Apache UIMA (Unstructured Information Management Architecture) v2.3.0 Release Notes

1. What is UIMA?
2. Major Changes in this Release
3. Migrating from IBM UIMA to Apache UIMA
4. How to Get Involved
5. How to Report Issues
6. List of JIRA Issues Fixed in this Release

1. What is UIMA?

Unstructured Information Management applications are software systems that analyze large volumes of unstructured information in order to discover knowledge that is relevant to an end user. UIMA is a framework and SDK for developing such applications. An example UIM application might ingest plain text and identify entities, such as persons, places, organizations; or relations, such as works-for or located-at. UIMA enables such an application to be decomposed into components, for example "language identification" -> "language specific segmentation" -> "sentence boundary detection" -> "entity detection (person/place names etc.)". Each component must implement interfaces defined by the framework and must provide self-describing metadata via XML descriptor files. The framework manages these components and the data flow between them. Components are written in Java or C++; the data that flows between components is designed for efficient mapping between these languages. UIMA additionally provides capabilities to wrap components as network services, and can scale to very large volumes by replicating processing pipelines over a cluster of networked nodes.

Apache UIMA is an Apache-licensed open source implementation of the UIMA specification (that specification is, in turn, being developed concurrently by a technical committee within OASIS , a standards organization). We invite and encourage you to participate in both the implementation and specification efforts.

UIMA is a component framework for analysing unstructured content such as text, audio and video. It comprises an SDK and tooling for composing and running analytic components written in Java and C++, with some support for Perl, Python and TCL.

2. Major Changes in this Release

Please see the README for this information.

3. Migrating from IBM UIMA to Apache UIMA

This section describes how to move from pre-Apache versions of UIMA to the Apache version (starting with Apache UIMA 2.1).

Note: Before running the migration utility, be sure to back up your files, just in case you encounter any problems, because the migration tool updates the files in place in the directories where it finds them.

The migration utility is run by executing the script file apache-uima/bin/ibmUimaToApacheUima.bat (Windows) or apache-uima/bin/ibmUimaToApacheUima.sh (UNIX). You must pass one argument: the directory containing the files that you want to be migrated. Subdirectories will be processed recursively.

The script scans your files and applies the necessary updates, for example replacing the com.ibm package names with the new org.apache package names.

The script will only attempt to modify files with the extensions: java, xml, xmi, wsdd, properties, launch, bat, cmd, sh, ksh, or csh; and files with no extension. Also, files with size greater than 1,000,000 bytes will be skipped. (If you want the script to modify files with other extensions, you can edit the script file and change the -ext argument appropriately.)

If the migration tool reports warnings, there may be a few additional steps to take. The following two sections explain some simple manual changes that you might need to make to your code.

3.1. JCas Cover Classes for DocumentAnnotation

If you have run JCasGen it is likely that you have the classes com.ibm.uima.jcas.tcas.DocumentAnnotation and com.ibm.uima.jcas.tcas.DocumentAnnotation_Type as part of your code. This package name is no longer valid, and the migration utility does not move your files between directories so it is unable to fix this.

If you have not made manual modifications to these classes, the best solution is usually to just delete these two classes (and their containing package). There is a default version in the uima-document-annotation.jar file that is included in Apache UIMA. If you have made custom changes, then you should not delete the file but instead move it to the correct package org.apache.uima.jcas.tcas. For more information about JCas and DocumentAnnotation please see Section 5.5.4, "Adding Features to DocumentAnnotation" in the UIMA References manual.

3.2. JCas.getDocumentAnnotation

The deprecated method JCas.getDocumentAnnotation has been removed. Its use must be replaced with JCas.getDocumentAnnotationFs. The method JCas.getDocumentAnnotationFs() returns type TOP, so your code must cast this to type DocumentAnnotation. The reasons for this are described in Section 5.5.4, "Adding Features to DocumentAnnotation" in the UIMA References manual.

