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seanfinan pushed a commit to branch main
in repository https://gitbox.apache.org/repos/asf/ctakes.git
The following commit(s) were added to refs/heads/main by this push:
new 6d359f6 Added SuppressWarnings unchecked for older code Copied
TemplateFillerAnnotator to ctakes-core, deprecated in ctakes-template-filler
since that module is otherwise empty changed signature on several methods,
private to protected, package protected to protected Made module names
consistent in poms
6d359f6 is described below
commit 6d359f605131aaf54a2eeafd8217ca125a957093
Author: Sean Finan <[email protected]>
AuthorDate: Tue Jan 24 11:54:35 2023 -0500
Added SuppressWarnings unchecked for older code
Copied TemplateFillerAnnotator to ctakes-core, deprecated in
ctakes-template-filler since that module is otherwise empty
changed signature on several methods, private to protected, package
protected to protected
Made module names consistent in poms
---
.../medfacts/cleartk/extractors/CueWordTest.java | 3 +-
.../medfacts/cleartk/extractors/CueWordTest2.java | 1 +
.../WindowedAssertionCleartkAnalysisEngine.java | 1 +
.../windowed/context/AbstractWindowedContext.java | 1 +
.../cleartk/windowed/context/PrecedingContext.java | 1 +
ctakes-chunker/pom.xml | 2 +-
ctakes-clinical-pipeline/pom.xml | 2 +-
ctakes-context-tokenizer/pom.xml | 2 +-
.../analysis_engine/AggregateTemplateFiller.xml | 78 +++++++++++++++++++
.../analysis_engine/TemplateFillerAnnotator.xml | 44 +++++++++++
ctakes-core/pom.xml | 2 +-
.../org/apache/ctakes/core/ae/CommandRunner.java | 4 +-
.../org/apache/ctakes/core/ae/CtakesRunner.java | 4 +-
.../ctakes/core/ae/PausableFileLoggerAE.java | 18 ++++-
.../ctakes/core/ae/SHARPKnowtatorXMLReader.java | 7 +-
.../ctakes/core}/ae/TemplateFillerAnnotator.java | 88 ++++++++--------------
.../ctakes/core/cc/jdbc/AbstractJdbcWriter.java | 1 +
.../org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java | 1 +
ctakes-dictionary-lookup-fast/pom.xml | 2 +-
ctakes-dictionary-lookup/pom.xml | 2 +-
.../algorithms/FirstTokenPermutationImpl.java | 1 +
ctakes-distribution/pom.xml | 4 +
.../ctakes/dockhand/build/LocalInstallBuilder.java | 6 +-
.../org/apache/ctakes/gui/progress/InfoPanel.java | 73 ++++++++++++++++++
.../ctakes/gui/progress/NoteProgressDialog.java | 26 +++++++
.../apache/ctakes/gui/wizard/util/SystemUtil.java | 2 +
.../drugner/fsm/machines/elements/DosagesFSM.java | 1 +
.../fsm/machines/elements/FractionStrengthFSM.java | 3 +-
ctakes-examples/pom.xml | 4 +
ctakes-fhir/pom.xml | 2 +-
ctakes-ne-contexts/pom.xml | 2 +-
ctakes-pos-tagger/pom.xml | 2 +-
.../ae/RelationExtractorAnnotator.java | 1 +
.../ae/features/NamedEntityFeaturesExtractor.java | 2 +
.../ae/features/PartOfSpeechFeaturesExtractor.java | 1 +
.../ae/features/TokenFeaturesExtractor.java | 1 +
.../org/apache/ctakes/sideeffect/util/SEUtil.java | 3 +-
ctakes-template-filler/pom.xml | 4 +-
.../filler/ae/TemplateFillerAnnotator.java | 6 ++
.../ctakes/temporal/ae/BackwardsTimeAnnotator.java | 2 +
...ecutiveSentencesEventTimeRelationAnnotator.java | 1 +
.../ae/ConstituencyBasedTimeAnnotator.java | 4 +-
.../apache/ctakes/temporal/ae/EventAnnotator.java | 2 +
.../ae/EventEventI2B2RelationAnnotator.java | 1 +
.../ae/TemporalRelationExtractorAnnotator.java | 1 +
.../temporal/ae/TimexAdmissionTimeAnnotator.java | 2 +
.../temporal/ae/TimexDischargeTimeAnnotator.java | 2 +
.../ae/feature/MultiTokenFeaturesExtractor.java | 1 +
.../feature/UnexpandedTokenFeaturesExtractor.java | 1 +
ctakes-type-system/pom.xml | 2 +-
ctakes-user-resources/pom.xml | 10 ++-
ctakes-utils/pom.xml | 2 +-
52 files changed, 351 insertions(+), 88 deletions(-)
diff --git
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
index 538ec7b..4194514 100644
---
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
+++
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest.java
@@ -58,7 +58,8 @@ public class CueWordTest
CueWordTest t = new CueWordTest();
t.execute();
}
-
+
+ @SuppressWarnings("unchecked")
public void execute() throws UIMAException, IOException
{
logger.info("starting");
diff --git
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
index 1b56d8d..72e00db 100644
---
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
+++
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/CueWordTest2.java
@@ -44,6 +44,7 @@ import org.cleartk.ml.feature.extractor.CombinedExtractor1;
import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
import org.cleartk.ml.feature.extractor.TypePathExtractor;
+@SuppressWarnings("unchecked")
public class CueWordTest2
{
Logger logger = Logger.getLogger(CueWordTest2.class.getName());
diff --git
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
index ef1ca8c..bffed96 100644
---
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
+++
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/WindowedAssertionCleartkAnalysisEngine.java
@@ -272,6 +272,7 @@ public abstract class
WindowedAssertionCleartkAnalysisEngine extends
entityTreeExtractors = new ArrayList<>();
}
+ @SuppressWarnings("unchecked")
@Override
public void process( JCas jCas ) throws AnalysisEngineProcessException {
String documentId = DocIdUtil.getDocumentID( jCas );
diff --git
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractWindowedContext.java
