Version 2.5.0
Copyright © 2012, 2020 The Apache Software Foundation
License and Disclaimer. The ASF licenses this documentation to you under the Apache License, Version 2.0 (the "License"); you may not use this documentation except in compliance with the License. You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, this documentation and its contents are distributed under the License on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Trademarks. All terms mentioned in the text that are known to be trademarks or service marks have been appropriately capitalized. Use of such terms in this book should not be regarded as affecting the validity of the the trademark or service mark.
April, 2020
Table of Contents
While uimaFIT provides many features for a UIMA developer, there are two overarching themes that most features fall under. These two sides of uimaFIT are,while complementary, largely independent of each other. One of the beauties of uimaFIT is that a developer that uses one side of uimaFIT extensively is not required to use the other side at all.
The first broad theme of uimaFIT provides features that simplify component
implementation. Our favorite example of this is the
@ConfigurationParameter annotation which allows you to annotate a
member variable as a configuration parameter. This annotation in combination with the method
ConfigurationParameterInitializer.initialize() completely automates
the process of initializing member variables with values from the
UimaContext passed into your analysis engine's initialize
method. Similarly, the annotation @ExternalResource annotation in
combination with the method ExternalResourceInitializer.initialize()
completely automates the binding of an external resource as defined in the
UimaContext to a member variable. Dispensing with manually
writing the code that performs these two tasks reduces effort, eliminates verbose and
potentially buggy boiler-plate code, and makes implementing a UIMA component more enjoyable.
Consider, for example, a member variable that is of type Locale. With
uimaFIT you can simply annotate the member variable with
@ConfigurationParameter and have your initialize method automatically
initialize the variable correctly with a string value in the
UimaContext such as en_US.
The second broad theme of uimaFIT provides features that simplify component instantiation. Working with UIMA, have you ever said to yourself “but I just want to tag some text!?” What does it take to “just tag some text?” Here's a list of things you must do with the traditional approach:
wrap your tagger as a UIMA analysis engine
write a descriptor file for your analysis engine
write a CAS consumer that produces the desired output
write another descriptor file for the CAS consumer
write a descriptor file for a collection reader
write a descriptor file that describes a pipeline
invoke the Collection Processing Manager with your pipeline descriptor file
Each of these steps has its own pitfalls and can be rather time consuming. This is a rather unsatisfying answer to our simple desire to just tag some text. With uimaFIT you can literally eliminate all of these steps.
Here's a simple snippet of Java code that illustrates “tagging some text” with uimaFIT:
import static org.apache.uima.fit.factory.JCasFactory.createJCas;
import static org.apache.uima.fit.pipeline.SimplePipeline.runPipeline;
import static
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription;
JCas jCas = createJCas();
jCas.setDocumentText("some text");
runPipeline(jCas,
createEngineDescription(MyTokenizer.class),
createEngineDescription(MyTagger.class));
for(Token token : iterate(jCas, Token.class)){
System.out.println(token.getTag());
}
This code uses several static method imports for brevity. And while the terseness of this code won't make a Python programmer blush - it is certainly much easier than the seven steps outlined above!
uimaFIT provides mechanisms to instantiate and run UIMA components programmatically with
or without descriptor files. For example, if you have a descriptor file for your analysis
engine defined by MyTagger (as shown above), then you can instead
instantiate the analysis engine with:
AnalysisEngineDescription tagger = createEngineDescription(
"mypackage.MyTagger");
This will find the descriptor file mypackage/MyTagger.xml by name.
Similarly, you can find a descriptor file by location with
createEngineDescriptionFromPath(). However, if you want to dispense
with XML descriptor files altogether (and you probably do), you can use the method
createEngineDescription() as shown above. One of the driving motivations
for creating the second side of uimaFIT is our frustration with descriptor files and our
desire to eliminate them. Descriptor files are difficult to maintain because they are
generally tightly coupled with java code, they decay without warning, they are wearisome to
test, and they proliferate, among other reasons.
One question that is often raised by new uimaFIT users is whether or not it breaks the
UIMA way. That is, does adopting uimaFIT lead me down a path of
creating UIMA components and systems that are incompatible with the traditional UIMA approach?
The answer to this question is no. For starters, uimaFIT does not skirt
the UIMA mechanism of describing components - it only skips the XML part of it. For example,
when the method createEngineDescription() is called (as shown above) an
AnalysisEngineDescription is created for the analysis engine.
This is the same object type that is instantiated when a descriptor file is used. So, instead
of parsing XML to instantiate an analysis engine description from XML, uimaFIT uses a factory
method to instantiate it from method parameters. One of the happy benefits of this approach is
that for a given AnalysisEnginedDescription you can generate
an XML descriptor file using AnalysisEngineDescription.toXML(). So,
uimaFIT actually provides a very simple and direct path for generating
XML descriptor files rather than manually creating and maintaining them!
It is also useful to clarify that if you only want to use one side or the other of
uimaFIT, then you are free to do so. This is possible precisely because uimaFIT does not
workaround UIMA's mechanisms for describing components but rather uses them directly. For
example, if the only thing you want to use in uimaFIT is the
@ConfigurationParameter, then you can do so without worrying about
what effect this will have on your descriptor files. This is because your analysis engine will
be initialized with exactly the same UimaContext regardless of
whether you instantiate your analysis engine in the UIMA way or use one
of uimaFIT's factory methods. Similarly, a UIMA component does not need to be annotated with
@ConfiguratioParameter for you to make use of the
createEngineDescription() method. This is because when you pass
configuration parameter values in to the createEngineDescription() method,
they are added to an AnalysisEngineDescription which is used by
UIMA to populate a UimaContext - just as it would if you used a
descriptor file.
Because uimaFIT can be used to simplify component implementation and instantiation it is easy to assume that you can't do one without the other. This page has demonstrated that while these two sides of uimaFIT complement each other, they are not coupled together and each can be effectively used without the other. Similarly, by understanding how uimaFIT uses the UIMA component description mechanisms directly, one can be assured that uimaFIT enables UIMA development that is compatible and consistent with the UIMA standard and APIs.