3.3. Rare Cases Where Additional Manual Migration is Necessary

For most users there should not be any additional migration steps necessary. However, if the migration tool reported an additional warning or if you are having trouble getting your code to compile or run after running the migration, please see Section 1.4.2. "Rare Cases Where Additional Manual Migration is Necessary," in the Overview and Setup manual.

Bug

[UIMA-629] - Default file names produced by XmiWriterCasConsumer don't have .xmi extension and can't be read by XmiCollectionReader
[UIMA-781] - CPE test case CpmCasConsumer_ErrorTest intermittently failing
[UIMA-852] - jcasgen.sh has trouble with import by name
[UIMA-853] - jcasgen.sh returns success even if the run fails
[UIMA-941] - No ProcessTrace events for process calls that take 0ms
[UIMA-958] - Document Analyzer not showing PersonTitle when running with xml tagged source
[UIMA-978] - CDE eclipse plugin contains upper-case GIF file extension
[UIMA-982] - SofaFS class level Javadocs misleading
[UIMA-985] - Javdocs for getSofaData calls do not say null may be returned
[UIMA-988] - Performance bug: CAS heap reset wasteful use of Arrays.fill()
[UIMA-989] - CVD hangs on start-up
[UIMA-1012] - addSourceToJars.[bat/sh] is not executable in distribution
[UIMA-1024] - change version number from 2.2.2-incubating to 2.3-incubating-SNAPSHOT
[UIMA-1027] - Classes from uima-document-annotator.jar are not in Eclipse plugin
[UIMA-1036] - runAE help message needs to document available options for language and encoding
[UIMA-1045] - "Recently used" file lists in CVD do not work correctly
[UIMA-1058] - synch issue in FSClassRegistry.generators
[UIMA-1086] - CpmPanel displayProgress has bad logic
[UIMA-1099] - The Cas Editor leaks memory with each opened file.
[UIMA-1100] - Token annotation rendering style does not work.
[UIMA-1105] - CPE is sutck trying to retrieve a free CAS from the pool
[UIMA-1107] - Annotator context not set when annotator loaded from PEAR
[UIMA-1111] - Calling jcas.getType for a type that is not defined in the descriptor causes a lot of object allocation
[UIMA-1114] - DocumentAnalyzer: html view doesn't work for aggregates
[UIMA-1116] - Missing override to protect SofaNum feature from modification
[UIMA-1142] - FileUtils.saveString2File() should use try/finally block to close output stream
[UIMA-1150] - Pear isolation broken, test case failing
[UIMA-1158] - Some shell scripts don't work on Ubuntu Linux
[UIMA-1175] - CasEditor should work well with eclipse 3.4
[UIMA-1180] - Opening a CAS file should open the annotation editor. Not the text editor.
[UIMA-1181] - Deleting a CAS file should also close the annotation editor. This occurs when the file is opened in text editor and annotation editor and cas file is deleted.
[UIMA-1202] - Test cases fail because of incorrect/missing text encoding handling
[UIMA-1203] - Add source code encoding to master pom
[UIMA-1208] - How to get the element type of a uima.cas.FSList feature
[UIMA-1228] - Merging results from a parallel step fails when a feature is an array of pre-existing annotations
[UIMA-1242] - Array-valued features are written out incorrectly when serializing type system
[UIMA-1244] - PDF for Tutorials and Users' Guides printing fails on page 32
[UIMA-1247] - MBean Registration not thread-safe
[UIMA-1250] - Some initialization messages may not appear as the Logger object changes during initialization
[UIMA-1251] - If one delegate in an aggregate uses a JMS service descriptor and another fails to initialize, the JVM fails to terminate
