You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@uima.apache.org by re...@apache.org on 2020/10/27 21:24:24 UTC
[uima-uimafit] 01/01: Merge branch 'master' into
origin/bugfix/UIMA-6286-select-following-finds-zero-width-annotation-at-reference-end-position
This is an automated email from the ASF dual-hosted git repository.
rec pushed a commit to branch origin/bugfix/UIMA-6286-select-following-finds-zero-width-annotation-at-reference-end-position
in repository https://gitbox.apache.org/repos/asf/uima-uimafit.git
commit 285aa0a211c7b860b8ad517abadb3003fbceb184
Merge: ebb1ecb 2f009d8
Author: Richard Eckart de Castilho <re...@apache.org>
AuthorDate: Tue Oct 27 22:24:06 2020 +0100
Merge branch 'master' into origin/bugfix/UIMA-6286-select-following-finds-zero-width-annotation-at-reference-end-position
* master: (134 commits)
[UIMA-6275] InitializableFactory is not smart enough to find a suitable classloader
No issue: ASF Jenkins Windows nodes seem to have trouble ('nohup' not found) - excluding Windows build nodes for the moment.
[UIMA-6270] Add selectOverlapping to (J)CasUtil
[UIMA-6270] Add selectOverlapping to (J)CasUtil
[UIMA-6263] CAS validation support
[UIMA-6264] Switch from DocBook to Asciidoc
[UIMA-6257] Jenkinsfile for uimaFIT
[UIMA-6257] Jenkinsfile for uimaFIT
[UIMA-6257] Jenkinsfile for uimaFIT
[UIMA-6257] Jenkinsfile for uimaFIT
[maven-release-plugin] prepare for next development iteration
[maven-release-plugin] prepare release uimafit-3.1.0
[maven-release-plugin] prepare for next development iteration
[maven-release-plugin] prepare release uimafit-3.1.0
[NO JIRA] Adjust UIMA version in the NOTICE file of the binary distribution
[maven-release-plugin] prepare for next development iteration
[maven-release-plugin] prepare release uimafit-3.1.0
[NO JIRA] Update documentation to changed API in ExternalResourceFactory and removed a spurious character
[NO JIRA] Adjusted comparison version for API change report
[NO JIRA] Updated README file for release.
...
% Conflicts:
% uimafit-core/src/main/java/org/apache/uima/fit/util/CasUtil.java
CONTRIBUTING.md | 3 +-
README | 36 +-
api-change-report.html | 13 +-
pom.xml | 56 +-
src/main/assembly/bin.xml | 28 +-
src/main/dist-bin/LICENSE | 2 +-
src/main/dist-bin/NOTICE | 16 +-
uimafit-assertj/pom.xml | 4 +-
uimafit-benchmark/pom.xml | 23 +-
.../org/apache/uima/fit/benchmark/Benchmark.java | 2 +-
.../uima/fit/benchmark/RunnableWithExceptions.java | 4 +-
.../uima/fit/benchmark/CasUtilBenchmark.java | 62 ++
.../uima/fit/benchmark/JCasUtilBenchmark.java | 69 +++
.../src/test/resources/simplelogger.properties | 1 +
uimafit-core/NOTICE | 4 +
uimafit-core/pom.xml | 52 +-
.../uima/fit/component/CasAnnotator_ImplBase.java | 15 -
.../component/CasCollectionReader_ImplBase.java | 12 +-
.../uima/fit/component/CasConsumer_ImplBase.java | 15 -
.../fit/component/CasFlowController_ImplBase.java | 15 -
.../uima/fit/component/CasMultiplier_ImplBase.java | 15 -
.../uima/fit/component/ExternalResourceAware.java | 8 +-
.../uima/fit/component/JCasAnnotator_ImplBase.java | 15 -
.../component/JCasCollectionReader_ImplBase.java | 13 +-
.../uima/fit/component/JCasConsumer_ImplBase.java | 15 -
.../fit/component/JCasFlowController_ImplBase.java | 15 -
.../fit/component/JCasMultiplier_ImplBase.java | 15 -
.../uima/fit/component/Resource_ImplBase.java | 14 +-
.../uima/fit/factory/AnalysisEngineFactory.java | 10 +-
.../org/apache/uima/fit/factory/CasFactory.java | 34 +-
.../uima/fit/factory/CollectionReaderFactory.java | 50 +-
.../fit/factory/ConfigurationParameterFactory.java | 13 +-