This quick start tutorial demonstrates how to use uimaFIT to define and set a configuration parameter in an analysis engine, run it, and generate a descriptor file for it. The complete code for this example can be found in the uimaFIT-examples module.
The following instructions describe how to add uimaFIT to your project's classpath.
If you use Maven, then uimaFIT can be added to your project by simply adding uimaFIT as a project dependency by adding the following snippet of XML to your pom.xml file:
<dependency> <groupId>org.apache.uima</groupId> <artifactId>uimafit-core</artifactId> <version>2.5.0</version> </dependency>
uimaFIT distributions are hosted by Maven Central and so no repository needs to be added to your pom.xml file.
If you do not build with Maven, then download uimaFIT from the Apache UIMA downloads page. The file
name should be uimafit-2.5.0-bin.zip. Download and unpack this file.
The contents of the resulting upacked directory will contain a directory called
lib. Add all of the files in this directory to your classpath.
Here is the complete analysis engine implementation for this example.
public class GetStartedQuickAE
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
public static final String PARAM_STRING = "stringParam";
@ConfigurationParameter(name = PARAM_STRING)
private String stringParam;
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
System.out.println("Hello world! Say 'hi' to " + stringParam);
}
}
The first thing to note is that the member variable stringParam is
annotated with @ConfigurationParameter which tells uimaFIT that this is
an analysis engine configuration parameter. It is best practice to create a public constant
for the parameter name, here PARAM_STRING The second thing to note is that we
extend uimaFIT's version of the JCasAnnotator_ImplBase. The initialize
method of this super class calls:
ConfigurationParameterInitializer.initializeConfigurationParameters( Object, UimaContext)
which populates the configuration parameters with the appropriate contents of the
UimaContext. If you do not want to extend uimaFIT's
JCasAnnotator_ImplBase, then you can call this method directly in the
initialize method of your analysis engine or any class that
implements Initializable. You can call this method for an
instance of any class that has configuration parameters.
The following lines of code demonstrate how to instantiate and run the analysis engine from a main method:
JCas jCas = JCasFactory.createJCas(); AnalysisEngine analysisEngine = AnalysisEngineFactory.createEngine( GetStartedQuickAE.class, GetStartedQuickAE.PARAM_STRING, "uimaFIT"); analysisEngine.process(jCas);
In a more involved example, we would probably instantiate a collection reader and run this
analysis engine over a collection of documents. Here, it suffices to simply create a
JCas. Line 3 instantiates the analysis engine using
AnalysisEngineFactory and sets the string parameter named
stringParam to the value uimaFIT. Running this
simple program sends the following output to the console:
Hello world! Say 'hi' to uimaFIT
Normally you would be using a type system with your analysis components. When using
uimaFIT, it is easiest to keep your type system descriptors in your source folders and make
them known to uimaFIT. To do so, create a file
META-INF/org.apache.uima.fit/types.txt in a source folder and add references to
all your type descriptors to the file, one per line. You can also use wildcards. For example:
classpath*:org/apache/uima/fit/examples/type/Token.xml classpath*:org/apache/uima/fit/examples/type/Sentence.xml classpath*:org/apache/uima/fit/examples/tutorial/type/*.xml
The following lines of code demonstrate how a descriptor file can be generated using the class definition:
AnalysisEngine analysisEngine = AnalysisEngineFactory.createEngine(
GetStartedQuickAE.class,
GetStartedQuickAE.PARAM_STRING, "uimaFIT");
analysisEngineDescription.toXML(
new FileOutputStream("GetStartedQuickAE.xml"));
If you open the resulting descriptor file you will see that the configuration parameter
stringParam is defined with the value set to
uimaFIT. We could now instantiate an analysis engine using this
descriptor file with a line of code like this:
AnalysisEngineFactory.createEngine("GetStartedQuickAE");
But, of course, we really wouldn't want to do that now that we can instantiate analysis engines using the class definition as was done above!
This chapter, of course, did not demonstrate every feature of uimaFIT which provides support for annotating external resources, creating aggregate engines, running pipelines, testing components, among others.
UIMA is a component-based architecture that allows composing various processing components into a complex processing pipeline. A pipeline typically involves a collection reader which ingests documents and analysis engines that do the actual processing.
Normally, you would run a pipeline using a UIMA Collection Processing Engine or using UIMA AS. uimaFIT offers a third alternative that is much simpler to use and well suited for embedding UIMA pipelines into applications or for writing tests.
As uimaFIT does not supply any readers or processing components, we just assume that we have written three components:
TextReader - reads text files from a directory
Tokenizer - annotates tokens
TokenFrequencyWriter - writes a list of tokens and their
frequency to a file
We create descriptors for all components and run them as a pipeline:
CollectionReaderDescription reader =
CollectionReaderFactory.createReaderDescription(
TextReader.class,
TextReader.PARAM_INPUT, "/home/uimafit/documents");
AnalysisEngineDescription tokenizer =
AnalysisEngineFactory.createEngineDescription(
Tokenizer.class);
AnalysisEngineDescription tokenFrequencyWriter =
AnalysisEngineFactory.createEngineDescription(
TokenFrequencyWriter.class,
TokenFrequencyWriter.PARAM_OUTPUT, "counts.txt");
SimplePipeline.runPipeline(reader, tokenizer, writer);
Instead of running the full pipeline end-to-end, we can also process one document at a time and inspect the analysis results:
CollectionReaderDescription reader =
CollectionReaderFactory.createReaderDescription(
TextReader.class,
TextReader.PARAM_INPUT, "/home/uimafit/documents");
AnalysisEngineDescription tokenizer =
AnalysisEngineFactory.createEngineDescription(
Tokenizer.class);
for (JCas jcas : SimplePipeline.iteratePipeline(reader, tokenizer)) {
System.out.printf("Found %d tokens%n",
JCasUtil.select(jcas, Token.class).size());
}
The uimafit-examples module contains a package org.apache.uima.fit.examples.experiment.pos which demonstrates a very simple experimental setup for testing a part-of-speech tagger. You may find this example more accessible if you check out the code from subversion and build it in your own environment.