[UIMA-1256] - UIMA-AS XMI serialization loses items appended to an FSList
[UIMA-1266] - AnalysisEngineMetaData.getTypeSystem() returns null
[UIMA-1268] - Pear installer can't detect encoding of UTF-8 XML file
[UIMA-1273] - Pear runtime pulls in all jar files in pear lib directory, no matter if they're on the classpath or not
[UIMA-1275] - Mistake in CAS Multiplier documentation
[UIMA-1277] - CasEditor line length setting is ignored
[UIMA-1280] - Missing message key in CPM at FINEST logging
[UIMA-1281] - Parameter overrides ignored for C++ annotators
[UIMA-1287] - deployAsyncService.sh does not work if UIMA_HOME contains a whitespace
[UIMA-1291] - FileNotFoundException with addSourceToJars under Windows when UIMA_HOME contains whitespace
[UIMA-1302] - PerformanceReports for PEAR not being generated in a CPE
[UIMA-1304] - Error handling parameters in CPE with a Vinci processor
[UIMA-1325] - jVinci pom.xml should have relative path to parent pom
[UIMA-1340] - PearAnalysisEngineWrapper does not expose Management Interface of the wrapped AE
[UIMA-1344] - XCAS Serialization doesn't handle StringArrays with null elements
[UIMA-1349] - Documentation does not mention that resource implementation should implement
[UIMA-1352] - java.lang.ClassCastException using find() with a SET index
[UIMA-1365] - Code trying to ensure reverse iterators list items in the opposite order of forward ones is present but not working
[UIMA-1373] - SimpleUimaAsService needs a POM
[UIMA-1380] - SwingWorker is Sun code that can't be relicensed under Apache license and needs to be removed
[UIMA-1386] - Cas Editor: BackgroundDrawingStrategy throws IllegalArgumentException
[UIMA-1388] - TypeSystem2Xml creates an incompatible type system descriptor
[UIMA-1400] - Uima aggregate with embedded Cas Multiplier fails if one attempts to create multiple instances of it in the same JVM
[UIMA-1404] - It is not possible to set feature values with subtypes of the feature type.
[UIMA-1408] - Annotation highlightning does not work with background drawing strategy
[UIMA-1411] - Instructions for building eclipse update site are wrong
[UIMA-1415] - Unix shell scripts should not use -vx debug arguments
[UIMA-1418] - Find/Annotate dialog annotation type should be synchronized with editor mode
[UIMA-1420] - Annotation Editor updates are too slow when it displays a huge number of annotations
[UIMA-1421] - Removing a huge number of annoations is slow
[UIMA-1422] - Improve/fix build process for Eclipse Plugins
[UIMA-1423] - Document import broken
[UIMA-1425] - Cas Editor plugin tests cannot be executed
[UIMA-1430] - XmiCasDeserializerHandler.readFS(String, String, String, Attributes) should throw an instantiated exception
[UIMA-1431] - Fix some potential overflow errors
[UIMA-1432] - Function SOAP AxisAnalysisEngineServiceStub.callAnalysisEngineMetaData() fails and should be removed
[UIMA-1438] - Don't delete src/main/resources/META-INF
[UIMA-1441] - Incorrect use of Collection.binarySearch in UnambiguousIteratorImpl
[UIMA-1458] - Remove the Cas Editor from the sandbox page.
[UIMA-1465] - running a pearSpecifier as a top level component fails with NullPointerException
[UIMA-1466] - Instantiating top level pearSpecifier: reconfigure throwing NPE and need to set Session
[UIMA-1467] - PearAnalysisEngineWrapper should forward remaining methods in its interfaces to the contained AE including reconfigure and management interfaces
[UIMA-1468] - Saving of annotations and relations does not always work properly
[UIMA-1470] - Annotation Editor tries to place cursor on invalid position
