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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 a97258b Cleared compile wanrings in bin.xml and the 4 java classes
pom switched from user resources copy in package phase to prepare-package phase
a97258b is described below
commit a97258b01d455f7816994070cf64deb311b29acc
Author: Sean Finan <[email protected]>
AuthorDate: Fri Dec 23 13:57:54 2022 -0500
Cleared compile wanrings in bin.xml and the 4 java classes
pom switched from user resources copy in package phase to prepare-package
phase
---
.../ae/ExtractionPrepAnnotator.java | 59 +++++-----------------
.../runtime/BagOfAnnotationsGenerator.java | 4 +-
ctakes-distribution/src/main/assembly/bin.xml | 8 +--
.../ctakes/ytex/tools/DBAnnotationViewerMain.java | 38 ++++++--------
.../docanalyzer/DBAnnotationViewerDialog.java | 24 +++------
pom.xml | 3 +-
6 files changed, 46 insertions(+), 90 deletions(-)
diff --git
a/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
b/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
index 4543474..f6dc6be 100644
---
a/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
+++
b/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ae/ExtractionPrepAnnotator.java
@@ -19,6 +19,8 @@
package org.apache.ctakes.clinicalpipeline.ae;
import org.apache.ctakes.core.pipeline.PipeBitInfo;
+import org.apache.ctakes.core.util.annotation.IdentifiedAnnotationUtil;
+import org.apache.ctakes.core.util.annotation.OntologyConceptUtil;
import org.apache.ctakes.core.util.annotation.WordTokenUtil;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
@@ -31,6 +33,7 @@ import org.apache.uima.UimaContext;
import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.FSIterator;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.jcas.cas.FSArray;
@@ -38,9 +41,7 @@ import org.apache.uima.jcas.cas.TOP;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.ResourceInitializationException;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
+import java.util.*;
/**
* UIMA annotator that prepares the CAS for output - performs
@@ -148,50 +149,18 @@ public class ExtractionPrepAnnotator extends
JCasAnnotator_ImplBase {
* Assigns OID and segmentID values to NamedEntities
*/
private void assignNamedEntityFeats( JCas jcas ) {
- JFSIndexRepository indexes = jcas.getJFSIndexRepository();
- // Set keySet = new HashSet();
- // List dupList = new ArrayList();
-
- Set segmentSet = new HashSet();
- Iterator segmentItr = indexes.getAnnotationIndex( Segment.type
).iterator();
- while ( segmentItr.hasNext() ) {
- segmentSet.add( segmentItr.next() );
- }
-
- // For each NE, assign segment ID and assign ontology concept OIDs if
applicable
- Iterator neItr = indexes.getAnnotationIndex( IdentifiedAnnotation.type
).iterator();
- while ( neItr.hasNext() ) {
-
- IdentifiedAnnotation neAnnot = (IdentifiedAnnotation)neItr.next();
-
- // assign segment ID
- Iterator segItr = segmentSet.iterator();
- while ( segItr.hasNext() ) {
- Segment seg = (Segment)segItr.next();
- // see if NE is inside this segment
- if ( (neAnnot.getBegin() >= seg.getBegin())
- && (neAnnot.getEnd() <= seg.getEnd()) ) {
- // found segment for this NE
- neAnnot.setSegmentID( seg.getId() );
- break;
- }
- }
-
- // assign ontology concept OID values
- FSArray ocArr = neAnnot.getOntologyConceptArr();
- if ( ocArr != null ) {
- for ( int i = 0; i < ocArr.size(); i++ ) {
- OntologyConcept oc = (OntologyConcept)ocArr.get( i );
- String code = oc.getCode();
- String scheme = oc.getCodingScheme();
-
- StringBuffer oid = new StringBuffer();
- oid.append( code );
- oid.append( "#" );
- oid.append( scheme );
- oc.setOid( oid.toString() );
+ final Map<Segment,Collection<IdentifiedAnnotation>> sectionAnnotationsMap
+ = JCasUtil.indexCovered( jcas, Segment.class,
IdentifiedAnnotation.class );