The documentation for this example can be found in the code itself. Please refer to
RunExperiment as a starting point. The following is copied from the
javadoc comments of that file:
RunExperimentdemonstrates a very common (though simplified) experimental setup in which gold standard data is available for some task and you want to evaluate how well your analysis engine works against that data. Here we are evaluatingBaselineTaggerwhich is a (ridiculously) simple part-of-speech tagger against the part-of-speech tags found insrc/main/resources/org/apache/uima/fit/examples/pos/sample-gold.txt
The basic strategy is as follows:
post the data as is into the default view,
parse the gold-standard tokens and part-of-speech tags and put the results into another view we will call GOLD_VIEW,
create another view called SYSTEM_VIEW and copy the text and
Token annotations from the GOLD_VIEW into this
view,
run the BaselineTagger on the SYSTEM_VIEW
over the copied Token annoations,
evaluate the part-of-speech tags found in the SYSTEM_VIEW with those in the GOLD_VIEW.
uimaFIT facilitates working with the CAS and JCas by offering various convenient methods for accessing and navigating annotations and feature structures. Additionally, the the convenience methods for JCas access are fully type-safe and return the JCas type or a collection of the JCas type which you wanted to access.
uimaFIT supports the following convenience methods for accessing CAS and JCas structures. All methods respect the UIMA index definitions and return annotations or feature structures in the order defined by the indexes. Unless the default UIMA index for annotations has been overwritten, annotations are returned sorted by begin (increasing) and end (decreasing).
select(cas, type) - fetch all annotations of the given type from the
CAS/JCas. Variants of this method also exist to fetch annotations from a
FSList or FSArray.
selectAll(cas) - fetch all annotations from the CAS or fetch all feature
structures from the JCas.
selectBetween(type, annotation1, annotation2)* - fetch all annotations
between the given two annotations.
selectCovered(type, annotation)* - fetch all annotations covered by the
given annotation. If this operation is used intensively, indexCovered(...)
should be used to pre-calculate annotation covering information.
selectCovering(type, annotation)* - fetch all annotations covering the
given annotation. If this operation is used intensively, indexCovering(...)
should be used to pre-calculate annotation covering information.
selectByIndex(cas, type, n) - fetch the n-th feature structure of the
given type.
selectSingle(cas, type) - fetch the single feature structure of the given
type. An exception is thrown if there is not exactly one feature structure of the type.
selectSingleRelative(type, annotation, n)* - fetch a single annotation
relative to the given annotation. A positive n fetches the n-th
annotation right of the specified annotation, while the a negative
n fetches to the left.
selectPreceding(type, annotation, n)* - fetch the n annotations preceding
the given annotation. If there are less then n preceding annotations, all preceding
annotations are returned.
selectFollowing(type, annotation, n)* - fetch the n annotations following
the given annotation. If there are less then n following annotations, all following
annotations are returned.
For historical reasons, the method marked with * also exist in a version that accepts a CAS/JCas as the first argument. These may not work as expected when the annoation arguments provided to the method are from a different CAS/JCas/view. Also, for any method accepting two annotations, these should come from the same CAS/JCas/view. In future, the potentially problematic signatures may be deprecated, removed, or throw exeptions if these conditions are not met.
You should expect the structures returned by these methods to be backed by the CAS/JCas
contents. In particular, if you remove any feature structures from the CAS while iterating
over these structures may cause failures. For this reason, you should also not hold on to
these structures longer than necessary, as is the case for UIMA FSIterators as
well.
Depending on whether one works with a CAS or JCas, the respective methods are available from the JCasUtil or CasUtil classes.
JCasUtil expect a JCas wrapper class for the type argument, e.g.
select(jcas, Token.class) and return this type or a collection using this
generic type. Any subtypes of the specified type are returned as well. CasUtil expects a UIMA
Type instance. For conveniently getting these, CasUtil offers the methods
getType(CAS, Class<?>) or getType(CAS, String) which fetch a
type either by its JCas wrapper class or by its name.
Unless annotations are specifically required, e.g. because begin/end offsets are required,
the JCasUtil methods can be used to access any feature structure inheriting from
TOP, not only annotations. The CasUtil methods generally work only on
annotations. Alternative methods ending in "FS" are provided for accessing arbitrary feature
structures, e.g. selectFS.
Examples:
// CAS version
Type tokenType = CasUtil.getType(cas, "my.Token");
for (AnnotationFS token : CasUtil.select(cas, tokenType)) {
...
}
// JCas version
for (Token token : JCasUtil.select(jcas, Token.class)) {
...
}
uimaFIT defines the @ConfigurationParameter annotation which can be
used to annotate the fields of an analysis engine or collection reader. The purpose of this
annotation is twofold:
injection of parameters from the UIMA context into fields
declaration of parameter metadata (mandatory, default value, description) which can be used to generate XML descriptors
In a regular UIMA component, parameters need to be manually extracted from the UIMA context, typically requiring a type cast.
class MyAnalysisEngine extends CasAnnotator_ImplBase {
public static final String PARAM_SOURCE_DIRECTORY = "sourceDirectory";
private File sourceDirectory;
public void initialize(UimaContext context)
throws ResourceInitializationException {
sourceDirectory = new File((String) context.getConfigParameterValue(
PARAM_SOURCE_DIRECTORY));
}
}
The component has no way to declare a default value or to declare if a parameter is optional or mandatory. In addition, any documentation needs to be maintained in !JavaDoc and in the XML descriptor for the component.
With uimaFIT, all this information can be declared in the component using the
@ConfigurationParameter annotation.
Table 6.1. @ConfigurationParameter annotation
| Parameter | Description | Default |
|---|---|---|
| name | parameter name | name of annotated field |
| description | description of the parameter | |
| mandatory | whether a non-null value must be specified | true |
| defaultValue | the default value if no value is specified |
class MyAnalysisEngine
extends org.apache.uima.fit.component.CasAnnotator_ImplBase {
/**
* Directory to read the data from.
*/
public static final String PARAM_SOURCE_DIRECTORY = "sourceDirectory";
@ConfigurationParameter(name=PARAM_SOURCE_DIRECTORY, defaultValue=".")
private File sourceDirectory;
}
Note, that it is no longer necessary to implement the initialize()
method. uimaFIT takes care of locating the parameter sourceDirectory in
the UIMA context. It recognizes that the File class has a
String constructor and uses that to instantiate a new
File object from the parameter. A parameter is mandatory unless
specified otherwise. If a mandatory parameter is not specified in the context, an exception is
thrown.