[UIMA-1473] - mvn assembly:assembly failing with msg about illegal character in path name to ant in repo
[UIMA-1483] - Incorrect generification of JCas interface
[UIMA-1485] - UIMA Tutorial and Developers guide in sub title 1.3.2 should be AAE and not AE
[UIMA-1491] - Correct generics in org.apache.uima.cas.text
[UIMA-1493] - Findbugs reporting inconsistent synchronization in ResourceManager - pear wrapper
[UIMA-1494] - PearWrapper - don't forward finalize method
[UIMA-1499] - Potential ClassCastException in CasPool
[UIMA-1512] - some subproject POMs missing dependency on JUnit
[UIMA-1516] - Deleted annotations remain highlighted
[UIMA-1521] - File encoding is platform dependent
[UIMA-1523] - Generics: FSIterator.moveTo(T) should be moveTo(FeatureStructure)
[UIMA-1525] - Running an AE inside the Cas Editor does not marks editor as dirty if document is opened
[UIMA-1532] - Generics in FSIndex maybe incorrect
[UIMA-1536] - move RunWithJarPath into its own project
[UIMA-1543] - Missing <version> tags in uimaj-distr POM
[UIMA-1548] - Include LICENSE/NOTICE/DISCLAIMER files from local sources ahead of common sources
[UIMA-1549] - uimaj-core has dependency on log4j coded incorrectly
[UIMA-1560] - Fix problems reported by FindBugs
[UIMA-1561] - UIMA Reference docs 5.5.4 DocumentAnnotation is misspelled
[UIMA-1562] - CasMultiplier doesn't work for PEARs
[UIMA-1566] - build breaks for some components having no source files
[UIMA-1569] - Marker should be make invalid when CAS is reset.
[UIMA-1573] - setUimaClassPath fixes
[UIMA-1576] - The AnnotationEditor does not remember the shown annotations when the Cas Editor is restarted
[UIMA-1584] - Document Delta CAS XMI format
[UIMA-1599] - Outline view may throws ClassCastException in TypeGroupedContentProvider
[UIMA-1600] - Background drawing style does not draw correctly if an annotation contains a tab
[UIMA-1606] - On eclipse 3.3.1.1 package not automatically added to the list of imported packages
[UIMA-1609] - binary assembly wrongly including FOP files
[UIMA-1615] - make build-from-sources work
[UIMA-1618] - Rename CasEditor NLP category to "Cas Editor" and the NLP project to "Cas Editor Project"
[UIMA-1619] - Clarify that a Cas Editor Project is required to use the Cas Editor in the documentation
[UIMA-1621] - CVD should work when classes loaded dynamically
[UIMA-1631] - UimaBootstrap Loader approach fails to work for classes loaded by logger (and maybe other parts of Java)
[UIMA-1641] - Cas Processor integration was changed, but documentation not updated
[UIMA-1647] - Scripts fail to call runUimaClass.sh
[UIMA-1650] - Bug in common launcher script causing UIMA_CLASSPATH to be ignored
[UIMA-1663] - All directories in UIMA distribution should be 755
[UIMA-1664] - Windows command line files not working
[UIMA-1678] - Pear builder maven plugin should use "Package" mode of buildComponentClassPath
[UIMA-1679] - UIMA scripts set memory options that override user's setiings
[UIMA-1683] - fix copyright notice in the NOTICE files
[UIMA-1687] - correct top-level svn license/notice files
[UIMA-1688] - Cas Editor throws NPE when cleaning a document which is opened
[UIMA-1690] - After cleaning a document the outline view does not sync
[UIMA-1692] - add missing license headers to .project files etc. in uimaj-eclipse-... projects
[UIMA-1694] - Error 'scm url cannot be null' on uimaj POM
[UIMA-1708] - Trailing blank following log property level causing problems with IBM Java 6
[UIMA-1718] - The UIMA core code fails to unlock a CAS if there is an exception in CasMultiplier's next() or hasNext() methods

