Chapter 7
GATE Embedded [#]

7.1 Quick Start with GATE Embedded [#]

Embedding GATE-based language processing in other applications using GATE Embedded (the GATE API) is straightforward:

For example, this code will create the ANNIE extraction system:

If you want to use resources from any plugins, you need to load the plugins before calling createResource:

Instead of creating your processing resources individually using the Factory, you can create your application in GATE Developer, save it using the ‘save application state’ option (see Section 3.8.3), and then load the saved state from your code. This will automatically reload any plugins that were loaded when the state was saved, you do not need to load them manually.

There are many examples of using GATE Embedded available at http://gate.ac.uk/wiki/code-repository/.

7.2 Resource Management in GATE Embedded [#]

As outlined earlier, GATE defines three different types of resources:

Language Resources

: (LRs) entities that hold linguistic data.

Processing Resources

: (PRs) entities that process data.

Visual Resources

: (VRs) components used for building graphical interfaces.

These resources are collectively named CREOLE¹ resources.

All CREOLE resources have some associated meta-data in the form of an entry in a special XML file named creole.xml. The most important role of that meta-data is to specify the set of parameters that a resource understands, which of them are required and which not, if they have default values and what those are. The valid parameters for a resource are described in the resource’s section of its creole.xml file or in Java annotations on the resource class – see Section 4.7.

All resource types have creation-time parameters that are used during the initialisation phase. Processing Resources also have run-time parameters that get used during execution (see Section 7.5 for more details).

Controllers are used to define GATE applications and have the role of controlling the execution flow (see Section 7.6 for more details).

This section describes how to create and delete CREOLE resources as objects in a running Java virtual machine. This process involves using GATE’s Factory class², and, in the case of LRs, may also involve using a DataStore.

CREOLE resources are Java Beans; creation of a resource object involves using a default constructor, then setting parameters on the bean, then calling an init() method. The Factory takes care of all this, makes sure that the GATE Developer GUI is told about what is happening (when GUI components exist at runtime), and also takes care of restoring LRs from DataStores. A programmer using GATE Embedded should never call the constructor of a resource: always use the Factory!

Creating a resource involves providing the following information:

• fully qualified class name for the resource. This is the only required value. For all the rest, defaults will be used if actual values are not provided.
• values for the creation time parameters.^† 
• initial values for resource features.^†  For an explanation on features see Section 7.4.2.
• a name for the new resource;

^†  Parameters and features need to be provided in the form of a GATE Feature Map which is essentially a java Map (java.util.Map) implementation, see Section 7.4.2 for more details on Feature Maps.

Creating a resource via the Factory involves passing values for any create-time parameters that require setting to the Factory’s createResource method. If no parameters are passed, the defaults are used. So, for example, the following code creates a default ANNIE part-of-speech tagger:

Note that if the resource created here had any parameters that were both mandatory and had no default value, the createResource call would throw an exception. In this case, all the information needed to create a tagger is available in default values given in the tagger’s XML definition (in plugins/ANNIE/creole.xml):

Here the two parameters shown are either ‘runtime’ parameters, which are set before a PR is executed, or have a default value (in this case the default rules file is distributed with GATE itself).

When creating a Document, however, the URL of the source for the document must be provided³. For example:

Note that the document created here is transient: when you quit the JVM the document will no longer exist. If you want the document to be persistent, you need to store it in a DataStore (see Section 7.4.5).

Apart from createResource() methods with different signatures, Factory also provides some shortcuts for common operations, listed in table 7.1.

GATE maintains various data structures that allow the retrieval of loaded resources. When a resource is no longer required, it needs to be removed from those structures in order to remove all references to it, thus making it a candidate for garbage collection. This is achieved using the  deleteResource(Resource res) method on Factory.

Simply removing all references to a resource from the user code will NOT be enough to make the resource collect-able. Not calling  Factory.deleteResource() will lead to memory leaks!

7.3 Using CREOLE Plugins [#]

As shown in the examples above, in order to use a CREOLE resource the relevant CREOLE plugin must be loaded. Processing Resources, Visual Resources and Language Resources other than Document, Corpus and DataStore all require that the appropriate plugin is first loaded. When using Document, Corpus or DataStore, you do not need to first load a plugin. The following API calls listed in table 7.2 are relevant to working with CREOLE plugins.

If you are writing a GATE Embedded application and have a single resource class that will only be used from your embedded code (and so does not need to be distributed as a complete plugin), and all the configuration for that resource is provided as Java annotations on the class, then it is possible to register the class with the CreoleRegister at runtime without needing to package it in a JAR and provide a creole.xml file. You can pass the Class object representing your resource class to Gate.getCreoleRegister().registerComponent() method and then create instances of the resource in the usual way using Factory.createResource. Note that resources cannot be registered this way in the developer GUI, and cannot be included in saved application states (see section ?? below).

7.4 Language Resources [#]

This section describes the implementation of documents and corpora in GATE.

7.4.1 GATE Documents

Documents are modelled as content plus annotations (see Section 7.4.4) plus features (see Section 7.4.2).

The content of a document can be any implementation of the  gate.DocumentContent interface; the features are <attribute, value> pairs stored a Feature Map. Attributes are String values while the values can be any Java object.

The annotations are grouped in sets (see section 7.4.3). A document has a default (anonymous) annotations set and any number of named annotations sets.

Documents are defined by the gate.Document interface and there is also a provided implementation:

gate.corpora.DocumentImpl

: transient document. Can be stored persistently through Java serialisation.

Main Document functions are presented in table 7.3.

7.4.2 Feature Maps [#]

All CREOLE resources as well as the Controllers and the annotations can have attached meta-data in the form of Feature Maps.

A Feature Map is a Java Map (i.e. it implements the java.util.Map interface) and holds <attribute-name, attribute-value> pairs. The attribute names are Strings while the values can be any Java Objects.