The defaultValue is used when generating an UIMA component
description from the class. It should be pointed out in particular, that uimaFIT does not make
use of the default value when injecting parameters into fields. For this reason, it is possible
to have a parameter that is mandatory but does have a default value. The default value is used
as a parameter value when a component description is generated via the uimaFIT factories unless
a parameter is specified in the factory call. If a component description in created manually
without specifying a value for a mandatory parameter, uimaFIT will generate an exception.
You can use the enhance goal of the uimaFIT Maven plugin to pick up
the parameter description from the JavaDoc and post it to the
description field of the
@ConfigurationParameter annotation. This should be preferred to
specifying the description explicitly as part of the annotation.
The parameter injection mechanism is implemented in the
ConfigurationParameterInitializer class. uimaFIT provides several base
classes that already come with an initialize() method using the
initializer:
CasAnnotator_ImplBase`
CasCollectionReader_ImplBase
CasConsumer_ImplBase
CasFlowController_ImplBase
CasMultiplier_ImplBase
JCasAnnotator_ImplBase
JCasCollectionReader_ImplBase
JCasConsumer_ImplBase
JCasFlowController_ImplBase
JCasMultiplier_ImplBase
Resource_ImplBase
The ConfigurationParameterInitializer can also be used with shared
resources:
class MySharedResourceObject implements SharedResourceObject {
public static final String PARAM_VALUE = "Value";
@ConfigurationParameter(name = PARAM_VALUE, mandatory = true)
private String value;
public void load(DataResource aData)
throws ResourceInitializationException {
ConfigurationParameterInitializer.initialize(this, aData);
}
}
Fields that can be annotated with the @ConfigurationParameter
annotation are any array or collection types (including if they are only typed via interfaces
such as List or Set) of primitive types (int,
boolean, float, double). Enum types, as well as,
fields of the types
Charset,
File,
Locale,
Pattern,
URI, and
URL can also be used.
These can be initialized either using an object value (e.g. StandardChartsets.UTF_8)
or a string value (e.g. "UTF-8").
Additionally it is possible to inject any fields of types that define a constructor accepting
a single String. These must be initialized from a string value.
Multi-valued parameters can be initialized from single values without having to wrap these into a container.
An analysis engine often uses some data model. This may be as simple as word frequency counts or as complex as the model of a parser. Often these models can become quite large. If an analysis engine is deployed multiple times in the same pipeline or runs on multiple CPU cores, memory can be saved by using a shared instance of the data model. UIMA supports such a scenario by so-called external resources. The following sections illustrates how external resources can be used with uimaFIT.
First create a class for the shared data model. Usually this class would load its data from
some URI and then expose it via its methods. An example would be to load word frequency counts
and to provide a getFrequency() method. In our simple example we do not
load anything from the provided URI - we just offer a method to get the URI from which data be
loaded.
// Simple model that only stores the URI it was loaded from. Normally data
// would be loaded from the URI instead and made accessible through methods
// in this class. This simple example only allows accessing the URI.
public static final class SharedModel implements SharedResourceObject {
private String uri;
public void load(DataResource aData)
throws ResourceInitializationException {
uri = aData.getUri().toString();
}
public String getUri() { return uri; }
}
When an external resource is used in a regular UIMA component, it is usually fetched from the context, cast and copied to a class member variable.
class MyAnalysisEngine extends CasAnnotator_ImplBase {
final static String MODEL_KEY = "Model";
private SharedModel model;
public void initialize(UimaContext context)
throws ResourceInitializationException {
configuredResource = (SharedModel)
getContext().getResourceObject(MODEL_KEY);
}
}
uimaFIT can be used to inject external resources into such traditional components using
the createDependencyAndBind() method. To show that this works with
any off-the-shelf UIMA component, the following example uses uimaFIT to configure the
OpenNLP Tokenizer:
// Create descriptor AnalysisEngineDescription tokenizer = createEngineDescription( Tokenizer.class, UimaUtil.TOKEN_TYPE_PARAMETER, Token.class.getName(), UimaUtil.SENTENCE_TYPE_PARAMETER, Sentence.class.getName()); // Create the external resource dependency for the model and bind it createDependencyAndBind(tokenizer, UimaUtil.MODEL_PARAMETER, TokenizerModelResourceImpl.class, "http://opennlp.sourceforge.net/models-1.5/en-token.bin");
We recommend declaring parameter constants in the classes that use them, e.g. here
in Tokenizer. This way, the parameters for a class can be found
easily. However, OpenNLP declares parameters centrally in UimaUtil.
Thus, the example above is correct, although unconvential.
Note that uimaFIT is unable to perform type-coercion on parameters if a descriptor
is created from a class that does not contain @ConfigurationParameter
annotations, such as the OpenNLP Tokenizer. Such a descriptor does
not contain any parameter declarations! However, it is
still possible to configure such a component using uimaFIT by passing exactly the expected
types as parameter values. Thus, we need use the getName() method
to get the class name as a string, instead of simply passing the class itself. Also, setting
multi-valued parameter from a list or single value does not work here. Multi-values parameters
must be passed as an array of the required type. Only the default UIMA types are possible:
String, boolean, int, and float.
uimaFIT provides the @ExternalResource annotation to inject
external resources directly into class member variables.
Table 7.1. @ExternalResource annotation
| Parameter | Description | Default |
|---|---|---|
| key | Resource key | field name |
| api | Used when the external resource type is different from the field type, e.g. when using an ExternalResourceLocator | field type |
| mandatory | Whether a value must be specified | true |
// Example annotator that uses the SharedModel. In the process() we only
// test if the model was properly initialized by uimaFIT
public static class Annotator
extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
final static String MODEL_KEY = "Model";
@ExternalResource(key = MODEL_KEY)
private SharedModel model;
public void process(JCas aJCas) throws AnalysisEngineProcessException {
assertTrue(model.getUri().endsWith("gene_model_v02.bin"));
// Prints the instance ID to the console - this proves the same
// instance of the SharedModel is used in both Annotator instances.