Improvement

[UIMA-71] - New v2 features missing from tutorial chapters
[UIMA-420] - CVD should use encoding list provided by JVM
[UIMA-472] - CAS Editor: All annotation inside the editor should have a differnt default colors as its done in the "UIMA Annotation Viewer"
[UIMA-483] - JCas method like getSofaDataString that doesn't copy the chars from the StringHeap
[UIMA-518] - improve browser utilities to configured the used browser in UIMA
[UIMA-554] - Have produceResource for CollectionReaders operate like other Analysis Engines with respect to setup of type system
[UIMA-684] - update website with "How to do a release"
[UIMA-767] - Use eclipse content types to identify annotators descriptors (.ann) and consumer descriptors (.con)
[UIMA-841] - move Eclipse feature maven builds into feature projects
[UIMA-857] - Change startup of framework to support versioned Jars and simplified classpath
[UIMA-961] - Cleanup - remove unused things
[UIMA-984] - Improve way we get required jar file javax.activation:activation:jar:1.0.2 for building from the source
[UIMA-1015] - Example using deprecated method
[UIMA-1048] - Eliminate compiler warings in CVD
[UIMA-1067] - Remove char heap/ref heap in StringHeap of the CAS
[UIMA-1068] - Use of the JCas cache should be configurable
[UIMA-1119] - The XmiCasDeserializer throws NoSuchElementException if an XCAS is corrupted, but doesn't report the offending element.
[UIMA-1148] - CVD should ignore feature structures of unknown types
[UIMA-1163] - set svn:eol-style to native for source files in UIMA project
[UIMA-1177] - Consider making the default setting for "Auto Generate JCAS Java source files" be off.
[UIMA-1178] - Move the editing part of the Cas Editor to a new plugin
[UIMA-1179] - Outline view should have an option to show all annotations grouped by type
[UIMA-1182] - add info on how to verify using md5 signatures
[UIMA-1206] - Add the capability to browse subdirectories to org.apache.uima.examples.cpe.FileSystemCollectionReader
[UIMA-1212] - Optimize indexRepository methods getIndexedFS and flush
[UIMA-1221] - PEAR Installer : how to run?
[UIMA-1222] - PEAR Installer: environment variables
[UIMA-1225] - dot files should not be redistributed
[UIMA-1230] - When parsing an aggregate descriptor, should parse a shared type system file only once
[UIMA-1257] - Type System Merging Should Produce Consistent Ordering of Types
[UIMA-1258] - Optimize performance of CasCopier when input and output TypeSystems are the same
[UIMA-1260] - [SimpleServer] Expose some "private" variables and method as "protected" so that new subclasses for UIMA-AS can be defined
[UIMA-1262] - Make changes to superPoms active before they are *installed*
[UIMA-1283] - Improve POMs so that eclipse build no longer requery maven repos once a day
[UIMA-1306] - uimaj-examples: opennlp_wrappers not compatible with opennlp 1.4.x
[UIMA-1326] - Remove EMF dependency from uimaj-ep-runtime plugin
[UIMA-1333] - JCasFlow_ImplBase.setJCas() should be deprecated, and this action always done by framework
[UIMA-1341] - Introduce generics in UIMA core API
[UIMA-1342] - Use @Deprecated annotation also
[UIMA-1345] - Use generics in uimaj-core test code
[UIMA-1356] - Add source to UIMA Eclipse plugins
[UIMA-1362] - Cas Editor pom should use ${uimaj-release-version variable instead of hardcoded version string
[UIMA-1363] - Access to individual type index iterators
[UIMA-1364] - Concurrent modification checks dominate index iteration time.
[UIMA-1366] - Binary heap annotation iterator implementation
[UIMA-1368] - Compiler warnings in CAS index impl code
[UIMA-1396] - Use generics in uimaj-core org.apache.uima.analysis_component package
[UIMA-1397] - Extract CasEditor interface from AnnotationEditor
[UIMA-1398] - Refactor ICasDocument interface to be more generic for non-text cas editors
[UIMA-1417] - ResourceConfigurationException to be thrown from the initialize(context) method