The use of non-Serialisable objects as values is strongly discouraged.

Feature Maps are created using the gate.Factory.newFeatureMap() method.

The actual implementation for FeatureMaps is provided by the  gate.util.SimpleFeatureMapImpl class.

Objects that have features in GATE implement the gate.util.FeatureBearer interface which has only the two accessor methods for the object features: FeatureMap getFeatures() and void setFeatures(FeatureMap features).

7.4.3 Annotation Sets [#]

A GATE document can have one or more annotation layers — an anonymous one, (also called default), and as many named ones as necessary.

An annotation layer is organised as a Directed Acyclic Graph (DAG) on which the nodes are particular locations —anchors— in the document content and the arcs are made out of annotations reaching from the location indicated by the start node to the one pointed by the end node (see Figure 7.1 for an illustration). Because of the graph metaphor, the annotation layers are also called annotation graphs. In terms of Java objects, the annotation layers are represented using the Set paradigm as defined by the collections library and they are hence named annotation sets. The terms of annotation layer, graph and set are interchangeable and refer to the same concept when used in this book.

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An annotation set holds a number of annotations and maintains a series of indices in order to provide fast access to the contained annotations.

The GATE Annotation Sets are defined by the gate.AnnotationSet interface and there is a default implementation provided:

gate.annotation.AnnotationSetImpl

annotation set implementation used by transient documents.

The annotation sets are created by the document as required. The first time a particular annotation set is requested from a document it will be transparently created if it doesn’t exist.

Tables 7.4 and 7.5 list the most used Annotation Set functions.

7.4.4 Annotations [#]

An annotation, is a form of meta-data attached to a particular section of document content. The connection between the annotation and the content it refers to is made by means of two pointers that represent the start and end locations of the covered content. An annotation must also have a type (or a name) which is used to create classes of similar annotations, usually linked together by their semantics.

An Annotation is defined by:

start node

a location in the document content defined by an offset.

end node

a location in the document content defined by an offset.

type

a String value.

features

(see Section 7.4.2).

ID

an Integer value. All annotations IDs are unique inside an annotation set.

In GATE Embedded, annotations are defined by the gate.Annotation interface and implemented by the gate.annotation.AnnotationImpl class. Annotations exist only as members of annotation sets (see Section 7.4.3) and they should not be directly created by means of a constructor. Their creation should always be delegated to the containing annotation set.

7.4.5 GATE Corpora [#]

A corpus in GATE is a Java List (i.e. an implementation of java.util.List) of documents. GATE corpora are defined by the gate.Corpus interface and the following implementations are available:

gate.corpora.CorpusImpl

used for transient corpora.

gate.corpora.SerialCorpusImpl

used for persistent corpora that are stored in a serial datastore (i.e. as a directory in a file system).

Apart from implementation for the standard List methods, a Corpus also implements the methods in table 7.6.

Using a DataStore

Assuming that you have a DataStore already open called myDataStore, this code will ask the datastore to take over persistence of your document, and to synchronise the memory representation of the document with the disk storage:

When you want to restore a document (or other LR) from a datastore, you make the same createResource call to the Factory as for the creation of a transient resource, but this time you tell it the datastore the resource came from, and the ID of the resource in that datastore:

7.5 Processing Resources [#]

Processing Resources (PRs) represent entities that are primarily algorithmic, such as parsers, generators or ngram modellers.

They are created using the GATE Factory in manner similar the Language Resources. Besides the creation-time parameters they also have a set of run-time parameters that are set by the system just before executing them.

Analysers are a particular type of processing resources in the sense that they always have a document and a corpus among their run-time parameters.

The most used methods for Processing Resources are presented in table 7.7

7.6 Controllers [#]

Controllers are used to create GATE applications. A Controller handles a set of Processing Resources and can execute them following a particular strategy. GATE provides a series of serial controllers (i.e. controllers that run their PRs in sequence):

gate.creole.SerialController:

a serial controller that takes any kind of PRs.

gate.creole.SerialAnalyserController:

a serial controller that only accepts Language Analysers as member PRs.

gate.creole.ConditionalSerialController:

a serial controller that accepts all types of PRs and that allows the inclusion or exclusion of member PRs from the execution chain according to certain run-time conditions (currently features on the document being processed are used).

gate.creole.ConditionalSerialAnalyserController:

a serial controller that only accepts Language Analysers and that allows the conditional run of member PRs.

7.7 Duplicating a Resource [#]

Sometimes, particularly in a multi-threaded application, it is useful to be able to create an independent copy of an existing PR, controller or LR. The obvious way to do this is to call createResource again, passing the same class name, parameters, features and name, and for many resources this will do the right thing. However there are some resources for which this may be insufficient (e.g. controllers, which also need to duplicate their PRs), unsafe (if a PR uses temporary files, for instance), or simply inefficient. For example for a large gazetteer this would involve loading a second copy of the lists into memory and compiling them into a second identical state machine representation, but a much more efficient way to achieve the same behaviour would be to use a SharedDefaultGazetteer (see section 13.11), which can re-use the existing state machine.

The GATE Factory provides a duplicate method which takes an existing resource instance and creates and returns an independent copy of the resource. By default it uses the algorithm described above, extracting the parameter values from the template resource and calling createResource to create a duplicate. However, if a particular resource type knows of a better way to duplicate itself it can implement the CustomDuplication interface, and provide its own duplicate method which the factory will use instead of performing the default duplication algorithm. A caller who needs to duplicate an existing resource can simply call Factory.duplicate to obtain a copy, which will be constructed in the appropriate way depending on the resource type.

Note that the duplicate object returned by Factory.duplicate will not necessarily be of the same class as the original object. However the contract of Factory.duplicate specifies that where the original object implements any of a list of core GATE interfaces, the duplicate can be assumed to implement the same ones – if you duplicate a DefaultGazetteer the result may not be an instance of DefaultGazetteer but it is guaranteed to implement the Gazetteer interface.