System.out.println(model);
}
}
Note, that it is no longer necessary to implement the
initialize() method. uimaFIT takes care of locating the external
resource Model in the UIMA context and assigns it to the field
model. If a mandatory resource is not present in the context, an
exception is thrown.
The resource injection mechanism is implemented in the
ExternalResourceInitializer class. uimaFIT provides several base
classes that already come with an initialize() method using the
initializer:
CasAnnotator_ImplBase
CasCollectionReader_ImplBase
CasConsumer_ImplBase
CasFlowController_ImplBase
CasMultiplier_ImplBase
JCasAnnotator_ImplBase
JCasCollectionReader_ImplBase
JCasConsumer_ImplBase
JCasFlowController_ImplBase
JCasMultiplier_ImplBase
Resource_ImplBase
When building a pipeline, external resources can be set of a component just like configuration parameters. External resources and configuration parameters can be mixed and appear in any order when creating a component description.
Note that in the following example, we create only one external resource description and use it to configure two different analysis engines. Because we only use a single description, also only a single instance of the external resource is created and shared between the two engines.
ExternalResourceDescription extDesc = createExternalResourceDescription(
SharedModel.class, new File("somemodel.bin"));
// Binding external resource to each Annotator individually
AnalysisEngineDescription aed1 = createEngineDescription(
Annotator.class,
Annotator.MODEL_KEY, extDesc);
AnalysisEngineDescription aed2 = createEngineDescription(
Annotator.class,
Annotator.MODEL_KEY, extDesc);
// Check the external resource was injected
AnalysisEngineDescription aaed = createEngineDescription(aed1, aed2);
AnalysisEngine ae = createEngine(aaed);
ae.process(ae.newJCas());
This example is given as a full JUnit-based example in the the uimaFIT-examples project.
One kind of resources extend Resource_ImplBase. These are the
easiest to handle, because uimaFIT's version of Resource_ImplBase
already implements the necessary logic. Just be sure to call
super.initialize() when overriding
initialize(). Also mind that external resources are not available
yet when initialize() is called. For any initialization logic that
requires resources, override and implement
afterResourcesInitialized(). Other than that, injection of
external resources works as usual.
public static class ChainableResource extends Resource_ImplBase {
public final static String PARAM_CHAINED_RESOURCE = "chainedResource";
@ExternalResource(key = PARAM_CHAINED_RESOURCE)
private ChainableResource chainedResource;
public void afterResourcesInitialized() {
// init logic that requires external resources
}
}
The other kind of resources implement
SharedResourceObject. Since this is an interface, uimaFIT
cannot provide the initialization logic, so you have to implement a couple of things in the
resource:
implement ExternalResourceAware
declare a configuration parameter
ExternalResourceFactory.PARAM_RESOURCE_NAME and return its value
in getResourceName()
invoke ConfigurationParameterInitializer.initialize() in
the load() method.
Again, mind that external resource not properly initialized until uimaFIT invokes
afterResourcesInitialized().
public class TestSharedResourceObject implements
SharedResourceObject, ExternalResourceAware {
@ConfigurationParameter(name=ExternalResourceFactory.PARAM_RESOURCE_NAME)
private String resourceName;
public final static String PARAM_CHAINED_RESOURCE = "chainedResource";
@ExternalResource(key = PARAM_CHAINED_RESOURCE)
private ChainableResource chainedResource;
public String getResourceName() {
return resourceName;
}
public void load(DataResource aData)
throws ResourceInitializationException {
ConfigurationParameterInitializer.initialize(this, aData);
// rest of the init logic that does not require external resources
}
public void afterResourcesInitialized() {
// init logic that requires external resources
}
}
Nested resources are only initialized if they are used in a pipeline which contains at
least one component that calls
ConfigurationParameterInitializer.initialize(). Any component
extending uimaFIT's component base classes qualifies. If you use nested resources in a
pipeline without any uimaFIT-aware components, you can just add uimaFIT's
NoopAnnotator to the pipeline.
Normally, in UIMA an external resource needs to implement either
SharedResourceObject or
Resource. In order to inject arbitrary objects, uimaFIT has
the concept of ExternalResourceLocator. When a resource
implements this interface, not the resource itself is injected, but the method
getResource() is called on the resource and the result is injected.
The following example illustrates how to inject an object from JNDI into a UIMA
component:
class MyAnalysisEngine2 extends JCasAnnotator_ImplBase {
static final String RES_DICTIONARY = "dictionary";
@ExternalResource(key = RES_DICTIONARY)
Dictionary dictionary;
}
AnalysisEngineDescription desc = createEngineDescription(
MyAnalysisEngine2.class);
bindResource(desc, MyAnalysisEngine2.RES_DICTIONARY,
JndiResourceLocator.class,
JndiResourceLocator.PARAM_NAME, "dictionaries/german");
UIMA requires that types that are used in the CAS are defined in XML files - so-called type system descriptions (TSD). Whenever a UIMA component is created, it must be associated with such a type system. While it is possible to manually load the type system descriptors and pass them to each UIMA component and to each created CAS, it is quite inconvenient to do so. For this reason, uimaFIT supports the automatic detection of such files in the classpath. Thus is becomes possible for a UIMA component provider to have component's type automatically detected and thus the components becomes immediately usable by adding it to the classpath.
The provider of a type system should create a file
META-INF/org.apache.uima.fit/types.txt in the classpath. This file
should define the locations of the type system descriptions. Assume that a type
org.apache.uima.fit.type.Token is specified in the TSD
org/apache/uima/fit/type/Token.xml, then the file should have the
following contents:
classpath*:org/apache/uima/fit/type/Token.xml
Mind that the file types.txt is must be located in
META-INF/org.apache.uima.fit where
org.apache.uima.fit is the name of a sub-directory inside
META-INF. We are not using the Java package notation
here!