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractWindowedContext.java
index 608e1e6..7ed79ae 100644
---
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractWindowedContext.java
+++
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/AbstractWindowedContext.java
@@ -44,6 +44,7 @@ abstract public class AbstractWindowedContext implements
CleartkExtractor.Contex
return this.name;
}
+ @SuppressWarnings("unchecked")
protected <T extends Annotation> List<T> selectCovered( final Annotation
covering, final Class<T> coveredClass ) {
// System.out.print( "LastCoveredContext focusAnnotation "
// + covering.getClass().getName() + " " +
covering.getCoveredText()
diff --git
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/PrecedingContext.java
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/PrecedingContext.java
index 36d1a83..52e93f6 100644
---
a/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/PrecedingContext.java
+++
b/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/windowed/context/PrecedingContext.java
@@ -23,6 +23,7 @@ public class PrecedingContext extends
AbstractRightToLeftContext {
super( begin, end );
}
+ @SuppressWarnings("unchecked")
protected <T extends Annotation> List<T> select( final JCas jCas,
final Annotation
focusAnnotation,
final Class<T>
annotationClass,
diff --git a/ctakes-chunker/pom.xml b/ctakes-chunker/pom.xml
index fabf3af..b9fab05 100644
--- a/ctakes-chunker/pom.xml
+++ b/ctakes-chunker/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-chunker</artifactId>
- <name>Apache cTAKES chunker</name>
+ <name>Apache cTAKES Chunker</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-clinical-pipeline/pom.xml b/ctakes-clinical-pipeline/pom.xml
index 87fbc21..d550cd1 100644
--- a/ctakes-clinical-pipeline/pom.xml
+++ b/ctakes-clinical-pipeline/pom.xml
@@ -12,7 +12,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-clinical-pipeline</artifactId>
- <name>Apache cTAKES ctakes-clinical-pipeline</name>
+ <name>Apache cTAKES Default Clinical Pipeline</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-context-tokenizer/pom.xml b/ctakes-context-tokenizer/pom.xml
index 65caccc..21797af 100644
--- a/ctakes-context-tokenizer/pom.xml
+++ b/ctakes-context-tokenizer/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-context-tokenizer</artifactId>
- <name>Apache cTAKES context dependent tokenizer</name>
+ <name>Apache cTAKES Context Dependent Tokenizer</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-core/desc/analysis_engine/AggregateTemplateFiller.xml
b/ctakes-core/desc/analysis_engine/AggregateTemplateFiller.xml
new file mode 100644
index 0000000..63608e9
--- /dev/null
+++ b/ctakes-core/desc/analysis_engine/AggregateTemplateFiller.xml
@@ -0,0 +1,78 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed 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.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier";>
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>false</primitive>
+ <delegateAnalysisEngineSpecifiers>
+ <delegateAnalysisEngine key="RelationExtractorAnnotator">
+ <import location="RelationExtractorAggregateWithoutOrangeBook.xml"/>
+ </delegateAnalysisEngine>
+ <delegateAnalysisEngine key="TemplateFillerAnnotator">
+ <import location="TemplateFillerAnnotator.xml"/>
+ </delegateAnalysisEngine>
+ </delegateAnalysisEngineSpecifiers>
+ <analysisEngineMetaData>
+ <name>AggregateTemplateFiller</name>
+ <description>Find named entities and relations using RelationExtractor,
then fill xxxxxxMention templates</description>
+ <version/>
+ <vendor/>
+ <configurationParameters searchStrategy="language_fallback">
+ </configurationParameters>
+ <configurationParameterSettings>
+ </configurationParameterSettings>
+ <flowConstraints>
+ <fixedFlow>
+ <node>RelationExtractorAnnotator</node>
+ <node>TemplateFillerAnnotator</node>
+ </fixedFlow>
+ </flowConstraints>
+ <typePriorities>
+ <name>Ordering</name>
+ <description>For subiterator</description>
+ <version>1.0</version>
+ <priorityList>
+ <type>org.apache.ctakes.typesystem.type.textspan.Segment</type>
+ <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+ <type>org.apache.ctakes.typesystem.type.syntax.BaseToken</type>
+ </priorityList>
+ <priorityList>
+ <type>org.apache.ctakes.typesystem.type.textspan.Sentence</type>
+
<type>org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation</type>
+ </priorityList>
+ </typePriorities>
+ <fsIndexCollection/>
+ <capabilities>
+ <capability>
+ <inputs/>
+ <outputs>
+ </outputs>
+ <languagesSupported/>
+ </capability>
+ </capabilities>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+ <resourceManagerConfiguration/>
+</analysisEngineDescription>
diff --git a/ctakes-core/desc/analysis_engine/TemplateFillerAnnotator.xml
b/ctakes-core/desc/analysis_engine/TemplateFillerAnnotator.xml
new file mode 100644
index 0000000..48d9b8b
--- /dev/null
+++ b/ctakes-core/desc/analysis_engine/TemplateFillerAnnotator.xml
@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements. See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership. The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License. You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed 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.