Full details of how to implement a custom duplicate method in your own resource type can be found in the JavaDoc documentation for the CustomDuplication interface and the Factory.duplicate method.

7.8 Persistent Applications [#]

GATE Embedded allows the persistent storage of applications in a format based on XML serialisation. This is particularly useful for applications management and distribution. A developer can save the state of an application when he/she stops working on its design and continue developing it in a next session. When the application reaches maturity it can be deployed to the client site using the same method.

When an application (i.e. a Controller) is saved, GATE will actually only save the values for the parameters used to create the Processing Resources that are contained in the application. When the application is reloaded, all the PRs will be re-created using the saved parameters.

Many PRs use external resources (files) to define their behaviour and, in most cases, these files are identified using URLs. During the saving process, all the URLs are converted relative URLs based on the location of the application file. This way, if the resources are packaged together with the application file, the entire application can be reliably moved to a different location.

API access to application saving and loading is provided by means of two static methods on the gate.util.persistence.PersistenceManager class, listed in table 7.8.

7.9 Ontologies

Starting from GATE version 3.1, support for ontologies has been added. Ontologies are nominally Language Resources but are quite different from documents and corpora and are detailed in chapter 14.

Classes related to ontologies are to be found in the gate.creole.ontology package and its sub-packages. The top level package defines an abstract API for working with ontologies while the sub-packages contain concrete implementations. A client program should only use the classes and methods defined in the API and never any of the classes or methods from the implementation packages.

The entry point to the ontology API is the gate.creole.ontology.Ontology interface which is the base interface for all concrete implementations. It provides methods for accessing the class hierarchy, listing the instances and the properties.

Ontology implementations are available through plugins. Before an ontology language resource can be created using the gate.Factory and before any of the classes and methods in the API can be used, one of the implementing ontology plugins must be loaded. For details see chapter 14.

7.10 Creating a New Annotation Schema [#]

An annotation schema (see Section 3.4.6) can be brought inside GATE through the creole.xml file. By using the AUTOINSTANCE element, one can create instances of resources defined in creole.xml. The gate.creole.AnnotationSchema (which is the Java representation of an annotation schema file) initializes with some predefined annotation definitions (annotation schemas) as specified by the GATE team.

Example from GATE’s internal creole.xml (in src/gate/resources/creole):

In order to create a gate.creole.AnnotationSchema object from a schema annotation file, one must use the gate.Factory class;

Note: All the elements and their values must be written in lower case, as XML is defined as case sensitive and the parser used for XML Schema inside GATE searches is case sensitive.

In order to be able to write XML Schema definitions, the ones defined in GATE (resources/creole/schema) can be used as a model, or the user can have a look at http://www.w3.org/2000/10/XMLSchema for a proper description of the semantics of the elements used.

Some examples of annotation schemas are given in Section 5.4.1.

7.11 Creating a New CREOLE Resource [#]

To create a new resource you need to:

• write a Java class that implements GATE’s beans model;
• compile the class, and any others that it uses, into a Java Archive (JAR) file;
• write some XML configuration data for the new resource;
• tell GATE the URL of the new JAR and XML files.

GATE Developer helps you with this process by creating a set of directories and files that implement a basic resource, including a Java code file and a Makefile. This process is called ‘bootstrapping’.

For example, let’s create a new component called GoldFish, which will be a Processing Resource that looks for all instances of the word ‘fish’ in a document and adds an annotation of type ‘GoldFish’.

First start GATE Developer (see Section 2.2). From the ‘Tools’

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menu select ‘BootStrap Wizard’, which will pop up the dialogue in figure 7.2. The meaning of the data entry fields:

• The ‘resource name’ will be displayed when GATE Developer loads the resource, and will be the name of the directory the resource lives in. For our example: GoldFish.
• ‘Resource package’ is the Java package that the class representing the resource will be created in. For our example: sheffield.creole.example.
• ‘Resource type’ must be one of Language, Processing or Visual Resource. In this case we’re going to process documents (and add annotations to them), so we select ProcessingResource.
• ‘Implementing class name’ is the name of the Java class that represents the resource. For our example: GoldFish.
• The ‘interfaces implemented’ field allows you to add other interfaces (e.g. gate.creole.ControllerAwarePR⁴) that you would like your new resource to implement. In this case we just leave the default (which is to implement the gate.ProcessingResource interface).
• The last field selects the directory that you want the new resource created in. For our example: z:/tmp.

Now we need to compile the class and package it into a JAR file. The bootstrap wizard creates an Ant build file that makes this very easy – so long as you have Ant set up properly, you can simply run

This will compile the Java source code and package the resulting classes into GoldFish.jar. If you don’t have your own copy of Ant, you can use the one bundled with GATE - suppose your GATE is installed at /opt/gate-5.0-snapshot, then you can use /opt/gate-5.0-snapshot/bin/ant jar to build.

You can now load this resource into GATE; see Section 3.6. The default Java code that was created for our GoldFish resource looks like this:

The default XML configuration for GoldFish looks like this:

The directory structure containing these files

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is shown in figure 7.3. GoldFish.java lives in the src/sheffield/creole/example directory. creole.xml and build.xml are in the top GoldFish directory. The lib directory is for libraries; the classes directory is where Java class files are placed; the doc directory is for documentation. These last two, plus GoldFish.jar are created by Ant.

This process has the advantage that it creates a complete source tree and build structure for the component, and the disadvantage that it creates a complete source tree and build structure for the component. If you already have a source tree, you will need to chop out the bits you need from the new tree (in this case GoldFish.java and creole.xml) and copy it into your existing one.

See the example code at http://gate.ac.uk/wiki/code-repository/.