To specify multiple TSDs, add additonal lines to the file. If you have a large number of
TSDs, you may prefer to add a pattern. Assume that we have a large number of TSDs under
org/apache/uima/fit/type, we can use the following pattern which
recursively scans the package org.apache.uima.fit.type and all sub-packages
for XML files and tries to load them as TSDs.
classpath*:org/apache/uima/fit/type/**/*.xml
Try to design your packages structure in a way that TSDs and JCas wrapper classes generated from them are separate from the rest of your code.
If it is not possible or inconvenient to add the `types.txt` file, patterns can also be
specified using the system property
org.apache.uima.fit.type.import_pattern. Multiple patterns may be
specified separated by semicolon:
-Dorg.apache.uima.fit.type.import_pattern=\ classpath*:org/apache/uima/fit/type/**/*.xml
The \ in the example is used as a line-continuation indicator. It
and all spaces following it should be ommitted.
Auto-detection also works for index definitions and type priority definitions. For
index definitions, the respective file where to register the index definition XML files is
META-INF/org.apache.uima.fit/fsindexes.txt and for type priorities, it
is META-INF/org.apache.uima.fit/typepriorities.txt.
The auto-detected type system can be obtained from the
TypeSystemDescriptionFactory:
TypeSystemDescription tsd = TypeSystemDescriptionFactory.createTypeSystemDescription()
Popular factory methods also support auto-detection:
AnalysisEngine ae = createEngine(MyEngine.class);
uimaFIT supports multiple types.txt files in the classpath (e.g. in differnt JARs). The
types.txt files are located via Spring using the classpath search
pattern:
TYPE_MANIFEST_PATTERN = "classpath*:META-INF/org.apache.uima.fit/types.txt"
This resolves to a list URLs pointing to ALL types.txt files. The
resolved URLs are unique and will point either to a specific point in the file system or into
a specific JAR. These URLs can be handled by the standard Java URL loading mechanism.
Example:
jar:/path/to/syntax-types.jar!/META-INF/org.apache.uima.fit/types.txt jar:/path/to/token-types.jar!/META-INF/org.apache.uima.fit/types.txt
uimaFIT then reads all patters from all of these URLs and uses these to search the
classpath again. The patterns now resolve to a list of URLs pointing to the individual type
system XML descriptors. All of these URLs are collected in a set to avoid duplicate loading
(for performance optimization - not strictly necessary because the UIMA type system merger can
handle compatible duplicates). Then the descriptors are loaded into memory and merged using
the standard UIMA type system merger
(CasCreationUtils.mergeTypeSystems()). Example:
jar:/path/to/syntax-types.jar!/desc/types/Syntax.xml jar:/path/to/token-types.jar!/org/foobar/typesystems/Tokens.xml
Voilá, the result is a type system covering all types could be found in the classpath.
It is recommended
to put type system descriptors into packages resembling a namespace you "own" and to use a package-scoped wildcard search
classpath*:org/apache/uima/fit/type/**/*.xml`
or when putting descriptors into a "well-known" package like
desc.type, that types.txt file should
explicitly list all type system descriptors instead of using a wildcard
search
classpath*:desc/type/Token.xml classpath*:desc/type/Syntax.xml
Method 1 should be preferred. Both methods can be mixed.
Currently uimaFIT evaluates the patterns for TSDs once and caches the locations, but not
the actual merged type system description. A rescan can be forced using
TypeSystemDescriptionFactory.forceTypeDescriptorsScan(). This may
change in future.
The mechanism works fine. However, there are specific issues with Java in general that one should be aware of.
There seems to be a bug in some older versions of m2eclipse that causes resources not
always to be copied to target/classes. If UIMA complains about type
definitions missing at runtime, try to clean/rebuild your project and
carefully check the m2eclipse console in the console view for error messages that might
cause m2eclipse to abort.
A problem can occur if you end up having multiple incompatible versions of the same type
system in the classpath. This is a general problem and not related to the auto-detection
feature. It is the same as when you have incompatible version of a particular class (e.g.
JCas wrapper or some third-party-library) in the classpath.
The behavior of the Java Classloader is undefined in that case. The detection will do its
best to try and load everything it can find, but the UIMA type system merger may barf or you
may end up with undefined behavior at runtime because one of the class versions is used at
random.
It is bad practice to place classes into the default (unnamed) package. In fact it is not possible to import classes from the default package in another class. Similarly it is a bad idea to put resources at the root of the classpath. The Spring documentation on resources explains this in detail.
For this reason the types.txt resides in
/META-INF/org.apache.uima.fit and it is suggest that type system
descriptors reside either in a proper package like
/org/foobar/typesystems/XXX.xml or in
/desc/types/XXX.xml.
Building an executable JAR including uimaFIT components typically requires extra care. Per
convention, uimaFIT expects certain information in specific locations on the classpath, e.g. the
types.txt file that controls the automatic type system detection mechanism must
reside at META-INF/org.apache.uima.fit/types.txt. It often occurs that a
project has several dependencies, each supplying its own configuration files at these standard
locations. However, this causes a problem with naive approaches to creating an executable
fat-jar merging all dependencies into a single JAR file. Without extra
care, the files supplied by the different dependencies overwrite each other during the packaging
process and only one file wins in the end. As a consequence, the types
configured in the other files cannot be detected at runtime. Such a native approach is taken,
for example, by the Maven Assembly Plugin.
The Maven Shade Plugin provides a convenient alternative for the creation of executable
fat-jars, as it provides a mechanism to concatenate the configuration files from different
dependencies while creating the fat-jar. To use the Maven Shade Plugin with uimaFIT, use the
following configuration section in your POM file and make sure to change the
mainClass as required for your project:
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.2</version>
<executions>
<execution>
<phase>package</phase>
<goals><goal>shade</goal></goals>
<configuration>
<transformers>
<!-- Set the main class of the executable JAR -->
<transformer
implementation="org.apache.maven.plugins.shade.\
resource.ManifestResourceTransformer">
<mainClass>org.apache.uima.fit.example.Main</mainClass>
</transformer>
<!-- Merge the uimaFIT configuration files -->
<transformer
implementation="org.apache.maven.plugins.shade.\
resource.AppendingTransformer">
<resource>\
META-INF/org.apache.uima.fit/fsindexes.txt\
</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.\
resource.AppendingTransformer">
<resource>\
META-INF/org.apache.uima.fit/types.txt\
</resource>
</transformer>
<transformer
implementation="org.apache.maven.plugins.shade.\
resource.AppendingTransformer">
<resource>\
META-INF/org.apache.uima.fit/typepriorities.txt\
</resource>
</transformer>
</transformers>
<!--
Prevent huge shaded artifacts from being deployed
to a Maven repository (remove if not desired)
-->
<outputFile>\
${project.build.directory}/\
${artifactId}-${version}-standalone.jar\
</outputFile>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
Due to formatting constraints in the PDF version of this manual, the example above uses
\ to indicate a line continuation. Remove these and join the lines when you
copy/paste this example.