+
+-->
+<analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier";>
+ <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+ <primitive>true</primitive>
+
<annotatorImplementationName>org.apache.ctakes.template.filler.ae.TemplateFillerAnnotator</annotatorImplementationName>
+ <analysisEngineMetaData>
+ <name>TemplateFillerAnnotator</name>
+ <description></description>
+ <version>unknown</version>
+ <vendor></vendor>
+ <configurationParameters>
+ </configurationParameters>
+ <configurationParameterSettings>
+ </configurationParameterSettings>
+ <typeSystemDescription/>
+ <fsIndexCollection/>
+ <capabilities/>
+ <operationalProperties>
+ <modifiesCas>true</modifiesCas>
+ <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+ <outputsNewCASes>false</outputsNewCASes>
+ </operationalProperties>
+ </analysisEngineMetaData>
+</analysisEngineDescription>
diff --git a/ctakes-core/pom.xml b/ctakes-core/pom.xml
index 43bbc50..43800b7 100644
--- a/ctakes-core/pom.xml
+++ b/ctakes-core/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-core</artifactId>
- <name>Apache cTAKES core</name>
+ <name>Apache cTAKES Core</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
index 0c8e9b3..c61ec88 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CommandRunner.java
@@ -83,7 +83,7 @@ public class CommandRunner extends PausableFileLoggerAE {
private String _logName;
- boolean processPerDoc() {
+ protected boolean processPerDoc() {
return _perDoc.equalsIgnoreCase( "yes" ) || _perDoc.equalsIgnoreCase(
"true" );
}
@@ -132,7 +132,7 @@ public class CommandRunner extends PausableFileLoggerAE {
}
- void runCommand() throws IOException {
+ protected void runCommand() throws IOException {
final String command = ( _cmdDir == null || _cmdDir.isEmpty() ) ? _cmd :
_cmdDir + File.separator + _cmd;
final SystemUtil.CommandRunner runner = new SystemUtil.CommandRunner(
command );
final String logFile = getLogFile();
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
index 39dbdee..03765da 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/CtakesRunner.java
@@ -40,7 +40,7 @@ public class CtakesRunner extends PausableFileLoggerAE {
private String _logFile;
- boolean processPerDoc() {
+ protected boolean processPerDoc() {
return false;
}
@@ -97,7 +97,7 @@ public class CtakesRunner extends PausableFileLoggerAE {
return piper;
}
- void runCommand() throws IOException {
+ protected void runCommand() throws IOException {
final String java_home = System.getProperty( "java.home" );
final SystemUtil.CommandRunner runner =
new SystemUtil.CommandRunner( "\"" + java_home + File.separator +
"bin" + File.separator
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java
index f09aec1..57360ee 100644
---
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java
+++
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/PausableFileLoggerAE.java
@@ -24,11 +24,23 @@ abstract public class PausableFileLoggerAE extends
PausableAE {
)
private String _logFile;
- abstract boolean processPerDoc();
+ /**
+ *
+ * @return true if the process should be run for each document.
+ */
+ abstract protected boolean processPerDoc();
- abstract void runCommand() throws IOException;
+ /**
+ * Some command to run.
+ * @throws IOException -
+ */
+ abstract protected void runCommand() throws IOException;
- final protected String getLogFile() {
+ /**
+ *
+ * @return the path of a file to which logs should be written.
+ */
+ protected String getLogFile() {
return _logFile;
}
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
index 372a2d8..39c2c0e 100644
---
a/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
+++
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/SHARPKnowtatorXMLReader.java
@@ -22,6 +22,7 @@ import com.google.common.base.Charsets;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import com.google.common.io.Files;
+import org.apache.ctakes.core.cc.FileTreeXmiWriter;
import org.apache.ctakes.core.knowtator.KnowtatorAnnotation;
import org.apache.ctakes.core.knowtator.KnowtatorXMLParser;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
@@ -40,7 +41,7 @@ import org.apache.uima.cas.Feature;
import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
-import org.apache.uima.fit.util.CasIOUtil;
+//import org.apache.uima.fit.util.CasIOUtil;
import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
@@ -1506,7 +1507,9 @@ public class SHARPKnowtatorXMLReader extends
JCasAnnotator_ImplBase {
documentID.addToIndexes();
engine.process(jCas);
documentID.setDocumentID(textFile.getName());
- CasIOUtil.writeXmi(jCas, new File("/tmp",
textFile.toURI().toString()));
+// CasIOUtil.writeXmi(jCas, new File("/tmp",
textFile.toURI().toString()));
+ final FileTreeXmiWriter writer = new FileTreeXmiWriter();
+ writer.writeFile( jCas, "/tmp/" + textFile.toURI(),
textFile.getName(), textFile.getName() );
}
}
diff --git
a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
similarity index 81%
copy from
ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
copy to
ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
index 13c0239..7bc0301 100644
---
a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
+++
b/ctakes-core/src/main/java/org/apache/ctakes/core/ae/TemplateFillerAnnotator.java
@@ -16,13 +16,15 @@
* specific language governing permissions and limitations
* under the License.