.../uima/fit/factory/ExternalResourceFactory.java | 371 ++++++++----
.../uima/fit/factory/FlowControllerFactory.java | 10 +-
.../apache/uima/fit/factory/FsIndexFactory.java | 10 +-
.../org/apache/uima/fit/factory/JCasFactory.java | 49 +-
.../uima/fit/factory/TypePrioritiesFactory.java | 19 +-
.../fit/factory/TypeSystemDescriptionFactory.java | 11 +-
.../apache/uima/fit/internal/ExtendedLogger.java | 450 ---------------
.../org/apache/uima/fit/internal/MetaDataUtil.java | 2 +-
.../uima/fit/internal/ResourceManagerFactory.java | 77 ++-
.../apache/uima/fit/pipeline/SimplePipeline.java | 47 +-
.../uima/fit/testing/factory/TokenBuilder.java | 1 -
.../apache/uima/fit/util/AnnotationPredicates.java | 217 +++++++
.../java/org/apache/uima/fit/util/CasUtil.java | 182 ++++--
.../apache/uima/fit/util/FSCollectionFactory.java | 322 +++++++----
.../main/java/org/apache/uima/fit/util/FSUtil.java | 53 +-
.../java/org/apache/uima/fit/util/JCasUtil.java | 54 +-
.../AnalysisEngineFactoryExternalResourceTest.java | 61 +-
...ollectionReaderFactoryExternalResourceTest.java | 7 +-
.../factory/ExternalResourceConfiguratorTest.java | 4 +-
.../fit/factory/ExternalResourceFactoryTest.java | 173 ++++--
.../FlowControllerFactoryExternalResourceTest.java | 5 +-
.../org/apache/uima/fit/factory/LoggingTest.java | 375 -------------
.../fit/factory/TypePrioritiesFactoryTest.java | 30 +-
.../apache/uima/fit/pipeline/JCasIterableTest.java | 10 +-
.../uima/fit/pipeline/SimplePipelineTest.java | 6 +-
.../uima/fit/util/AnnotationPredicatesTest.java | 382 +++++++++++++
.../uima/fit/util/FSCollectionFactoryTest.java | 76 ++-
.../java/org/apache/uima/fit/util/FSUtilTest.java | 27 +-
.../org/apache/uima/fit/util/JCasUtilTest.java | 290 +++++++++-
.../{JCasUtilTest.java => JCasUtilv3Test.java} | 413 +++++++-------
.../resources/data/reference/JCasBuilderTest.dump | 22 +-
.../test/resources/data/reference/test.xmi.dump | 28 +-
uimafit-core/src/test/resources/log4j.properties | 5 -
.../src/test/resources/simplelogger.properties | 1 +
.../.settings/org.eclipse.core.resources.prefs | 1 +
uimafit-cpe/pom.xml | 82 +--
.../java/org/apache/uima/fit/cpe/CpePipeline.java | 27 +-
.../uima/fit/cpe/ExternalResourceFactoryTest.java | 30 +-
.../src/test/resources/simplelogger.properties | 1 +
uimafit-doc/pom.xml | 2 +-
.../asciidoc/tools.uimafit.externalresources.adoc | 2 +-
.../src/main/asciidoc/tools.uimafit.migration.adoc | 154 ++---
{uimafit-junit => uimafit-docbook}/pom.xml | 31 +-
.../tools.uimafit.configurationparameters.xml | 185 ++++++
.../docbook/tools.uimafit.externalresources.xml | 321 +++++++++++
.../src/docbook/tools.uimafit.migration.xml | 273 +++++++++
uimafit-examples/NOTICE | 3 +
uimafit-examples/pom.xml | 267 ++++-----
.../examples/resource/ExternalResourceExample.java | 7 +-
.../resource/ExternalResourceExample2.java | 7 +-
.../resource/ExternalResourceExample3.java | 6 +-
.../examples/tutorial/ex2/RoomNumberAnnotator.java | 3 +-
.../tutorial/ex6/UimaAcronymAnnotator.java | 8 +-
.../tutorial/ex6/UimaMeetingAnnotator.java | 8 +-
.../src/main/resources/simplelogger.properties | 1 +
.../fit/examples/tutorial/ex6/Example6Test.java | 8 +-
uimafit-junit/pom.xml | 4 +-
.../.settings/org.eclipse.jdt.core.prefs | 288 ----------
.../.settings/org.eclipse.jdt.ui.prefs | 3 -
uimafit-legacy-support/NOTICE | 8 -
...marker-file-identifying-api-compatibility-check | 1 -
uimafit-legacy-support/pom.xml | 144 -----
.../uima/fit/legacy/AnnotationConverter.java | 44 --
.../uima/fit/legacy/LegacySupportPluginImpl.java | 158 ------
.../fit/legacy/converter/AnnotationLiteral.java | 277 ---------