7.12 Adding Support for a New Document Format [#]

In order to add a new document format, one needs to extend the gate.DocumentFormat class and to implement an abstract method called:

This method is supposed to implement the functionality of each format reader and to create annotations on the document. Finally the document’s old content will be replaced with a new one containing only the text between markups.

If one needs to add a new textual reader will extend the gate.corpora.TextualDocumentFormat and override the unpackMarkup(doc) method.

This class needs to be implemented under the Java bean specifications because it will be instantiated by GATE using Factory.createResource() method.

The init() method that one needs to add and implement is very important because in here the reader defines its means to be selected successfully by GATE. What one needs to do is to add some specific information into certain static maps defined in DocumentFormat class, that will be used at reader detection time.

After that, a definition of the reader will be placed into the one’s creole.xml file and the reader will be available to GATE.

We present for the rest of the section a complete three step example of adding such a reader. The reader we describe in here is an XML reader.

Step 1

Create a new class called XmlDocumentFormat that extends
gate.corpora.TextualDocumentFormat.

Step 2

Implement the unpackMarkup(Document doc) which performs the required functionality for the reader. Add XML detection means in init() method:

More details about the information from those maps can be found in Section 5.5.1

Step 3

Add the following creole definition in the creole.xml document.

More information on the operation of GATE’s document format analysers may be found in Section 5.5.

7.13 Using GATE Embedded in a Multithreaded Environment [#]

GATE Embedded can be used in multithreaded applications, so long as you observe a few restrictions. First, you must initialise GATE by calling Gate.init() exactly once in your application, typically in the application startup phase before any concurrent processing threads are started.

Secondly, you must not make calls that affect the global state of GATE (e.g. loading or unloading plugins) in more than one thread at a time. Again, you would typically load all the plugins your application requires at initialisation time. It is safe to create instances of resources in multiple threads concurrently.

Thirdly, it is important to note that individual GATE processing resources, language resources and controllers are by design not thread safe – it is not possible to use a single instance of a controller/PR/LR in multiple threads at the same time – but for a well written resource it should be possible to use several different instances of the same resource at once, each in a different thread. When writing your own resource classes you should bear the following in mind, to ensure that your resource will be useable in this way.

• Avoid static data. Where possible, you should avoid using static fields in your class, and you should try and take all configuration data via the CREOLE parameters you declare in your creole.xml file. System properties may be appropriate for truly static configuration, such as the location of an external executable, but even then it is generally better to stick to CREOLE parameters – a user may wish to use two different instances of your PR, each talking to a different executable.
• Read parameters at the correct time. Init-time parameters should be read in the init() (and reInit()) method, and for processing resources runtime parameters should be read at each execute().
• Use temporary files correctly. If your resource makes use of external temporary files you should create them using File.createTempFile() at init or execute time, as appropriate. Do not use hardcoded file names for temporary files.
• If there are objects that can be shared between different instances of your resource, make sure these objects are accessed either read-only, or in a thread-safe way. In particular you must be very careful if your resource can take other resource instances as init or runtime parameters (e.g. the Flexible Gazetteer, Section 13.7).

Of course, if you are writing a PR that is simply a wrapper around an external library that imposes these kinds of limitations there is only so much you can do. If your resource cannot be made safe you should document this fact clearly.

All the standard ANNIE PRs are safe when independent instances are used in different threads concurrently, as are the standard transient document, transient corpus and controller classes. A typical pattern of development for a multithreaded GATE-based application is:

• Develop your GATE processing pipeline in GATE Developer.
• Save your pipeline as a .gapp file.
• In your application’s initialisation phase, load n copies of the pipeline using PersistenceManager.loadObjectFromFile() (see the Javadoc documentation for details), or load the pipeline once and then make copies of it using Factory.duplicate as described in section 7.7, and either give one copy to each thread or store them in a pool (e.g. a LinkedList).
• When you need to process a text, get one copy of the pipeline from the pool, and return it to the pool when you have finished processing.

Alternatively you can use the Spring Framework as described in the next section to handle the pooling for you.

7.14 Using GATE Embedded within a Spring Application [#]

GATE Embedded provides helper classes to allow GATE resources to be created and managed by the Spring framework. For Spring 2.0 or later, GATE Embedded provides a custom namespace handler that makes them extremely easy to use. To use this namespace, put the following declarations in your bean definition file:

You can have Spring initialise GATE:

The gate-home, user-config-file, etc. and the <value> elements under <gate:preload-plugins> are interpreted as Spring “resource” paths. If the value is not an absolute URL then Spring will resolve the path in an appropriate way for the type of application context — in a web application they are taken as being relative to the web app root, and you would typically use locations within WEB-INF as shown in the example above. To use an absolute path for gate-home it is not sufficient to use a leading slash (e.g. /opt/gate), for backwards-compatibility reasons Spring will still resolve this relative to your web application. Instead you must specify it as a full URL, i.e. file:/opt/gate.

To create a GATE resource, use the <gate:resource> element.

The children of <gate:parameters> are Spring <entry/> elements, just as you would write when configuring a bean property of type Map<String,Object>. <gate:url> provides a way to construct a java.net.URL from a resource path as discussed above. If it is possible to resolve the resource path as a file: URL then this form will be preferred, as there are a number of areas within GATE which work better with file: URLs than with other types of URL (for example plugins that run external processes, or that use a URL parameter to point to a directory in which they will create new files).

A note about types: The <gate:parameters> and <gate:features> elements define GATE FeatureMaps. When using the simple <entry key="..." value="..." /> form, the entry values will be treated as strings; Spring can convert strings into many other types of object using the standard Java Beans property editor mechanism, but since a FeatureMap can hold any kind of values you must use an explicit <value type="...">...</value> to tell Spring what type the value should be.