*/
-package org.apache.ctakes.template.filler.ae;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+package org.apache.ctakes.core.ae;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.refsem.*;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
+import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textsem.*;
import org.apache.log4j.Logger;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
@@ -35,54 +37,24 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
-import org.apache.ctakes.typesystem.type.constants.CONST;
-import org.apache.ctakes.typesystem.type.refsem.Date;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDosage;
-import org.apache.ctakes.typesystem.type.refsem.MedicationDuration;
-import org.apache.ctakes.typesystem.type.refsem.MedicationForm;
-import org.apache.ctakes.typesystem.type.refsem.MedicationFrequency;
-import org.apache.ctakes.typesystem.type.refsem.MedicationRoute;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStatusChange;
-import org.apache.ctakes.typesystem.type.refsem.MedicationStrength;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
-import org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation;
-import org.apache.ctakes.typesystem.type.relation.RelationArgument;
-import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
-import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.EventMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDosageModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationDurationModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFormModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationFrequencyModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
-import org.apache.ctakes.typesystem.type.textsem.MedicationRouteModifier;
-import
org.apache.ctakes.typesystem.type.textsem.MedicationStatusChangeModifier;
-import org.apache.ctakes.typesystem.type.textsem.MedicationStrengthModifier;
-import org.apache.ctakes.typesystem.type.textsem.Modifier;
-import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
-import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
-import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
public class TemplateFillerAnnotator extends JCasAnnotator_ImplBase{
// LOG4J logger based on class name
- private Logger logger = Logger.getLogger(getClass().getName());
- private UimaContext uimaContext;
+ static private final Logger LOGGER = Logger.getLogger(
"TemplateFillerAnnotator" );
+ /**
+ * {@inheritDoc}
+ */
@Override
- public void initialize(UimaContext aContext) throws
ResourceInitializationException {
-
- super.initialize(aContext);
- uimaContext = aContext;
-
- logger.info("Initializing " + TemplateFillerAnnotator.class.getName());
-
+ public void initialize( final UimaContext aContext ) throws
ResourceInitializationException {
+ super.initialize( aContext );
}
/**
@@ -92,7 +64,7 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
* attributes like dosage from the MedicationEventMention attributes.
* @param mention The annotation to copy values to
* @param original The annotation to copy values from
- * @throws CASException
+ * @throws CASException -
*/
private void setAttributesFromOriginal(IdentifiedAnnotation mention,
IdentifiedAnnotation original) throws CASException {
mention.setBegin(original.getBegin());
@@ -189,7 +161,7 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
@Override
public void process(JCas jcas) throws AnalysisEngineProcessException {
- logger.debug("process(JCas) in " +
TemplateFillerAnnotator.class.getName());
+ LOGGER.debug( "process(JCas) in " +
TemplateFillerAnnotator.class.getName() );
// Get all IdentifiedAnnotations
FSIterator<Annotation> identifiedAnnotationsIter =
getAllAnnotations(jcas, IdentifiedAnnotation.type);
@@ -276,9 +248,9 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
AnatomicalSiteMention asm =
(AnatomicalSiteMention) loc;
//asm.setBodyLocation(binaryTextRelation); // uncomment iff
AnatomicalSiteMention ends up with a bodyLocation attribute
} else {
- logger.error("Need to implement cases
for handling EntityMention " + entityMention + " within relation: " + relation);
- logger.error(" loc " + loc + " in
relation " + relation + " with/to " + entityMention);
- logger.error(" Using covered text:
loc " + loc.getCoveredText() + " in relation " + relation + " with/to " +
entityMention.getCoveredText());
+ LOGGER.error( "Need to implement cases
for handling EntityMention " + entityMention + " within relation: " + relation
);
+ LOGGER.error( " loc " + loc + " in
relation " + relation + " with/to " + entityMention );
+ LOGGER.error( " Using covered text:
loc " + loc.getCoveredText() + " in relation " + relation + " with/to " +
entityMention.getCoveredText() );
}
} else {
@@ -295,12 +267,12 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
SignSymptomMention ssm =
(SignSymptomMention) eventMention;
ssm.setBodyLocation(locationOfTextRelation);
} else {
- logger.error("Need to implement more
cases for handling EventMention " + eventMention + " within relation: " +
relation);
+ LOGGER.error( "Need to implement more
cases for handling EventMention " + eventMention + " within relation: " +
relation );
}
}
} else {
- logger.error("Need to implement more cases for
relation: " + relation);
+ LOGGER.error( "Need to implement more cases for
relation: " + relation );
}
}
}
@@ -335,9 +307,9 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
IdentifiedAnnotation ia = mapToMentions.get(arg1Arg);
if (ia instanceof EntityMention) {
EntityMention entityMention = (EntityMention)
ia;
- logger.error("Need to implement cases for
handling EntityMention " + entityMention + " within relation: " + relation);
- logger.error(" severity " + severity + " in
relation " + relation + " with/to " + entityMention);
- logger.error(" Using covered text: severity "
+ severity.getCoveredText() + " in relation " + relation + " with/to " +
entityMention.getCoveredText());
+ LOGGER.error( "Need to implement cases for
handling EntityMention " + entityMention + " within relation: " + relation );
+ LOGGER.error( " severity " + severity + " in
relation " + relation + " with/to " + entityMention );
+ LOGGER.error( " Using covered text: severity
" + severity.getCoveredText() + " in relation " + relation + " with/to " +
entityMention.getCoveredText() );
} else {
EventMention eventMention = (EventMention) ia;
if (eventMention instanceof
DiseaseDisorderMention) {
@@ -347,7 +319,7 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
SignSymptomMention ssm =
(SignSymptomMention) eventMention;
ssm.setSeverity(degreeOfTextRelation);
} else {
- logger.error("Need to implement more
cases for handling EventMention " + eventMention + " within relation: " +
relation);
+ LOGGER.error( "Need to implement more
cases for handling EventMention " + eventMention + " within relation: " +
relation );
}
}
@@ -357,7 +329,7 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
// location_of has its own loop.
} else {
- logger.error("Need to implement more cases for
relation: " + relation);
+ LOGGER.error( "Need to implement more cases for
relation: " + relation );
}
}
}
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
index d046de4..5211eea 100644
---
a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
+++
b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/AbstractJdbcWriter.java
@@ -156,6 +156,7 @@ abstract public class AbstractJdbcWriter<T> extends
JCasAnnotator_ImplBase {
* @param data data to be written.
* @throws SQLException if anything goes wrong.
*/
+ @SuppressWarnings("unchecked")
public void writeJdbc( final T data ) throws SQLException {
for ( JdbcTable<T> table : getJdbcTables( (Class<T>)data.getClass() ) ) {
table.writeValue( data );
diff --git
a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java
b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java
index 4ffa517..d904bc1 100644
--- a/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java
+++ b/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/JdbcDb.java
@@ -28,6 +28,7 @@ public interface JdbcDb {
* @param dataClass class of data.
