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Posted to commits@ctakes.apache.org by se...@apache.org on 2018/11/07 15:08:01 UTC
svn commit: r1846041 - in /ctakes/trunk: ./ ctakes-distribution/
ctakes-distribution/src/main/assembly/ ctakes-examples/
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/
ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/ ctakes-gui/src...
Author: seanfinan
Date: Wed Nov 7 15:08:00 2018
New Revision: 1846041
URL: http://svn.apache.org/viewvc?rev=1846041&view=rev
Log:
CTAKES-526 : Add shutdown hook to close hsql database
Add ctakes-fhir to main build and distribution and examples
Enlarge Piper File Submitter Gui
Switch fhir id divider char to dash
Modified:
ctakes/trunk/ctakes-distribution/pom.xml
ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
ctakes/trunk/ctakes-examples/pom.xml
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java
ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java
ctakes/trunk/pom.xml
Modified: ctakes/trunk/ctakes-distribution/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/pom.xml?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/pom.xml (original)
+++ ctakes/trunk/ctakes-distribution/pom.xml Wed Nov 7 15:08:00 2018
@@ -138,6 +138,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-gui</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-fhir</artifactId>
+ </dependency>
</dependencies>
<build>
Modified: ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml (original)
+++ ctakes/trunk/ctakes-distribution/src/main/assembly/bin.xml Wed Nov 7 15:08:00 2018
@@ -47,6 +47,7 @@
<include>org.apache.ctakes:ctakes-dictionary-lookup-fast</include>
<include>org.apache.ctakes:ctakes-drug-ner</include>
<include>org.apache.ctakes:ctakes-gui</include>
+ <include>org.apache.ctakes:ctakes-fhir</include>
<include>org.apache.ctakes:ctakes-lvg</include>
<include>org.apache.ctakes:ctakes-ne-contexts</include>
<include>org.apache.ctakes:ctakes-pos-tagger</include>
Modified: ctakes/trunk/ctakes-examples/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-examples/pom.xml?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-examples/pom.xml (original)
+++ ctakes/trunk/ctakes-examples/pom.xml Wed Nov 7 15:08:00 2018
@@ -35,6 +35,10 @@
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-gui</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-fhir</artifactId>
+ </dependency>
<dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-coreference</artifactId>
@@ -72,12 +76,15 @@
<executions>
<execution>
<goals>
- <goal>java</goal>
+ <goal>exec</goal>
</goals>
</execution>
</executions>
<configuration>
- <workingDirectory>${project.parent.basedir}</workingDirectory>
+ <executable>java</executable>
+ <includeProjectDependencies>true</includeProjectDependencies>
+ <includePluginDependencies>true</includePluginDependencies>
+ <workingDirectory>${project.parent.basedir}</workingDirectory>
<arguments>
<argument>-classpath</argument>
<classpath/>
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementFactory.java Wed Nov 7 15:08:00 2018
@@ -43,6 +43,8 @@ final public class FhirElementFactory {
static public final String CODING_TUI = "tui";
static public final String CODING_SEMANTIC = "semantic-group";
+ static public final char DIVIDER_CHAR = '-';
+
private FhirElementFactory() {
}
@@ -141,7 +143,7 @@ final public class FhirElementFactory {
* @return fhir id containing name and code.