+ for ( Map.Entry<Segment,Collection<IdentifiedAnnotation>>
sectionAnnotations
+ : sectionAnnotationsMap.entrySet() ) {
+ final String segmentId = sectionAnnotations.getKey().getId();
+ for ( IdentifiedAnnotation annotation : sectionAnnotations.getValue()
) {
+ annotation.setSegmentID( segmentId );
+ for ( OntologyConcept concept :
OntologyConceptUtil.getOntologyConcepts( annotation ) ) {
+ concept.setOid( concept.getCode() + '#' +
concept.getCodingScheme() );
}
}
}
}
+
}
\ No newline at end of file
diff --git
a/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
b/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
index 380b866..b47ac94 100644
---
a/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
+++
b/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/runtime/BagOfAnnotationsGenerator.java
@@ -46,8 +46,8 @@ public abstract class BagOfAnnotationsGenerator<T extends
Annotation,K> {
private Class<T> classOfT;
/**
- * @throws IOException
- * @throws UIMAException
+ * @throws IOException -
+ * @throws UIMAException -
*/
public BagOfAnnotationsGenerator(String inputDir, String outputDir)
throws UIMAException, IOException{
this(inputDir, outputDir, null);
diff --git a/ctakes-distribution/src/main/assembly/bin.xml
b/ctakes-distribution/src/main/assembly/bin.xml
index 7ff1741..49de896 100644
--- a/ctakes-distribution/src/main/assembly/bin.xml
+++ b/ctakes-distribution/src/main/assembly/bin.xml
@@ -76,18 +76,18 @@
<exclude>org.apache.ctakes:ctakes-coreference-models</exclude>
<exclude>org.apache.ctakes:ctakes-core-models</exclude>
<exclude>org.apache.ctakes:ctakes-dependency-parser-models</exclude>
-
<exclude>org.apache.ctakes:ctakes-dependency-parser-models-clear</exclude>
+<!--
<exclude>org.apache.ctakes:ctakes-dependency-parser-models-clear</exclude>-->
<exclude>org.apache.ctakes:ctakes-pos-tagger-models</exclude>
<exclude>org.apache.ctakes:ctakes-relation-extractor-models</exclude>
<exclude>org.apache.ctakes:ctakes-side-effect-models</exclude>
<exclude>org.apache.ctakes:ctakes-smoking-status-models</exclude>
<exclude>org.apache.ctakes:ctakes-temporal-models</exclude>
- <!-- exclude non-asf compliant
dependencies used by ytex -->
+ <!-- exclude non-asf compliant
dependencies used by ctakes-ytex -->
<exclude>org.hibernate:*</exclude>
<exclude>nz.ac.waikato.cms.weka:*</exclude>
<exclude>mysql:*</exclude>
- <exclude>com.microsoft.sqlserver:*</exclude>
- <exclude>oracle.jdbc:*</exclude>
+<!-- <exclude>com.microsoft.sqlserver:*</exclude>-->
+<!-- <exclude>oracle.jdbc:*</exclude>-->
</excludes>
<outputDirectory>lib</outputDirectory>
<unpack>false</unpack>
diff --git
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java
index 5c73d5e..5d75344 100644
---
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java
+++
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/DBAnnotationViewerMain.java
@@ -420,11 +420,11 @@ public class DBAnnotationViewerMain extends JFrame {
}
/**
- * @param tae
+ * @param tad -
* // *
- * @param taeDescFileName
- * @return
- * @throws IOException
+ * @param descFileName -
+ * @return -
+ * @throws IOException -
*/
private File getStyleMapFile(AnalysisEngineDescription tad,
String descFileName) throws IOException {
@@ -444,11 +444,11 @@ public class DBAnnotationViewerMain extends JFrame {
}
/**
- * @param tae
+ * @param tsd -
* // *
- * @param taeDescFileName
- * @return
- * @throws IOException
+ * @param descFileName -
+ * @return -
+ * @throws IOException -
*/
private File getStyleMapFile(TypeSystemDescription tsd, String
descFileName)
throws IOException {
@@ -717,10 +717,10 @@ public class DBAnnotationViewerMain extends JFrame {
*/
public void getColorsForTypesFromFile(CasAnnotationViewer viewer,
File aStyleMapFile) {
- List colorList = new ArrayList();
- ArrayList typeList = new ArrayList();