* @return all registered tables that handle that type of data.
*/
+ @SuppressWarnings("unchecked")
default <T> Collection<JdbcTable<T>> getTables( final Class<T> dataClass ) {
final Collection<JdbcTable<T>> tables = new ArrayList<>();
for ( JdbcTable<?> table : getTables() ) {
diff --git a/ctakes-dictionary-lookup-fast/pom.xml
b/ctakes-dictionary-lookup-fast/pom.xml
index 2995a51..9cc37a1 100644
--- a/ctakes-dictionary-lookup-fast/pom.xml
+++ b/ctakes-dictionary-lookup-fast/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-dictionary-lookup-fast</artifactId>
- <name>Apache cTAKES dictionary lookup fast</name>
+ <name>Apache cTAKES Fast Dictionary Lookup</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-dictionary-lookup/pom.xml b/ctakes-dictionary-lookup/pom.xml
index e6f4e93..96768f9 100644
--- a/ctakes-dictionary-lookup/pom.xml
+++ b/ctakes-dictionary-lookup/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-dictionary-lookup</artifactId>
- <name>Apache cTAKES dictionary lookup</name>
+ <name>Apache cTAKES Dictionary Lookup (deprecated)</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git
a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
index ffe30b1..8a53a92 100644
---
a/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
+++
b/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/algorithms/FirstTokenPermutationImpl.java
@@ -184,6 +184,7 @@ public class FirstTokenPermutationImpl implements
LookupAlgorithm {
return namedMetaDataHits;
}
+ @SuppressWarnings("unchecked")
private Collection<LookupHit> getLookupHits( final Collection<MetaDataHit>
firstTokenHits,
final List<LookupToken>
wLookupTokenList,
final int firstTokenIndex )
throws Exception {
diff --git a/ctakes-distribution/pom.xml b/ctakes-distribution/pom.xml
index bd108bd..7681c5b 100644
--- a/ctakes-distribution/pom.xml
+++ b/ctakes-distribution/pom.xml
@@ -150,6 +150,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-fhir</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pbj</artifactId>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-tiny-rest</artifactId>
diff --git
a/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
b/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
index 348aee2..40650fa 100644
---
a/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
+++
b/ctakes-dockhand/src/main/java/org/apache/ctakes/dockhand/build/LocalInstallBuilder.java
@@ -62,9 +62,9 @@ final public class LocalInstallBuilder implements Runnable {
if ( finished ) {
DialogUtil.showInstalledDialog( INSTALL_TYPE, installPath );
}
- if ( DialogUtil.showStartGui() ) {
- startGui( "Running Apache cTAKES ...<BR> RunPiperGui", installPath
+ "/" + INSTALL_DIRNAME );
- }
+// if ( DialogUtil.showStartGui() ) {
+// startGui( "Running Apache cTAKES ...<BR> RunPiperGui",
installPath + "/" + INSTALL_DIRNAME );
+// }
}
static private boolean cleanup( final String installPath ) {
diff --git
a/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/InfoPanel.java
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/InfoPanel.java
new file mode 100644
index 0000000..773341b
--- /dev/null
+++
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/InfoPanel.java
@@ -0,0 +1,73 @@
+package org.apache.ctakes.gui.progress;
+
+
+import javax.swing.*;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.Document;
+import java.io.IOException;
+import java.io.OutputStream;
+
+/**
+ * @author SPF , chip-nlp
+ * @since {1/12/2023}
+ */
+final public class InfoPanel extends JScrollPane {
+
+ static private final int MAX_DOC_LENGTH = Integer.MAX_VALUE - 5000;
+
+ private final OutputStream _stream;
+ private final Document _textAreaDoc;
+
+ public InfoPanel() {
+ final JTextArea textArea = new JTextArea();
+ textArea.setEditable( false );
+ super.setViewportView( textArea );
+ _textAreaDoc = textArea.getDocument();
+ _stream = new InfoStream();
+ }
+
+ public OutputStream getStream() {
+ return _stream;
+ }
+
+ /**
+ * @param text to append to the text displayed in this gui
+ */
+ public void appendText( final String text ) {
+ SwingUtilities.invokeLater( () -> {
+ try {
+ if (_textAreaDoc.getLength() >= MAX_DOC_LENGTH ) {
+ // clear log if it gets too long. Not the best solution, but
good enough for now.
