAMETERS>
        <FILE>$main_root/desc/DelegateComponentDescriptor.xml</FILE>
        <FIND_STRING>
local_root_directory_for_1st_delegate_component/resources/dict/
        </FIND_STRING>
        <REPLACE_WITH>
          $first_delegate_component_id$root/resources/dict/
        </REPLACE_WITH>
        <COMMENTS>
          Specify actual dictionary location in the descriptor of the 1st
          delegate component
        </COMMENTS>
      </PARAMETERS>
    </PROCESS>

    <!-- Specifications of environment variables that should be set prior
         to running the main component and all other reused components.
         <VAR_VALUE> values may use the $main_root or one of the
         $component_id$root variables. -->

    <PROCESS>
      <ACTION>set_env_variable</ACTION>
      <PARAMETERS>
        <VAR_NAME>env_variable_name</VAR_NAME>
        <VAR_VALUE>env_variable_value</VAR_VALUE>
        <COMMENTS>Set environment variable value</COMMENTS>
      </PARAMETERS>
    </PROCESS>

  </INSTALLATION>
</COMPONENT_INSTALLATION_DESCRIPTOR>

<SUBMITTED_COMPONENT>
  <ID>submitted_component_id</ID>
  <NAME>Submitted component name</NAME>
  <DESC>$main_root/desc/ComponentDescriptor.xml</DESC>

<DEPLOYMENT>standard</DEPLOYMENT>

<DEPLOYMENT>service</DEPLOYMENT>
<SERVICE_COMMAND>$main_root/bin/startService.bat</SERVICE_COMMAND>
<SERVICE_WORKING_DIR>$main_root</SERVICE_WORKING_DIR>
<SERVICE_COMMAND_ARGS>
  <ARGUMENT>
    <VALUE>1st_parameter_value</VALUE>
    <COMMENTS>1st parameter description</COMMENTS>
  </ARGUMENT>
  <ARGUMENT>
    <VALUE>2nd_parameter_value</VALUE>
    <COMMENTS>2nd parameter description</COMMENTS>
  </ARGUMENT>
</SERVICE_COMMAND_ARGS>

<DEPLOYMENT>network</DEPLOYMENT>
<NETWORK_PARAMETERS>
  <VNS_SPECS VNS_HOST="vns_host_IP" VNS_PORT="vns_port_No" />
</NETWORK_PARAMETERS>

The last step of the PEAR process is to simply zip the content of the PEAR root folder (not including the root folder itself) to a PEAR file with the extension “.pear”.

To do this you can either use the PEAR packaging tools that are described in “Chapter 7, PEAR Packager User's Guide in UIMA Tools Guide and Reference” or you can use the PEAR packaging API that is shown below.

To use the PEAR packaging API you first have to create the necessary information for the PEAR package:

    //define PEAR data  
    String componentID = "AnnotComponentID";
    String mainComponentDesc = "desc/mainComponentDescriptor.xml";
    String classpath ="$main_root/bin;";
    String datapath ="$main_root/resources;";
    String mainComponentRoot = "/home/user/develop/myAnnot";
    String targetDir = "/home/user/develop";
    Properties annotatorProperties = new Properties();
    annotatorProperties.setProperty("sysProperty1", "value1");

To create a complete PEAR package in one step call:

PackageCreator.generatePearPackage(
   componentID, mainComponentDesc, classpath, datapath, 
   mainComponentRoot, targetDir, annotatorProperties);

The created PEAR package has the file name <componentID>.pear and is located in the <targetDir>.

To create just the PEAR installation descriptor in the main component root directory call:

PackageCreator.createInstallDescriptor(componentID, mainComponentDesc,
   classpath, datapath, mainComponentRoot, annotatorProperties);

To package a PEAR file with an existing installation descriptor call:

PackageCreator.createPearPackage(componentID, mainComponentRoot,
   targetDir);

The created PEAR package has the file name <componentID>.pear and is located in the <targetDir>.

The example below shows how to use the PEAR APIs to install a PEAR package and access the installed PEAR package data. For more details about the PackageBrowser API, please refer to the Javadocs for the org.apache.uima.pear.tools package.

File installDir = new File("/home/user/uimaApp/installedPears");
File pearFile = new File("/home/user/uimaApp/testpear.pear");
boolean doVerification = true;

try {
  // install PEAR package
  PackageBrowser instPear = PackageInstaller.installPackage(
 	installDir, pearFile, doVerification);

  // retrieve installed PEAR data
  // PEAR package classpath
  String classpath = instPear.buildComponentClassPath();
  // PEAR package datapath
  String datapath = instPear.getComponentDataPath();
  // PEAR package main component descriptor
  String mainComponentDescriptor = instPear
     	.getInstallationDescriptor().getMainComponentDesc();
  // PEAR package component ID
  String mainComponentID = instPear
     	.getInstallationDescriptor().getMainComponentId();
  // PEAR package pear descriptor
  String pearDescPath = instPear.getComponentPearDescPath();

  // print out settings
  System.out.println("PEAR package class path: " + classpath);
  System.out.println("PEAR package datapath: " + datapath);
  System.out.println("PEAR package mainComponentDescriptor: " 
   	+ mainComponentDescriptor);
  System.out.println("PEAR package mainComponentID: " 
   	+ mainComponentID);
  System.out.println("PEAR package specifier path: " + pearDescPath); 	

  } catch (PackageInstallerException ex) {
    // catch PackageInstallerException - PEAR installation failed
    ex.printStackTrace();
    System.out.println("PEAR installation failed");
  } catch (IOException ex) {
    ex.printStackTrace();
    System.out.println("Error retrieving installed PEAR settings");
  }

To run a PEAR package after it was installed using the PEAR API see the example below. It use the generated PEAR specifier that was automatically created during the PEAR installation. For more details about the APIs please refer to the Javadocs.