.../converter/ConfigurationParameterConverter.java | 98 ----
.../ContextlessAnnotationConverterBase.java | 41 --
.../converter/ExternalResourceConverter.java | 92 ---
.../converter/FsIndexCollectionConverter.java | 67 ---
.../fit/legacy/converter/FsIndexConverter.java | 92 ---
.../fit/legacy/converter/FsIndexKeyConverter.java | 63 ---
.../legacy/converter/NoConversionConverter.java | 59 --
.../converter/OperationalPropertiesConverter.java | 67 ---
.../legacy/converter/SofaCapabilityConverter.java | 75 ---
.../legacy/converter/TypeCapabilityConverter.java | 75 ---
.../org/apache/uima/fit/ComponentTestBase.java | 89 ---
.../uima/fit/component/CasDumpWriterTest.java | 61 --
.../JCasCollectionReader_ImplBaseTest.java | 88 ---
.../fit/component/ViewCreatorAnnotatorTest.java | 182 ------
.../fit/component/ViewTextCopierAnnotatorTest.java | 92 ---
.../ConfigurationParameterInitializerTest.java | 472 ----------------
.../apache/uima/fit/data/CreateSampleXCASFile.java | 59 --
.../apache/uima/fit/data/CreateSampleXMIFile.java | 54 --
.../uima/fit/descriptor/TypeCapabilityTest.java | 57 --
.../uima/fit/factory/AggregateBuilderTest.java | 209 -------
.../uima/fit/factory/AggregateWithReaderTest.java | 198 -------
.../AnalysisEngineFactoryExternalResourceTest.java | 404 --------------
.../fit/factory/AnalysisEngineFactoryTest.java | 467 ----------------
.../uima/fit/factory/AnnotationFactoryTest.java | 45 --
...ollectionReaderFactoryExternalResourceTest.java | 91 ---
.../fit/factory/CollectionReaderFactoryTest.java | 127 -----
.../factory/ConfigurationParameterFactoryTest.java | 221 --------
.../factory/ExternalResourceConfiguratorTest.java | 82 ---
.../fit/factory/ExternalResourceFactoryTest.java | 411 --------------
.../FlowControllerFactoryExternalResourceTest.java | 93 ---
.../uima/fit/factory/FsIndexFactoryTest.java | 132 -----
.../apache/uima/fit/factory/JCasBuilderTest.java | 73 ---
.../apache/uima/fit/factory/JCasFactoryTest.java | 71 ---
.../org/apache/uima/fit/factory/LoggingTest.java | 311 -----------
.../ResourceCreationSpecifierFactoryTest.java | 56 --
.../uima/fit/factory/SofaMappingFactoryTest.java | 40 --
.../fit/factory/TypePrioritiesFactoryTest.java | 47 --
.../factory/TypeSystemDescriptionFactoryTest.java | 48 --
.../uima/fit/factory/UimaContextFactoryTest.java | 70 ---
.../initializable/InitializableFactoryTest.java | 123 ----
.../uima/fit/factory/testAes/Annotator1.java | 50 --
.../uima/fit/factory/testAes/Annotator2.java | 63 ---
.../uima/fit/factory/testAes/Annotator3.java | 57 --
.../uima/fit/factory/testAes/Annotator4.java | 45 --
.../apache/uima/fit/factory/testAes/FlowAE1.java | 38 --
.../apache/uima/fit/factory/testAes/FlowAE2.java | 45 --
.../apache/uima/fit/factory/testAes/FlowAE3.java | 48 --
.../uima/fit/factory/testAes/ParameterizedAE.java | 409 --------------
.../uima/fit/factory/testAes/ParameterizedAE2.java | 56 --
.../testAes/ReversableTestFlowController.java | 88 ---
.../apache/uima/fit/factory/testAes/ViewNames.java | 38 --
.../fit/factory/testCrs/SingleFileXReader.java | 127 -----
.../fit/factory/testCrs/SingleFileXReaderTest.java | 117 ----
.../fit/factory/testRes/TestExternalResource.java | 41 --
.../factory/testRes/TestSharedResourceObject.java | 48 --
.../uima/fit/testing/factory/TokenBuilderTest.java | 242 --------
.../java/org/apache/uima/fit/util/CasUtilTest.java | 188 -------
.../apache/uima/fit/util/ContainmentIndexTest.java | 69 ---
.../apache/uima/fit/util/DisableLoggingTest.java | 106 ----
.../uima/fit/util/FSCollectionFactoryTest.java | 211 -------
.../org/apache/uima/fit/util/HideOutputTest.java | 72 ---