[UIMA-1419] - Find/Annotate dialog should have buttons to adjust annoation span
[UIMA-1428] - Remove unused private constructors from org.apache.uima.cas.impl package classes
[UIMA-1440] - Documentation build: add ant script that copies the docbook prereqs from a known location
[UIMA-1442] - RedBlackTree should use generics
[UIMA-1443] - RedBlackTree should implement Iterable
[UIMA-1444] - cas.impl package should use generics
[UIMA-1445] - Refactor FSTypeConstraintImpl
[UIMA-1448] - Add generics to LinearTypeOrderBuilderImpl
[UIMA-1451] - findbugs changes for ep-configurator (CDE)
[UIMA-1452] - add generic type info to some classes in uima-core
[UIMA-1453] - some findbugs cleanup in uimaj-core
[UIMA-1474] - review POMs for specification of obsolete, out-of-date levels of components
[UIMA-1488] - Generics for org.apache.uima.resoruce classes
[UIMA-1489] - Generify FSIndexRepository
[UIMA-1496] - Generics for CasCreationUtils
[UIMA-1500] - Deprecate UIMA 1.x classes in org.apache.uima.analysis_engine.annotator
[UIMA-1501] - more refactoring and updating - parent POMs
[UIMA-1504] - Generify the additionalParams Map through the uimaj-core codebase
[UIMA-1505] - Generics for org.apache.uima.analysis_engine classes
[UIMA-1507] - BaseCollectionReader should extend Resource
[UIMA-1508] - Generify uimaj-core
[UIMA-1509] - Generify the aResourceClass Class through the uimaj-core codebase
[UIMA-1510] - improve uimaj-distr assembly
[UIMA-1513] - Update Cas Editor documentation for 2.3.0 release
[UIMA-1517] - Don't set executable bits on non-executables, when building assemblies
[UIMA-1519] - Generify JFSIndexRepository
[UIMA-1520] - An annotation created with the edit view should use span of editor selection
[UIMA-1537] - License Notice Disclaimer copying
[UIMA-1538] - Common Build Step: build source Jars for java Jars
[UIMA-1544] - make bootstrap launcher take directories which have .class files in them
[UIMA-1545] - UimaBootstrap loader - print out the resulting classpath by default
[UIMA-1567] - Maven build: add <prerequisites> to uimaj to specify minimum Maven release level
[UIMA-1568] - Remove no longer used assemble-plugin files from uimaj-ep- projects
[UIMA-1575] - Change eclipse update site and feature generation to use common maven mechanisms
[UIMA-1585] - Run RAT on projects, fix missing licenses, add RAT running to POM, document exclusions
[UIMA-1590] - fix extractAndBuild scripts
[UIMA-1591] - Sandbox build - fix copying & cleaning of docs/ for website interaction with SVN
[UIMA-1592] - PearPackagingMavenPlugin - correct documentation and add usage from command line, and add plugin prefix
[UIMA-1613] - run Rat consistently for all maven assemblies
[UIMA-1689] - fix some miscompares between svn export and source-distribution
[UIMA-1691] - change checkout to export in extract and build scripts
[UIMA-1695] - Eclipse tooling: CDE fully instantiates components of aggregates, resulting in OutOfMemory issues

New Feature

[UIMA-1046] - CVD should support an ini file parameter on the command line
[UIMA-1129] - XMI serialization support for delta CAS
[UIMA-1151] - Make CVD load a CAS from command line
[UIMA-1167] - CVD should be able to call CollectionProcessComplete
[UIMA-1188] - More constraints for primitive types
[UIMA-1207] - Support for Delta CAS format in binary (blob) serialization
[UIMA-1210] - XmiCollectionReader fails when it encounters unknown types
[UIMA-1267] - Pear installer: expose the ability to install pear file without intermediate component ID

Task

[UIMA-1360] - Graduate the Cas Editor out of the sandbox
[UIMA-1387] - Cas Editor: Remove pde log viewer from perspective
[UIMA-1414] - Add Cas Editor to uima distribution
[UIMA-1424] - Remove .launch files from Cas Editor
[UIMA-1497] - change build for pear packaging maven plugin
[UIMA-1614] - update 2.3.0-incubating-SNAPSHOT to drop the snapshot in prep for release

Test

[UIMA-1389] - Remove OpenNLP example wrapper