- ArrayList notCheckedList = new ArrayList();
- ArrayList hiddenList = new ArrayList();
+ List<Color> colorList = new ArrayList<>();
+ ArrayList<String> typeList = new ArrayList<>();
+ ArrayList<String> notCheckedList = new ArrayList<>();
+ ArrayList<String> hiddenList = new ArrayList<>();
hiddenList.add("uima.cpm.FileLocation");
if (aStyleMapFile.exists()) {
@@ -732,16 +732,10 @@ public class DBAnnotationViewerMain extends JFrame {
DocumentBuilder db =
DocumentBuilderFactory.newInstance()
.newDocumentBuilder();
parse = db.parse(stream);
- } catch (FileNotFoundException e) {
- throw new UIMARuntimeException(e);
- } catch (ParserConfigurationException e) {
- throw new UIMARuntimeException(e);
- } catch (FactoryConfigurationError e) {
- throw new UIMARuntimeException(e);
- } catch (SAXException e) {
- throw new UIMARuntimeException(e);
- } catch (IOException e) {
- throw new UIMARuntimeException(e);
+ } catch ( ParserConfigurationException
+ | FactoryConfigurationError
+ | SAXException | IOException multE ) {
+ throw new UIMARuntimeException( multE );
}
Node node0 = parse.getDocumentElement();
// Node node1 =
getFirstChildByName(parse.getDocumentElement(),
diff --git
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java
index 6025ba7..1e2848c 100644
---
a/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java
+++
b/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/tools/docanalyzer/DBAnnotationViewerDialog.java
@@ -140,10 +140,10 @@ public class DBAnnotationViewerDialog extends JDialog
implements ActionListener
*
* @param aParentFrame
* frame containing this panel
- * @param aTitle
+ * @param aDialogTitle
* title to display for the dialog
- * @param aInputDir
- * directory containing input files (in XCAS foramt) to read
+// * @param aInputDir
+// * directory containing input files (in XCAS foramt) to read
* @param aStyleMapFile
* filename of style map to be used to view files in HTML
* @param aPerformanceStats
@@ -519,10 +519,10 @@ public class DBAnnotationViewerDialog extends JDialog
implements ActionListener
*/
public void getColorsForTypesFromFile(CasAnnotationViewer viewer, File
aStyleMapFile) {
- List colorList = new ArrayList();
- ArrayList typeList = new ArrayList();
- ArrayList notCheckedList = new ArrayList();
- ArrayList hiddenList = new ArrayList();
+ List<Color> colorList = new ArrayList<>();
+ ArrayList<String> typeList = new ArrayList<>();
+ ArrayList<String> notCheckedList = new ArrayList<>();
+ ArrayList<String> hiddenList = new ArrayList<>();
hiddenList.add("uima.cpm.FileLocation");
if (aStyleMapFile.exists()) {
@@ -533,15 +533,7 @@ public class DBAnnotationViewerDialog extends JDialog
implements ActionListener
stream = new FileInputStream(aStyleMapFile);
DocumentBuilder db =
DocumentBuilderFactory.newInstance().newDocumentBuilder();
parse = db.parse(stream);
- } catch (FileNotFoundException e) {
- throw new UIMARuntimeException(e);
- } catch (ParserConfigurationException e) {
- throw new UIMARuntimeException(e);
- } catch (FactoryConfigurationError e) {
- throw new UIMARuntimeException(e);
- } catch (SAXException e) {
- throw new UIMARuntimeException(e);
- } catch (IOException e) {
+ } catch ( ParserConfigurationException | FactoryConfigurationError |
SAXException | IOException e) {
throw new UIMARuntimeException(e);
}
Node node0 = parse.getDocumentElement();
diff --git a/pom.xml b/pom.xml
index 0565bb3..76d4a75 100644
--- a/pom.xml
+++ b/pom.xml
@@ -816,7 +816,8 @@
<!-- Copy resources
that should be user-editable to ctakes-user-resources -->
<!-- This makes
these resources available as a jar in maven central. -->
<id>copy-to-user-resources</id>
- <phase>package</phase>
+<!--
<phase>package</phase>-->
+
<phase>prepare-package</phase>
<goals>
<goal>copy-resources</goal>
</goals>