There is an additional twist for <gate:parameters> – GATE has its own internal logic to convert strings to other types required for resource parameters (see the discussion of default parameter values in section 4.7.1). So for parameter values you have a choice, you can either use an explicit <value type="..."> to make Spring do the conversion, or you can pass the parameter value as a string and let GATE do the conversion. For resource parameters whose type is java.net.URL, if you pass a string value that is not an absolute URL (starting file:, http:, etc.) then GATE will treat the string as a path relative to the creole.xml file of the plugin that defines the resource type whose parameter you are setting. If this is not what you intended then you should use <gate:url> to cause Spring to resolve the path to a URL before passing it to GATE. For example, for a JAPE transducer, <entry key="grammarURL" value="grammars/main.jape" /> would resolve to something like file:/path/to/webapp/WEB-INF/plugins/ANNIE/grammars/main.jape, whereas

would resolve to file:/path/to/webapp/grammars/main.jape.

You can load a GATE saved application with

‘Customisers’ are used to customise the application after it is loaded. In the example above, we load a singleton copy of an ontology which is then shared between all the separate instances of the (prototype) application. The <gate:set-parameter> customiser accepts all the same ways to provide a value as the standard Spring <property> element (a ”value” or ”ref” attribute, or a sub-element - <value>, <list>, <bean>, <gate:resource> …).

The <gate:add-pr> customiser provides support for the case where most of the application is in a saved state, but we want to create one or two extra PRs with Spring (maybe to inject other Spring beans as init parameters) and add them to the pipeline.

By default, the <gate:add-pr> customiser adds the target PR at the end of the pipeline, but an add-before or add-after attribute can be used to specify the name of a PR before (or after) which this PR should be placed. Alternatively, an index attribute places the PR at a specific (0-based) index into the pipeline. The PR to add can be specified either as a ‘ref’ attribute, or with a nested <bean> or <gate:resource> element.

7.14.1 Duplication in Spring [#]

The above example defines the <gate:application> as a prototype-scoped bean, which means the saved application state will be loaded afresh each time the bean is fetched from the bean factory (either explicitly using getBean or implicitly when it is injected as a dependency of another bean). However in many cases it is better to load the application once and then duplicate it as required (as described in section 7.7), as this allows resources to optimise their memory usage, for example by sharing a single in-memory representation of a large gazetteer list between several instances of the gazetteer PR. This approach is supported by the <gate:duplicate> tag.

The <gate:duplicate> tag acts like a prototype bean definition, in that each time it is fetched or injected it will call Factory.duplicate to create a new duplicate of its template resource (declared as a nested element or referenced by the template-ref attribute). However the tag also keeps track of all the duplicate instances it has returned over its lifetime, and will ensure they are released (using Factory.deleteResource) when the Spring context is shut down.

The <gate:duplicate> tag also supports customisers, which will be applied to the newly-created duplicate resource before it is returned. This is subtly different from applying the customisers to the template resource itself, which would cause them to be applied once to the original resource before it is first duplicated.

Finally, <gate:duplicate> takes an optional boolean attribute return-template. If set to false (or omitted, as this is the default behaviour), the tag always returns a duplicate — the original template resource is used only as a template and is not made available for use. If set to true, the first time the bean defined by the tag is injected or fetched, the original template resource is returned. Subsequent uses of the tag will return duplicates. Generally speaking, it is only safe to set return-template="true" when there are no customisers, and when the duplicates will all be created up-front before any of them are used. If the duplicates will be created asynchronously (e.g. with a dynamically expanding pool, see below) then it is possible that, for example, a template application may be duplicated in one thread whilst it is being executed by another thread, which may lead to unpredictable behaviour.

7.14.2 Spring pooling [#]

In a multithreaded application it is vital that individual GATE resources are not used in more than one thread at the same time. Because of this, multithreaded applications that use GATE Embedded often need to use some form of pooling to provided thread-safe access to GATE components. This can be managed by hand, but the Spring framework has built-in tools to support transparent pooling of Spring-managed beans. Spring can create a pool of identical objects, then expose a single “proxy” object (offering the same interface) for use by clients. Each method call on the proxy object will be routed to an available member of the pool in such a way as to guarantee that each member of the pool is accessed by no more than one thread at a time.

Since the pooling is handled at the level of method calls, this approach is not used to create a pool of GATE resources directly — making use of a GATE PR typically involves a sequence of method calls (at least setDocument(doc), execute() and setDocument(null)), and creating a pooling proxy for the resource may result in these calls going to different members of the pool. Instead the typical use of this technique is to define a helper object with a single method that internally calls the GATE API methods in the correct sequence, and then create a pool of these helpers. The interface gate.util.DocumentProcessor and its associated implementation gate.util.LanguageAnalyserDocumentProcessor are useful for this. The DocumentProcessor interface defines a processDocument method that takes a GATE document and performs some processing on it. LanguageAnalyserDocumentProcessor implements this interface using a GATE LanguageAnalyser (such as a saved “corpus pipeline” application) to do the processing. A pool of LanguageAnalyserDocumentProcessor instances can be exposed through a proxy which can then be called from several threads.

The machinery to implement this is all built into Spring, but the configuration typically required to enable it is quite fiddly, involving at least three co-operating bean definitions. Since the technique is so useful with GATE Embedded, GATE provides a special syntax to configure pooling in a simple way. Given the <gate:duplicate id="theApp"> definition from the previous section we can create a DocumentProcessor proxy that can handle up to five concurrent requests as follows:

The <gate:pooled-proxy> element decorates a singleton bean definition. It converts the original definition to prototype scope and replaces it with a singleton proxy delegating to a pool of instances of the prototype bean. The pool parameters are controlled by attributes of the <gate:pooled-proxy> element, the most important ones being:

max-size

The maximum size of the pool. If more than this number of threads try to call methods on the proxy at the same time, the others will (by default) block until an object is returned to the pool.

initial-size

The default behaviour of Spring’s pooling tools is to create instances in the pool on demand (up to the max-size). This attribute instead causes initial-size instances to be created up-front and added to the pool when it is first created.

when-exhausted-action-name

What to do when the pool is exhausted (i.e. there are already max-size concurrent calls in progress and another one arrives). Should be set to one of WHEN_EXHAUSTED_BLOCK (the default, meaning block the excess requests until an object becomes free), WHEN_EXHAUSTED_GROW (create a new object anyway, even though this pushes the pool beyond max-size) or WHEN_EXHAUSTED_FAIL (cause the excess calls to fail with an exception).