File installDir = new File("/home/user/uimaApp/installedPears");
File pearFile = new File("/home/user/uimaApp/testpear.pear");
boolean doVerification = true;

try {

  // Install PEAR package
  PackageBrowser instPear = PackageInstaller.installPackage(
  	installDir, pearFile, doVerification);

  // Create a default resouce manager
  ResourceManager rsrcMgr = UIMAFramework.newDefaultResourceManager();

  // Create analysis engine from the installed PEAR package using
  // the created PEAR specifier
  XMLInputSource in = 
        new XMLInputSource(instPear.getComponentPearDescPath());
  ResourceSpecifier specifier =
        UIMAFramework.getXMLParser().parseResourceSpecifier(in);
  AnalysisEngine ae = 
        UIMAFramework.produceAnalysisEngine(specifier, rsrcMgr, null);

  // Create a CAS with a sample document text
  CAS cas = ae.newCAS();
  cas.setDocumentText("Sample text to process");
  cas.setDocumentLanguage("en");

  // Process the sample document
  ae.process(cas);
  } catch (Exception ex) {
         ex.printStackTrace();
  }

In XMI, a multi-valued property is the most natural XMI representation for most cases. Consider the example where the FeatureStructure of type org.myproj.Baz has a feature myIntArray whose value is the integer array {2,4,6}. This can be mapped to:

<myproj:Baz xmi:id="3" myIntArray="2 4 6"/>

or equivalently:

<myproj:Baz xmi:id="3">
  <myIntArray>2</myIntArray>
  <myIntArray>4</myIntArray>
  <myIntArray>6</myIntArray>
</myproj:Baz>

Note that String arrays whose elements contain embedded spaces MUST use the latter mapping.

FSArray or FSList features are serialized in a similar way. For example an FSArray feature that contains references to the elements with xmi:id's “13” and “42” could be serialized as:

<myproj:Baz xmi:id="3" myFsArray="13 42"/>

or:

<myproj:Baz xmi:id="3">
  <myFsArray href="#13"/>
  <myFsArray href="#42"/>
</myproj:Baz>

The multi-valued-property representation described in the previous section does not allow multiple references to an array or list object. Therefore, it cannot be used for features that are defined to allow multiple references (i.e. features for which multipleReferencesAllowed = true in the Type System Description).

When multipleReferencesAllowed is set to true, array and list features are serialized as references, and the array or list objects are serialized as separate objects in the XMI. Consider again the example where the FeatureStructure of type org.myproj.Baz has a feature myIntArray whose value is the integer array {2,4,6}. If myIntArray is defined with multipleReferencesAllowed=true, the serialization will be as follows:

<myproj:Baz xmi:id="3" myIntArray="4"/>

or:

<myproj:Baz xmi:id="3">
  <myIntArray href="#4"/>
</myproj:Baz>

with the array object serialized as

<cas:IntegerArray xmi:id="4" elements="2 4 6"/>

or:

<cas:IntegerArray xmi:id="4">
  <elements>2</elements>
  <elements>4</elements>
  <elements>6</elements>
</cas:IntegerArray>

Note that in this case, the XML element name is formed from the CAS type name (e.g. “uima.cas.IntegerArray”) in the same way as for other FeatureStructures. The elements of the array are serialized either as a space-separated attribute named “elements” or as a series of child elements named “elements”.

List nodes are just standard FeatureStructures with “head” and “tail” features, and are serialized using the normal FeatureStructure serialization. For example, an IntegerList with the values 2, 4, and 6 would be serialized as the four objects:

<cas:NonEmptyIntegerList xmi:id="10" head="2" tail="11"/>
<cas:NonEmptyIntegerList xmi:id="11" head="4" tail="12"/>
<cas:NonEmptyIntegerList xmi:id="12" head="6" tail="13"/>
<cas:EmptyIntegerList xmi:id"13"/>

This representation of arrays allows multiple references to an array of list. It also allows a feature with range type TOP to refer to an array or list. However, it is a very unnatural representation in XMI and does not support interoperability with other XMI-based systems, so we instead recommend using the multi-valued-property representation described in the previous section whenever it is possible.

In UIMA, an element of an FSArray or FSList may be null. In XMI, multi-valued properties do not permit null values. As a workaround for this, we use a dummy instance of the special type cas:NULL, which has xmi:id 0. For example, in the following example the “myFsArray” feature refers to an FSArray whose second element is null:

<cas:NULL xmi:id="0"/>
<myproj:Baz xmi:id="3">
  <myFsArray href="#13"/>
  <myFsArray href="#0"/>
  <myFsArray href="#42"/>
</myproj:Baz>