+ _textAreaDoc.remove( 0, _textAreaDoc.getLength() );
+ }
+ _textAreaDoc.insertString( _textAreaDoc.getLength(), text, null );
+ } catch ( BadLocationException blE ) {
+ //
+ }
+ } );
+ }
+
+ public void clearText() {
+ SwingUtilities.invokeLater( () -> {
+ try {
+ _textAreaDoc.remove( 0, _textAreaDoc.getLength() );
+ } catch ( BadLocationException blE ) {
+ //
+ }
+ } );
+ }
+
+ private final class InfoStream extends OutputStream {
+ private final StringBuilder _sb = new StringBuilder();
+ @Override
+ public void write( final int b ) throws IOException {
+ _sb.append( b );
+ if ( b == '\n' ) {
+ appendText( _sb.toString() );
+ _sb.setLength( 0 );
+ }
+ }
+ }
+
+
+}
diff --git
a/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteProgressDialog.java
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteProgressDialog.java
index b44bbf3..e86d6c4 100644
---
a/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteProgressDialog.java
+++
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/progress/NoteProgressDialog.java
@@ -22,6 +22,7 @@ public enum NoteProgressDialog {
private JDialog _dialog;
private JLabel _processLabel;
private JLabel _progressLabel;
+// private final InfoPanel _infoPanel = new InfoPanel();;
private void createDialog() {
if ( _dialog != null ) {
@@ -57,6 +58,7 @@ public enum NoteProgressDialog {
panel.setBackground( Color.WHITE );
panel.add( notePanel, BorderLayout.WEST );
panel.add( labelPanel, BorderLayout.CENTER );
+// panel.add( _infoPanel, BorderLayout.CENTER );
_dialog.add( panel );
}
@@ -103,7 +105,31 @@ public enum NoteProgressDialog {
_dialog.setVisible( false );
_dialog.dispose();
_dialog = null;
+// _infoPanel.clearText();
}
+// public void setProcess( final Process process ) {
+// final ExecutorService executors = Executors.newFixedThreadPool( 2 );
+// executors.submit( new OutputLogger( process.getInputStream() ) );
+// executors.submit( new OutputLogger( process.getErrorStream() ) );
+// _dialog.setVisible( true );
+// ProgressNote.getInstance().startProgress();
+// }
+//
+// private class OutputLogger implements Runnable {
+// final private InputStream _stream;
+//
+// private OutputLogger( final InputStream stream ) {
+// _stream = stream;
+// }
+// public void run() {
+// try ( BufferedReader reader = new BufferedReader( new
InputStreamReader( _stream ) ) ) {
+// reader.lines()
+// .forEach( _infoPanel::appendText );
+// } catch ( IOException ioE ) {
+// //
+// }
+// }
+// }
}
diff --git
a/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
index 7aa56b8..7cb6046 100644
---
a/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
+++
b/ctakes-dockhand/src/main/java/org/apache/ctakes/gui/wizard/util/SystemUtil.java
@@ -158,6 +158,7 @@ final public class SystemUtil {
env.put( "JAVA_HOME", System.getProperty( "java.home" ) );
}
final Process process = processBuilder.start();
+// NoteProgressDialog.getInstance().setProcess( process );
int exitCode = process.waitFor();
return true;
}
@@ -174,6 +175,7 @@ final public class SystemUtil {
.redirectOutput( new File( outLog ) )
.redirectError( new File( errLog ) );
final Process process = processBuilder.start();
+// NoteProgressDialog.getInstance().setProcess( process );
int exitCode = process.waitFor();
return true;
}
diff --git
a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DosagesFSM.java
b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DosagesFSM.java
index 9b11020..10a99a0 100644
---
a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DosagesFSM.java
+++
b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/DosagesFSM.java
@@ -54,6 +54,7 @@ import net.openai.util.fsm.State;
*
* @author Mayo Clinic
*/
+@SuppressWarnings("unchecked")
public class DosagesFSM {
Set iv_soloTextSet = new HashSet();
diff --git
a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FractionStrengthFSM.java
b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FractionStrengthFSM.java
index e493c43..4dddb2b 100644
---
a/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FractionStrengthFSM.java
+++
b/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/fsm/machines/elements/FractionStrengthFSM.java
@@ -220,7 +220,8 @@ public class FractionStrengthFSM
* @return Set of FractionToken objects.
* @throws Exception
*/
- public Set execute(List tokens) throws Exception
+ @SuppressWarnings("unchecked")
+ public Set execute(List tokens) throws Exception
{
Set<FractionStrengthToken> fractionSet = new
HashSet<FractionStrengthToken>();
diff --git a/ctakes-examples/pom.xml b/ctakes-examples/pom.xml
index 4c4fa97..c817c22 100644
--- a/ctakes-examples/pom.xml
+++ b/ctakes-examples/pom.xml
@@ -38,6 +38,10 @@
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-fhir</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pbj</artifactId>
</dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
diff --git a/ctakes-fhir/pom.xml b/ctakes-fhir/pom.xml
index 8bdaac6..aaee8be 100644
--- a/ctakes-fhir/pom.xml
+++ b/ctakes-fhir/pom.xml
@@ -23,7 +23,7 @@
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-fhir</artifactId>
- <name>Apache cTAKES fhir support</name>
+ <name>Apache cTAKES FHIR Support</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-ne-contexts/pom.xml b/ctakes-ne-contexts/pom.xml
index 44bd7ad..3909205 100644
--- a/ctakes-ne-contexts/pom.xml
+++ b/ctakes-ne-contexts/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-ne-contexts</artifactId>
- <name>Apache cTAKES named entity contexts</name>
+ <name>Apache cTAKES Named Entity Contexts</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git a/ctakes-pos-tagger/pom.xml b/ctakes-pos-tagger/pom.xml
index 4f37ffb..7c18ac5 100644
--- a/ctakes-pos-tagger/pom.xml
+++ b/ctakes-pos-tagger/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-pos-tagger</artifactId>
- <name>Apache cTAKES part-of-speech tagger</name>
+ <name>Apache cTAKES Part-of-speech Tagger</name>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
index fc018dd..f89d2c8 100644
---
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
+++
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
@@ -91,6 +91,7 @@ private
List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation
*
* @return The list of feature extractors to use.