Many more options are available, corresponding to the properties of the Spring CommonsPoolTargetSource class. These allow you, for example, to configure a pool that dynamically grows and shrinks as necessary, releasing objects that have been idle for a set amount of time. See the JavaDoc documentation of CommonsPoolTargetSource (and the documentation for Apache commons-pool) for full details.

Note that the <gate:pooled-proxy> technique is not tied to GATE in any way, it is simply an easy way to configure standard Spring beans and can be used with any bean that needs to be pooled, not just objects that make use of GATE.

7.14.3 Further reading [#]

These custom elements all define various factory beans. For full details, see the JavaDocs for gate.util.spring (the factory beans) and gate.util.spring.xml (the gate: namespace handler). The main Spring framework API documentation is the best place to look for more detail on the pooling facilities provided by Spring AOP.

Note: the former approach using factory methods of the gate.util.spring.SpringFactory class will still work, but should be considered deprecated in favour of the new factory beans.

7.15 Using GATE Embedded within a Tomcat Web Application [#]

Embedding GATE in a Tomcat web application involves several steps.

1. Put the necessary JAR files (gate.jar and all or most of the jars in gate/lib) in your webapp/WEB-INF/lib.
2. Put the plugins that your application depends on in a suitable location (e.g. webapp/WEB-INF/plugins).
3. Create suitable gate.xml configuration files for your environment.
4. Set the appropriate paths in your application before calling Gate.init().

This process is detailed in the following sections.

7.15.1 Recommended Directory Structure

You will need to create a number of other files in your web application to allow GATE to work:

• Site and user gate.xml config files - we highly recommend defining these specifically for the web application, rather than relying on the default files on your application server.
• The plugins your application requires.

In this guide, we assume the following layout:

7.15.2 Configuration Files

Your gate.xml (the ‘site-wide configuration file’) should be as simple as possible:

Similarly, keep the user-gate.xml (the ‘user config file’) simple:

This way, you can control exactly which plugins are loaded in your webapp code.

7.15.3 Initialization Code

Given the directory structure shown above, you can initialize GATE in your web application like this:

Once initialized, you can create GATE resources using the Factory in the usual way (for example, see Section 7.1 for an example of how to create an ANNIE application). You should also read Section 7.13 for important notes on using GATE Embedded in a multithreaded application.

Instead of an initialization servlet you could also consider doing your initialization in a ServletContextListener, or using Spring (see Section 7.14).

7.16 Groovy for GATE [#]

Groovy is a dynamic programming language based on Java. Groovy is not used in the core GATE distribution, so to enable the Groovy features in GATE you must first load the Groovy plugin. Loading this plugin:

• provides access to the Groovy scripting console (configured with some extensions for GATE) from the GATE Developer “Tools” menu.
• provides a PR to run a Groovy script over documents.
• provides a controller which uses a Groovy DSL to define its execution strategy.
• enhances a number of core GATE classes with additional convenience methods that can be used from any Groovy code including the console, the script PR, and any Groovy class that uses the GATE Embedded API.

This section describes these features in detail, but assumes that the reader already has some knowledge of the Groovy language. If you are not already familiar with Groovy you should read this section in conjunction with Groovy’s own documentation at http://groovy.codehaus.org/.

7.16.1 Groovy Scripting Console for GATE [#]

Loading the Groovy plugin in GATE Developer will provide a “Groovy Console” item in the Tools/Groovy Tools menu. This menu item opens the standard Groovy console window (http://groovy.codehaus.org/Groovy+Console).

To help scripting GATE in Groovy, the console is pre-configured to import all classes from the gate, gate.annotation, gate.util, gate.jape and gate.creole.ontology packages of the core GATE API⁵. This means you can refer to classes and interfaces such as Factory, AnnotationSet, Gate, etc. without needing to prefix them with a package name. In addition, the following (read-only) variable bindings are pre-defined in the Groovy Console.

• corpora: a list of loaded corpora LRs (Corpus)
• docs: a list of all loaded document LRs (DocumentImpl)
• prs: a list of all loaded PRs
• apps: a list of all loaded Applications (AbstractController)

These variables are automatically updated as resources are created and deleted in GATE.

Here’s an example script. It finds all documents with a feature “annotator” set to “fred”, and puts them in a new corpus called “fredsDocs”.

You can find other examples (and add your own) in the Groovy script repository on the GATE Wiki: http://gate.ac.uk/wiki/groovy-recipes/.

Why won’t the ‘Groovy executing’ dialog go away? Sometimes, when you execute a Groovy script through the console, a dialog will appear, saying “Groovy is executing. Please wait”. The dialog fails to go away even when the script has ended, and cannot be closed by clicking the “Interrupt” button. You can, however, continue to use the Groovy Console, and the dialog will usually go away next time you run a script. This is not a GATE problem: it is a Groovy problem.

7.16.2 Groovy scripting PR [#]

The Groovy scripting PR enables you to load and execute Groovy scripts as part of a GATE application pipeline. The Groovy scripting PR is made available when you load the Groovy plugin via the plugin manager.

Parameters [#]

The Groovy scripting PR has a single initialisation parameter

• scriptURL: the path to a valid Groovy script

It has three runtime parameters

• inputASName: an optional annotation set intended to be used as input by the PR (but note that the PR has access to all annotation sets)
• outputASName: an optional annotation set intended to be used as output by the PR (but note that the PR has access to all annotation sets)
• scriptParams: optional parameters for the script. In a creole.xml file, these should be specified as key=value pairs, each pair separated by a comma. For example: ’name=fred,type=person’ . In the GATE GUI, these are specified via a dialog.