.../org/apache/uima/fit/util/JCasIterableTest.java | 43 --
.../org/apache/uima/fit/util/JCasUtilTest.java | 621 ---------------------
.../org/apache/uima/fit/util/LocaleUtilTest.java | 64 ---
.../apache/uima/fit/util/SimplePipelineTest.java | 48 --
.../org/apache/uima/fit/util/TypeSystemUtil.java | 46 --
.../resources/META-INF/org.uimafit/fsindexes.txt | 1 -
.../test/resources/META-INF/org.uimafit/types.txt | 1 -
.../resources/data/descriptor/DefaultValueAE1.xml | 36 --
.../resources/data/descriptor/DefaultValueAE2.xml | 36 --
.../src/test/resources/data/descriptor/README | 3 -
.../src/test/resources/data/docs/bad.xcas | 1 -
.../src/test/resources/data/docs/test.xcas | 1 -
.../src/test/resources/data/docs/test.xmi | 1 -
.../test/resources/data/docs/unix-newlines.txt.bin | 8 -
.../resources/data/docs/windows-newlines.txt.bin | 9 -
.../resources/data/reference/JCasBuilderTest.dump | 69 ---
.../test/resources/data/reference/test.xmi.dump | 92 ---
.../apache/uima/fit/component/NoOpAnnotator.xml | 48 --
.../uima/fit/factory/testCrs/SingleFileXReader.xml | 60 --
.../apache/uima/fit/index/AutoImportableIndex.xml | 38 --
.../org/apache/uima/fit/type/AnalyzedText.xml | 39 --
.../org/apache/uima/fit/type/Sentence.xml | 32 --
.../resources/org/apache/uima/fit/type/Token.xml | 44 --
uimafit-maven-plugin/pom.xml | 14 +-
uimafit-maven-plugin/src/it/default/pom.xml | 110 ++--
.../org/apache/uima/fit/maven/EnhanceMojo.java | 7 +-
.../uima/fit/maven/GenerateDescriptorsMojo.java | 2 +-
.../java/org/apache/uima/fit/maven/util/Util.java | 2 +-
uimafit-parent/pom.xml | 97 ++--
uimafit-spring/NOTICE | 3 +
uimafit-spring/pom.xml | 111 ++--
.../spring/SpringContextResourceManagerTest.java | 4 +-
.../src/test/resources/simplelogger.properties | 1 +
191 files changed, 3777 insertions(+), 12068 deletions(-)
diff --cc uimafit-core/src/main/java/org/apache/uima/fit/util/CasUtil.java
index eaa0e5c,187fe00..3e96190
--- a/uimafit-core/src/main/java/org/apache/uima/fit/util/CasUtil.java
+++ b/uimafit-core/src/main/java/org/apache/uima/fit/util/CasUtil.java
@@@ -1180,17 -1254,8 +1254,17 @@@ public final class CasUtil
}
// add annotations from the iterator into the result list
+ int refEnd = annotation.getEnd();
- List<AnnotationFS> followingAnnotations = new LinkedList<AnnotationFS>();
+ List<AnnotationFS> followingAnnotations = new ArrayList<AnnotationFS>();
for (int i = 0; i < count && itr.isValid(); i++, itr.moveToNext()) {
+ AnnotationFS fs = itr.get();
+ int begin = fs.getBegin();
+ int end = fs.getEnd();
+ if (begin == end && refEnd == begin) {
+ // Skip zero-width annotation at the end of the reference annotation. These are considered
+ // to be "coveredBy" instead of following
+ continue;
+ }
followingAnnotations.add(itr.get());
}
return followingAnnotations;
diff --cc uimafit-core/src/test/java/org/apache/uima/fit/util/JCasUtilTest.java
index afdbb52,12290b6..1932ecd
--- a/uimafit-core/src/test/java/org/apache/uima/fit/util/JCasUtilTest.java
+++ b/uimafit-core/src/test/java/org/apache/uima/fit/util/JCasUtilTest.java
@@@ -21,9 -21,10 +21,11 @@@
*/
package org.apache.uima.fit.util;
+import static java.lang.Integer.MAX_VALUE;
import static java.util.Arrays.asList;
+ import static java.util.stream.Collectors.toList;
import static org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription;
+ import static org.apache.uima.fit.util.AnnotationPredicates.overlaps;
import static org.apache.uima.fit.util.JCasUtil.contains;
import static org.apache.uima.fit.util.JCasUtil.exists;
import static org.apache.uima.fit.util.JCasUtil.getAnnotationType;