*/
+ @SuppressWarnings("unchecked")
protected
List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>
getFeatureExtractors()
throws ResourceInitializationException {
return Lists.newArrayList(
diff --git
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
index 49e28b0..9b542a1 100644
---
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
+++
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/NamedEntityFeaturesExtractor.java
@@ -60,9 +60,11 @@ public class NamedEntityFeaturesExtractor implements
RelationFeaturesExtractor<I
/**
* Number of named entities between the two mentions
*/
+ @SuppressWarnings("unchecked")
private DistanceExtractor nEntityMentionsBetween = new
DistanceExtractor(null, EntityMention.class);
@Override
+ @SuppressWarnings("unchecked")
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
throws AnalysisEngineProcessException {
diff --git
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
index e1fb9d2..b3e538a 100644
---
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
+++
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/PartOfSpeechFeaturesExtractor.java
@@ -33,6 +33,7 @@ import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.ml.feature.extractor.NamingExtractor1;
import org.cleartk.ml.feature.extractor.TypePathExtractor;
+@SuppressWarnings("unchecked")
public class PartOfSpeechFeaturesExtractor implements
RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
private FeatureExtractor1 pos = new TypePathExtractor(BaseToken.class,
"partOfSpeech");
diff --git
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
index 860c4ff..7e9d914 100644
---
a/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
+++
b/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/features/TokenFeaturesExtractor.java
@@ -45,6 +45,7 @@ import org.cleartk.ml.feature.extractor.DistanceExtractor;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.ml.feature.extractor.NamingExtractor1;
+@SuppressWarnings("unchecked")
public class TokenFeaturesExtractor implements
RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
private FeatureExtractor1 coveredText = new CoveredTextExtractor();
diff --git
a/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java
b/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java
index 7ec70f2..43324be 100644
---
a/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java
+++
b/ctakes-side-effect/src/main/java/org/apache/ctakes/sideeffect/util/SEUtil.java
@@ -233,8 +233,9 @@ public class SEUtil {
* @param end
* @return
*/
+ @SuppressWarnings( "unchecked" )
public static int getNumOfWordTokensInSpan(JCas jcas, int begin, int
end) {
- Set ignoreWords = new HashSet();
+ Set<String> ignoreWords = new HashSet();
ignoreWords.add("and");
ignoreWords.add("or");
diff --git a/ctakes-template-filler/pom.xml b/ctakes-template-filler/pom.xml
index 52517ee..9b829fd 100644
--- a/ctakes-template-filler/pom.xml
+++ b/ctakes-template-filler/pom.xml
@@ -22,8 +22,8 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-template-filler</artifactId>
- <name>Apache cTAKES template filler</name>
- <description>Fill CEM-based templates</description>
+ <name>Apache cTAKES Template Filler (deprecated)</name>
+ <description>Deprecated. There is a single AE
(TemplateFillerAnnotator) that has been moved to ctakes-core.</description>
<parent>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes</artifactId>
diff --git
a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
b/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
index 13c0239..b6923d2 100644
---
a/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
+++
b/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java
@@ -68,6 +68,10 @@ import
org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+/**
+ * @deprecated Use the TemplateFillerAnnotator in ctakes-core
+ */
+@Deprecated
public class TemplateFillerAnnotator extends JCasAnnotator_ImplBase{
// LOG4J logger based on class name
@@ -78,6 +82,8 @@ public class TemplateFillerAnnotator extends
JCasAnnotator_ImplBase{
@Override
public void initialize(UimaContext aContext) throws
ResourceInitializationException {
+ logger.warn( "TemplateFillerAnnotator in
ctakes-template-filler has been deprecated."
+ + " Please use the
TemplateFillerAnnotator in ctakes-core." );
super.initialize(aContext);
uimaContext = aContext;
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
index b6c0b19..54fa33e 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotator.java
@@ -152,6 +152,7 @@ public class BackwardsTimeAnnotator extends
TemporalEntityAnnotator_ImplBase {
private BioChunking<BaseToken, TimeMention> timeChunking;
+ @SuppressWarnings("unchecked")
@Override
public void initialize(UimaContext context) throws
ResourceInitializationException {
LOGGER.info( "Initializing ..." );
@@ -195,6 +196,7 @@ public class BackwardsTimeAnnotator extends
TemporalEntityAnnotator_ImplBase {
super.process( jCas );
}
+ @SuppressWarnings("unchecked")
@Override
public void process(JCas jCas, Segment segment) throws
AnalysisEngineProcessException {
// classify tokens within each sentence
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
index 0b23641..1888432 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConsecutiveSentencesEventTimeRelationAnnotator.java
@@ -70,6 +70,7 @@ public class ConsecutiveSentencesEventTimeRelationAnnotator
extends RelationExtr
new File(modelDirectory, "model.jar"));
}
+ @SuppressWarnings("unchecked")
@Override
protected
List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>
getFeatureExtractors()
throws ResourceInitializationException {
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
index 006a63b..4ef0458 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ConstituencyBasedTimeAnnotator.java
@@ -151,7 +151,8 @@ public class ConstituencyBasedTimeAnnotator extends
TemporalEntityAnnotator_Impl
private static final String LOOKUP_PATH =
"/org/apache/ctakes/temporal/time_word_types.txt";
private Map<String, String> wordTypes;
-
+
+ @SuppressWarnings("unchecked")
@Override
public void initialize(UimaContext context)
throws ResourceInitializationException {
@@ -211,6 +212,7 @@ public class ConstituencyBasedTimeAnnotator extends
TemporalEntityAnnotator_Impl
}
}
+ @SuppressWarnings("unchecked")
private double recursivelyProcessNode(JCas jCas, TreebankNode node,
Set<TimeMention> mentions, double parentScore) throws
AnalysisEngineProcessException {
// accumulate features:
double score=0.0;
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
index 176bfbb..e2853aa 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
@@ -191,6 +191,7 @@ public class EventAnnotator extends
TemporalEntityAnnotator_ImplBase {
return new File(outputDirectoryName, FEATURE_SELECTION_NAME +
"_Chi2_extractor.dat").toURI();
}
+ @SuppressWarnings("unchecked")
@Override
public void initialize(UimaContext context) throws
ResourceInitializationException {
LOGGER.info( "Initializing ..." );
@@ -240,6 +241,7 @@ public class EventAnnotator extends
TemporalEntityAnnotator_ImplBase {
super.process( jCas );
}
+ @SuppressWarnings("unchecked")
@Override
public void process(JCas jCas, Segment segment) throws
AnalysisEngineProcessException {
PredicateArgumentExtractor predicateArgumentExtractor = new
PredicateArgumentExtractor(jCas);
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java
index 5b75b20..cbf2e9a 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java
@@ -131,6 +131,7 @@ public class EventEventI2B2RelationAnnotator extends
RelationExtractorAnnotator
new File(modelDirectory, "model.jar"));
}
+ @SuppressWarnings("unchecked")
@Override
protected
List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>
getFeatureExtractors()
throws ResourceInitializationException {
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
index 0928713..8e9df5d 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TemporalRelationExtractorAnnotator.java
@@ -108,6 +108,7 @@ public abstract class TemporalRelationExtractorAnnotator
extends CleartkAnnotato
*
* @return The list of feature extractors to use.