You might want to consider also merging additional files, such as LICENSE, NOTICE, or DEPENDENCY files, configuration files for the Java Service Locator API, or files used by other frameworks that uses similar conventions for configuration file locations. Check the documentation of the Maven Shade Plugin, as different kinds of configuration files require different specialized transformers.
uimaFIT dynamically generates UIMA component descriptions from annotations in the Java source code. The uimaFIT Maven plugin provides the ability to automatically create such annotations in already compiled classes and to automatically generate XML descriptors from the annotated classes.
The goal enhance allows automatically augmenting compiled classes with uimaFIT annotations. Information like vendor, copyright, or version can be obtained from the Maven POM. Additionally, descriptions for parameters and components can be generated from Javadoc comments. Existing annotations are not overwritten unless forced.
<plugin>
<groupId>org.apache.uima</groupId>
<artifactId>uimafit-maven-plugin</artifactId>
<version>2.5.0</version> <!-- change to latest version -->
<configuration>
<!-- OPTIONAL -->
<!-- Override component description in generated descriptors. -->
<overrideComponentDescription>false</overrideComponentDescription>
<!-- OPTIONAL -->
<!-- Override version in generated descriptors. -->
<overrideComponentVersion>false</overrideComponentVersion>
<!-- OPTIONAL -->
<!-- Override vendor in generated descriptors. -->
<overrideComponentVendor>false</overrideComponentVendor>
<!-- OPTIONAL -->
<!-- Override copyright in generated descriptors. -->
<overrideComponentCopyright>false</overrideComponentCopyright>
<!-- OPTIONAL -->
<!-- Version to use in generated descriptors. -->
<componentVersion>${project.version}</componentVersion>
<!-- OPTIONAL -->
<!-- Vendor to use in generated descriptors. -->
<componentVendor>Apache Foundation</componentVendor>
<!-- OPTIONAL -->
<!-- Copyright to use in generated descriptors. -->
<componentCopyright>Apache Foundation 2013</componentCopyright>
<!-- OPTIONAL -->
<!-- Source file encoding. -->
<encoding>${project.build.sourceEncoding}</encoding>
<!-- OPTIONAL -->
<!-- Generate a report of missing meta data in
$project.build.directory/uimafit-missing-meta-data-report.txt -->
<generateMissingMetaDataReport>true</generateMissingMetaDataReport>
<!-- OPTIONAL -->
<!-- Fail on missing meta data. This setting has no effect unless
generateMissingMetaDataReport is enabled. -->
<failOnMissingMetaData>false</failOnMissingMetaData>
<!-- OPTIONAL -->
<!-- Constant name prefixes used for parameters and external resources,
e.g. "PARAM_". -->
<parameterNameConstantPrefixes>
<prefix>PARAM_<prefix/>
</parameterNameConstantPrefixes>
<!-- OPTIONAL -->
<!-- Fail on missing meta data. This setting has no effect unless
generateMissingMetaDataReport is enabled. -->
<externalResourceNameConstantPrefixes>
<prefix>KEY_<prefix/>
<prefix>RES_<prefix/>
</externalResourceNameConstantPrefixes>
<!-- OPTIONAL -->
<!-- Mode of adding type systems found on the classpath via the
uimaFIT detection mechanism at compile time to the generated
descriptor. By default, no type systems are added. -->
<addTypeSystemDescriptions>NONE</addTypeSystemDescriptions>
</configuration>
<executions>
<execution>
<id>default</id>
<phase>process-classes</phase>
<goals>
<goal>enhance</goal>
</goals>
</execution>
</executions>
</plugin>
When generating descriptions for configuration parameters or external resources, the
plugin supports a common practice of placing the Javadoc on a constant field instead of the
parameter or external resource field. Per default, parameter name constants must be prefixed
with PARAM_ and external resource key constants must be prefixed with RES_
or KEY_.
/** * Enable or disable my feature. */ public static final String PARAM_ENABLE_FEATURE = "enableFeature"; @ConfigurationParameter(name=PARAM_ENABLE_FEATURE) private boolean enableFeature; /** * My external resource. */ public static final String RES_MY_RESOURCE = "resource"; @ExternalResource(key=RES_MY_RESOURCE) private MyResource resource;
By enabling generateMissingMetaDataReport, the build can be made to fail if
meta data such as parameter descriptions are missing. A report about the missing data is
generated in uimafit-missing-meta-data-report.txt in the project build
directory.
The generate goal generates XML component descriptors for UIMA components.
<plugin>
<groupId>org.apache.uima</groupId>
<artifactId>uimafit-maven-plugin</artifactId>
<version>2.5.0</version> <!-- change to latest version -->
<configuration>
<!-- OPTIONAL -->
<!-- Path where the generated resources are written. -->
<outputDirectory>
${project.build.directory}/generated-sources/uimafit
</outputDirectory>
<!-- OPTIONAL -->
<!-- Skip generation of META-INF/org.apache.uima.fit/components.txt -->
<skipComponentsManifest>false</skipComponentsManifest>
<!-- OPTIONAL -->
<!-- Source file encoding. -->
<encoding>${project.build.sourceEncoding}</encoding>
</configuration>
<executions>
<execution>
<id>default</id>
<phase>process-classes</phase>
<goals>
<goal>generate</goal>
</goals>
</execution>
</executions>
</plugin>
In addition to the XML descriptors, a manifest file is written to
META-INF/org.apache.uima.fit/components.txt. This file can be used to
conveniently locate the XML descriptors, which are written in the packages next to the classes
they
describe.
classpath*:org/apache/uima/fit/examples/ExampleComponent.xml
It is recommended to use both, the enhance and the generate goal. Both goals should be specified in the same execution, first enhance, then generate:
<execution>
<id>default</id>
<phase>process-classes</phase>
<goals>
<goal>enhance</goal>
<goal>generate</goal>
</goals>
</execution>
This section provides helpful information on incompatible changes between versions.