Script bindings [#]

As with the Groovy console described above, and with JAPE right-hand-side Java code, Groovy scripts run by the scripting PR implicitly import all classes from the gate, gate.annotation, gate.util, gate.jape and gate.creole.ontology packages of the core GATE API. The Groovy scripting PR also makes available the following bindings, which you can use in your scripts:

• doc: the current document (Document)
• corpus: the corpus containing the current document
• content: the string content of the current document
• inputAS: the annotation set specified by inputASName in the PRs runtime parameters
• outputAS: the annotation set specified by outputASName in the PRs runtime parameters

Note that inputAS and outputAS are intended to be used as input and output AnnotationSets. This is, however, a convention: there is nothing to stop a script writing to or reading from any AnnotationSet. Also, although the script has access to the corpus containing the document it is running over, it is not generally necessary for the script to iterate over the documents in the corpus itself – the reference is provided to allow the script to access data stored in the FeatureMap of the corpus. Any other variables assigned to within the script code will be added to the binding, and values set while processing one document can be used while processing a later one.

Passing parameters to the script [#]

In addition to the above bindings, one further binding is available to the script:

• scriptParams: a FeatureMap with keys and values as specified by the scriptParams runtime parameter

For example, if you were to create a scriptParams runtime parameter for your PR, with the keys and values: ’name=fred,type=person’, then the values could be retrieved in your script via scriptParams.name and scriptParams.type

Controller callbacks [#]

A Groovy script may wish to do some pre- or post-processing before or after processing the documents in a corpus, for example if it is collecting statistics about the corpus. To support this, the script can declare methods beforeCorpus and afterCorpus, taking a single parameter. If the beforeCorpus method is defined and the script PR is running in a corpus pipeline application, the method will be called before the pipeline processes the first document. Similarly, if the afterCorpus method is defined it will be called after the pipeline has completed processing of all the documents in the corpus. In both cases the corpus will be passed to the method as a parameter. If the pipeline aborts with an exception the afterCorpus method will not be called, but if the script declares a method aborted(c) then this will be called instead.

Note that because the script is not processing a particular document when these methods are called, the usual doc, corpus, inputAS, etc. are not available within the body of the methods (though the corpus is passed to the method as a parameter). The scriptParams variable is available.

The following example shows how this technique could be used to build a simple tf/idf index for a GATE corpus. The example is available in the GATE distribution as plugins/Groovy/resources/scripts/tfidf.groovy. The script makes use of some of the utility methods described in section 7.16.4.

Examples [#]

The plugin directory Groovy/resources/scripts contains some example scripts. Below is the code for a naive regular expression PR.

The script needs to have the runtime parameter scriptParams set with keys and values as follows:

• regex: the Groovy regular expression that you want to match e.g. [^\s]*ing
• type: the type of the annotation to create for each regex match, e.g. regexMatch

When the PR is run over a document, the script will first make a matcher over the document content for the regular expression given by the regex parameter. It will iterate over all matches for this regular expression, adding a new annotation for each, with a type as given by the type parameter.

7.16.3 The Scriptable Controller [#]

The Groovy plugin’s “Scriptable Controller” is a more flexible alternative to the standard pipeline (SerialController) and corpus pipeline (SerialAnalyserController) applications and their conditional variants. Like the standard controllers, a scriptable controller contains a list of processing resources and can optionally be configured with a corpus, but unlike the standard controllers it does not necessarily execute the PRs in a linear order. Instead the execution strategy is controlled by a script written in a Groovy domain specific language (DSL), which is detailed in the following sections.

Running a single PR

To run a single PR from the scriptable controller’s list of PRs, simply use the PR’s name as a Groovy method call:

If the PR’s name contains spaces or any other character that is not valid in a Groovy identifier, or if the name is a reserved word (such as “import”) then you must enclose the name in single or double quotes. You may prefer to rename the PRs so their names are valid identifiers. Also, if there are several PRs in the controller’s list with the same name, they will all be run in the order in which they appear in the list.

You can optionally provide a Map of named parameters to the call, and these will override the corresponding runtime parameter values for the PR (the original values will be restored after the PR has been executed):

Iterating over the corpus

If a corpus has been provided to the controller then you can iterate over all the documents in the corpus using eachDocument:

The block of code (in fact a Groovy closure) is executed once for each document in the corpus exactly as a standard corpus pipeline application would operate. The current document is available to the script in the variable doc and the corpus in the variable corpus, and in addition any calls to PRs that implement the LanguageAnalyser interface will set the PR’s document and corpus parameters appropriately.

Running all the PRs in sequence

Calling allPRs() will execute all the controller’s PRs once in the order in which they appear in the list. This is rarely useful in practice but it serves to define the default behaviour: the initial script that is used by default in a newly instantiated scriptable controller is eachDocument { allPRs() }, which mimics the behaviour of a standard corpus pipeline application.

More advanced scripting

The basic DSL is extremely simple, but because the script is Groovy code you can use all the other facilities of the Groovy language to do conditional execution, grouping of PRs, etc. The control script has the same implicit imports as provided by the Groovy Script PR (section 7.16.2), and additional import statements can be added as required.

For example, suppose you have a pipeline for multi-lingual document processing, containing PRs named “englishTokeniser”, “englishGazetteer”, “frenchTokeniser”, “frenchGazetteer”, “genericTokeniser”, etc., and you need to choose which ones to run based on a document feature:

As another example, suppose you have a particular JAPE grammar that you know is slow on documents that mention a large number of locations, so you only want to run it on documents with up to 100 Location annotations, and use a faster but less accurate one on others:

You can have more than one call to eachDocument, for example a controller that pre-processes some documents, then collects some corpus-level statistics, then further processes the documents based on those statistics.