*/
+ @SuppressWarnings("unchecked")
protected
List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>
getFeatureExtractors()
throws ResourceInitializationException {
return Lists.newArrayList(
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java
index c5ef095..e3df4e1 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexAdmissionTimeAnnotator.java
@@ -123,6 +123,7 @@ public class TimexAdmissionTimeAnnotator extends
CleartkAnnotator<String> {
// private CoveredTextToValuesExtractor disSemExtractor;
// private DurationExpectationFeatureExtractor durationExtractor;
+ @SuppressWarnings("unchecked")
@Override
public void initialize(UimaContext context) throws
ResourceInitializationException {
super.initialize(context);
@@ -145,6 +146,7 @@ public class TimexAdmissionTimeAnnotator extends
CleartkAnnotator<String> {
// this.umlsExtractor = new UmlsSingleFeatureExtractor();
}
+ @SuppressWarnings("unchecked")
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
//get discharge Time id: T1:
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java
index 6f4b5fe..ca7aaa8 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexDischargeTimeAnnotator.java
@@ -121,6 +121,7 @@ public class TimexDischargeTimeAnnotator extends
CleartkAnnotator<String> {
// private CoveredTextToValuesExtractor disSemExtractor;
// private DurationExpectationFeatureExtractor durationExtractor;
+ @SuppressWarnings("unchecked")
@Override
public void initialize(UimaContext context) throws
ResourceInitializationException {
super.initialize(context);
@@ -143,6 +144,7 @@ public class TimexDischargeTimeAnnotator extends
CleartkAnnotator<String> {
// this.umlsExtractor = new
UmlsSingleFeatureExtractor();
}
+ @SuppressWarnings("unchecked")
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
//get discharge Time id: T1:
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
index 56a20f6..1166f47 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
@@ -45,6 +45,7 @@ import java.util.Map;
* @author CH151862
*
*/
+@SuppressWarnings("unchecked")
public class MultiTokenFeaturesExtractor implements
RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
private FeatureExtractor1 coveredText = new CoveredTextExtractor();
diff --git
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java
index 4f975cb..8f79142 100644
---
a/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java
+++
b/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/UnexpandedTokenFeaturesExtractor.java
@@ -23,6 +23,7 @@ import org.cleartk.ml.feature.extractor.NamingExtractor1;
import org.cleartk.ml.feature.extractor.FeatureExtractor1;
import org.cleartk.ml.feature.extractor.CombinedExtractor1;
+@SuppressWarnings("unchecked")
public class UnexpandedTokenFeaturesExtractor extends TokenFeaturesExtractor {
private FeatureExtractor1 coveredText = new CoveredTextExtractor();
diff --git a/ctakes-type-system/pom.xml b/ctakes-type-system/pom.xml
index f46bcef..1723384 100644
--- a/ctakes-type-system/pom.xml
+++ b/ctakes-type-system/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-type-system</artifactId>
- <name>Apache cTAKES common type system</name>
+ <name>Apache cTAKES Common Type System</name>
<description>Defines the cTAKES type system UIMA annotation
classes.</description>
<parent>
<groupId>org.apache.ctakes</groupId>
diff --git a/ctakes-user-resources/pom.xml b/ctakes-user-resources/pom.xml
index b3dc4a3..50833fb 100644
--- a/ctakes-user-resources/pom.xml
+++ b/ctakes-user-resources/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-user-resources</artifactId>
- <name>Apache cTAKES user resources</name>
+ <name>Apache cTAKES User Resources</name>
<description>For external projects to utilize user resources, e.g.
piper files and bsv definitions.</description>
<!-- This is not a normal module. There should not be main code or main
resources in this module. -->
<!-- This module creates a ctakes-user-resources jar that can be a
dependency for other projects. -->
@@ -153,6 +153,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-fhir</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-pbj</artifactId>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-tiny-rest</artifactId>
@@ -226,6 +230,10 @@
<directory>${project.basedir}/../ctakes-fhir/src/user/resources</directory>
<filtering>true</filtering>
</resource>
+ <resource>
+
<directory>${project.basedir}/../ctakes-pbj/src/user/resources</directory>
+
<filtering>true</filtering>
+ </resource>
<resource>
<directory>${project.basedir}/../ctakes-lvg/src/user/resources</directory>
<filtering>true</filtering>
diff --git a/ctakes-utils/pom.xml b/ctakes-utils/pom.xml
index ad3bedd..aa64ec0 100644
--- a/ctakes-utils/pom.xml
+++ b/ctakes-utils/pom.xml
@@ -22,7 +22,7 @@
<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/xsd/maven-4.0.0.xsd";>
<modelVersion>4.0.0</modelVersion>
<artifactId>ctakes-utils</artifactId>
- <name>Apache cTAKES utils</name>
+ <name>Apache cTAKES Utilities</name>
<parent>
<artifactId>ctakes</artifactId>
<groupId>org.apache.ctakes</groupId>