Version requirements. Depends on UIMA 2.10.2, Spring Framework 3.2.16 and Java 7.
Mind the updated version requirements. There should be no other potentially problematic changes in this upgrade.
CasIOUtil deprecated. The functionality of the uimaFIT CasIOUtil class has been superseded by the core UIMA class CasIOUtils added in UIMA 2.9.0. The method signatures in the new class are not the same, but provide more functionality. CasIOUtil has been deprecated and documentation has been added which of the CasIOUtils methods should be used instead.
Version requirements. Depends on UIMA 2.9.1, Spring Framework 3.2.16 and Java 7.
Mind the updated version requirements. There should be no other potentially problematic changes in this upgrade.
Version requirements. Depends on UIMA 2.8.1, Spring Framework 3.2.16 and Java 7.
Mind the updated version requirements. There should be no other potentially problematic changes in this upgrade.
Version requirements. Depends on UIMA 2.6.0 and Java 6.
AnnotationFactory.createAnnotation().
No longer throws UIMAExcption. If this exception was cought, some
IDEs may complain here after upgrading to uimaFIT 2.1.0.
Version requirements. Depends on UIMA 2.4.2.
Backwards compatibility. Compatibility with legacy annotation is provided by the Legacy support module.
Change of Maven groupId and artifactId.
The Maven group ID has changed from org.uimafit to
org.apache.uima.
The artifact ID of the main uimaFIT artifact has been changed from
uimafit to uimafit-core.
Change of package names.
The base package has been renamed from org.uimafit to
org.apache.uima.fit. A global search/replace on Java files with for
lines starting with import org.uimafit and replacing that with
import org.apache.uima.fit should work.
@ConfigurationParameter.
The default value for the mandatory attribute now is true. The
default name of configuration parameters is now the name of the annotated field only. The
classname is no longer prefixed. The method
ConfigurationParameterFactory.createConfigurationParameterName() that was
used to generate the prefixed name has been removed.
Type detection: META-INF/org.uimafit folder.
The META-INF/org.uimafit was renamed to
META-INF/org.apache.uima.fit.
JCasUtil.
The deprecated JCasUtil.iterate() methods have been removed.
JCasUtil.select() should be used instead.
AnalysisEngineFactory.
All createAggregateXXX and createPrimitiveXXX
methods have been renamed to createEngineXXX. The old names are
deprecated and will be removed in future versions.
All createAnalysisEngineXXX methods have been renamed to
createEngineXXX. The old names are deprecated and will be removed in
future versions.
CollectionReaderFactory.
All createDescriptionXXX methods have been renamed to
createReaderDescriptionXXX. The old names are deprecated and will be
removed in future versions.
All createCollectionReaderXXX methods have been renamed to
createReaderXXX. The old names are deprecated and will be removed in
future versions.
JCasIterable.
JCasIterable now only accepts reader and engine descriptions (no instances)
and no longer implements the Iterator interface. Instead, new
JCasIterator has been added, which replaces JCasIterable in that
respect.
CasDumpWriter.
org.uimafit.component.xwriter.CASDumpWriter has been renamed to
org.apache.uima.fit.component.CasDumpWriter.
CpePipeline.
CpePipeline has been moved to a separate module with the artifact ID
uimafit-cpe to reduce the dependencies incurred by the main uimaFIT
artifact.
XWriter removed.
The XWriter and associated file namers have been removed as they were
much more complex then acutally needed. As an alternative, CasIOUtil has
been introduced providing several convenience methods to read/write JCas/CAS data.
JCasFactory.
Methods only loading JCas data have been removed from JCasFactory.
The new methods in CasIOUtil can be used instead.
The compatibility layer should allow you to migrate to uimaFIT 2.5.0 without breaking anything. You should then be able to gradually change the codebase to be compatible with uimaFIT 2.5.0. As far as my tests go, uimaFIT 1.x and 2.5.0 can coexist peacefully on the classpath (and indeed both need to be on the classpath in order to use the legacy support module).
To enable the legacy support, make sure that you have a dependency on uimaFIT 1.x and then just add a dependency on the legacy module:
<dependency> <groupId>org.uimafit</groupId> <artifactId>uimafit</artifactId> <version>1.4.0</version> </dependency> <dependency> <groupId>org.apache.uima</groupId> <artifactId>uimafit-legacy-support</artifactId> <version>2.5.0</version> </dependency>
uimaFIT 2.5.0 automatically detects the presence of the legacy module and uses it - no additional configuration is necessary.
The following bash script may help to partially automatize the source code migration process. Please observe that it does not cover all of the necessary changes!
The script recursively changes all files under the current working directory! Make sure you are in the right directory before running it! Use the script at your own risk!
#!/bin/sh ############################################ # MAKE SURE TO BACKUP YOUR FILES FIRST! # SCRIPT RECURSIVELY CHANGES ALL JAVA FILES! # USE AT YOUR OWN RISK! ############################################ # Change of package names find . -name '*.java' -print | xargs perl -p -i -e 's/org.uimafit/org.apache.uima.fit/g' find . -name '*.java' -print | xargs perl -p -i -e 's/org.uimafit.component.xwriter.CASDumpWriter/\ org.apache.uima.fit.component.CasDumpWriter/g' # AnalysisEngineFactory find . -name '*.java' -print | xargs perl -p -i -e 's/createAggregate/createEngine/g' find . -name '*.java' -print | xargs perl -p -i -e 's/createPrimitive/createEngine/g' find . -name '*.java' -print | xargs perl -p -i -e 's/createAnalysisEngine/createEngine/g' # Readers find . -name '*.java' -print | xargs perl -p -i -e 's/createDescription/createReaderDescription/g' find . -name '*.java' -print | xargs perl -p -i -e 's/createCollectionReader/createReader/g'