As a final example, consider a controller to post-process data from a manual annotation task. Some of the documents have been annotated by one annotator, some by more than one (the annotations are in sets named “annotator1”, “annotator2”, etc., but the number of sets varies from document to document).

Nesting a scriptable controller in another application

Like the standard SerialAnalyserController, the scriptable controller implements the LanugageAnalyser interface and so can itself be nested as a PR in another pipeline. When used in this way, eachDocument does not iterate over the corpus but simply calls its closure once, with the “current document” set to the document that was passed to the controller as a parameter. This is the same logic as is used by SerialAnalyserController, which runs its PRs once only rather than once per document in the corpus.

The Scriptable Controller in GATE Developer

When you double-click on a scriptable controller in the resources tree of GATE Developer you see the same controller editor that is used by the standard controllers. This view allows you to add PRs to the controller and set their default runtime parameter values, and to specify the corpus over which the controller should run. A separate view is provided to allow you to edit the Groovy script, which is accessible via the “Control Script” tab (see figure 7.4). This tab provides a text editor which does basic Groovy syntax highlighting (the same editor used by the Groovy Console).

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7.16.4 Utility methods [#]

Loading the Groovy plugin adds some additional methods to several of the core GATE API classes and interfaces using the Groovy “mixin” mechanism. Any Groovy code that runs after the plugin has been loaded can make use of these additional methods, including snippets run in the Groovy console, scripts run using the Script PR, and any other Groovy code that uses the GATE Embedded API.

The methods that are injected come from two classes. The gate.Utils class (part of the core GATE API in gate.jar) defines a number of static methods that can be used to simplify common tasks such as getting the string covered by an annotation or annotation set, finding the start or end offset of an annotation (or set), etc. These methods do not use any Groovy-specific types, so they are usable from pure Java code in the usual way as well as being mixed in for use in Groovy. Additionally, the class gate.groovy.GateGroovyMethods (part of the Groovy plugin) provides methods that use Groovy types such as closures and ranges.

The added methods include:

• Unified access to the start and end offsets of an Annotation, AnnotationSet or Document: e.g. someAnnotation.start() or anAnnotationSet.end()
• Simple access to the DocumentContent or string covered by an annotation or annotation set: document.stringFor(anAnnotation), document.contentFor(annotationSet)
• Simple access to the length of an annotation or document, either as an int (annotation.length()) or a long (annotation.lengthLong()).
• A method to construct a FeatureMap from any map, to support constructions like def params = [sourceUrl:’http://gate.ac.uk’, encoding:’UTF-8’].toFeatureMap()
• A method to convert an annotation set into a List of annotations in the order they appear in the document, for iteration in a predictable order: annSet.inDocumentOrder().collect { it.type }
• The each, eachWithIndex and collect methods for a corpus have been redefined to properly load and unload documents if the corpus is stored in a datastore.
• Various getAt methods to support constructions like annotationSet["Token"] (get all Token annotations from the set), annotationSet[15..20] (get all annotations between offsets 15 and 20), documentContent[0..10] (get the document content between offsets 0 and 10).
• A withResource method for any resource, which calls a closure with the resource passed as a parameter, and ensures that the resource is properly deleted when the closure completes (analagous to the default Groovy method InputStream.withStream).

For full details, see the source code or javadoc documentation for these two classes.

7.17 Saving Config Data to gate.xml

Arbitrary feature/value data items can be saved to the user’s gate.xml file via the following API calls:

To get the config data: Map configData = Gate.getUserConfig().

To add config data simply put pairs into the map: configData.put("my new config key", "value");.

To write the config data back to the XML file: Gate.writeUserConfig();.

Note that new config data will simply override old values, where the keys are the same. In this way defaults can be set up by putting their values in the main gate.xml file, or the site gate.xml file; they can then be overridden by the user’s gate.xml file.

7.18 Annotation merging through the API [#]

If we have annotations about the same subject on the same document from different annotators, we may need to merge those annotations to form a unified annotation. Two approaches for merging annotations are implemented in the API, via static methods in the class gate.util.AnnotationMerging.

The two methods have very similar input and output parameters. Each of the methods takes an array of annotation sets, which should be the same annotation type on the same document from different annotators, as input. A single feature can also be specified as a parameter (or given asnull if no feature is to be specified).

The output is a map, the key of which is one merged annotation and the value of which represents the annotators (in terms of the indices of the array of annotation sets) who support the annotation. The methods also have a boolean input parameter to indicate whether or not the annotations from different annotators are based on the same set of instances, which can be determined by the static method public boolean isSameInstancesForAnnotators(AnnotationSet[] annsA) in the class gate.util.IaaCalculation. One instance corresponds to all the annotations with the same span. If the annotation sets are based on the same set of instances, the merging methods will ensure that the merged annotations are on the same set of instances.

The two methods corresponding to those described for the Annotation Merging plugin described in Section 19.12. They are:

• The Method public static void mergeAnnogation(AnnotationSet[] annsArr, String nameFeat,
  HashMap<Annotation,String>mergeAnns, int numMinK, boolean isTheSameInstances) merges the annotations stored in the array annsArr. The merged annotation is put into the map mergeAnns, with a key of the merged annotation and value of a string containing the indices of elements in the annotation set array annsArr which contain that annotation. NumMinK specifies the minimal number of the annotators supporting one merged annotation. The boolean parameter isTheSameInstances indicate if or not those annotation sets for merging are based on the same instances.
• Method public static void mergeAnnogationMajority(AnnotationSet[] annsArr, String nameFeat, HashMap<Annotation, String>mergeAnns, boolean isTheSameInstances) selects the annotations which the majority of the annotators agree on. The meanings of parameters are the same as those in the above method.