*/
static public String createId( final JCas jCas, final String name, final String code ) {
- return DocumentIDAnnotationUtil.getDocumentID( jCas ) + "_" + name + "_" + code;
+ return DocumentIDAnnotationUtil.getDocumentID( jCas ) + DIVIDER_CHAR + name + DIVIDER_CHAR + code;
}
// Identifiers are 0 .. 1 , so unnecessary
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/element/FhirElementParser.java Wed Nov 7 15:08:00 2018
@@ -32,7 +32,7 @@ final public class FhirElementParser {
}
static public String getIdName( final String id ) {
- final String[] splits = StringUtil.fastSplit( id, '_' );
+ final String[] splits = StringUtil.fastSplit( id, DIVIDER_CHAR );
if ( splits.length >= 3 ) {
return splits[ 1 ];
}
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/FhirPractitioner.java Wed Nov 7 15:08:00 2018
@@ -6,6 +6,7 @@ import org.hl7.fhir.dstu3.model.*;
import java.net.InetAddress;
import java.net.UnknownHostException;
+import static org.apache.ctakes.fhir.element.FhirElementFactory.DIVIDER_CHAR;
import static org.hl7.fhir.dstu3.model.Composition.CompositionAttesterComponent;
/**
@@ -65,7 +66,8 @@ public interface FhirPractitioner {
} catch ( UnknownHostException uhE ) {
hostname = "UnknownHost";
}
- practitioner.setId( getFamilyName() + '_' + getName() + '_' + getVersion() + "_" + hostname );
+ practitioner.setId(
+ getFamilyName() + DIVIDER_CHAR + getName() + DIVIDER_CHAR + getVersion() + DIVIDER_CHAR + hostname );
practitioner.setActive( true );
practitioner.addName( name );
practitioner.addTelecom( contact );
@@ -79,7 +81,7 @@ public interface FhirPractitioner {
final Organization organization = new Organization();
final Practitioner practitioner = getPractitioner();
final String id = practitioner.getId()
- .replace( '_' + getName(), "" );
+ .replace( DIVIDER_CHAR + getName(), "" );
organization.setId( id );
organization.setActive( practitioner.getActive() );
organization.setName( getFamilyName() );
Modified: ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java (original)
+++ ctakes/trunk/ctakes-fhir/src/main/java/org/apache/ctakes/fhir/resource/PractitionerCtakes.java Wed Nov 7 15:08:00 2018
@@ -5,6 +5,8 @@ import org.hl7.fhir.dstu3.model.Organiza
import org.hl7.fhir.dstu3.model.Practitioner;
import org.hl7.fhir.dstu3.model.Reference;
+import static org.apache.ctakes.fhir.element.FhirElementFactory.DIVIDER_CHAR;
+
/**
* https://www.hl7.org/fhir/practitioner.html
* Even though ctakes is not human, registering it as a Practitioner provides reference to information source and devlist contact
@@ -32,7 +34,7 @@ public enum PractitionerCtakes implement
@Override
public String getVersion() {
- return "4_0_1";
+ return "4" + DIVIDER_CHAR + "0" + DIVIDER_CHAR + "1";
}
@Override
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerGui.java Wed Nov 7 15:08:00 2018
@@ -27,7 +27,8 @@ final public class PiperRunnerGui {
// iPhone 5 : 1136 x 640 (under 16:9, unique to Apple)
// iPad 3&4 : 2048 x 1536 (4:3, QXGA)
// iPad Mini: 1024 x 768 (4:3, XGA)
- final Dimension size = new Dimension( 800, 600 );
+// final Dimension size = new Dimension( 800, 600 );
+ final Dimension size = new Dimension( 1024, 768 );
frame.setSize( size );
frame.setMinimumSize( size );
// System.setProperty( "apple.laf.useScreenMenuBar", "true" );
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/pipeline/PiperRunnerPanel.java Wed Nov 7 15:08:00 2018
@@ -142,7 +142,7 @@ final public class PiperRunnerPanel exte
private JComponent createMainPanel() {
final JComponent westPanel = createWestPanel();
final JComponent eastPanel = createEastPanel();
- final JSplitPane mainSplit = new JSplitPane( JSplitPane.HORIZONTAL_SPLIT, westPanel, eastPanel );
+ final JSplitPane mainSplit = new PositionedSplitPane( JSplitPane.HORIZONTAL_SPLIT, westPanel, eastPanel );
mainSplit.setDividerLocation( 0.5 );
return mainSplit;
}
@@ -169,9 +169,9 @@ final public class PiperRunnerPanel exte
_cliTable = new SmoothTipTable( new CliOptionModel() );
_cliTable.setRowHeight( 20 );
_cliTable.setAutoResizeMode( JTable.AUTO_RESIZE_LAST_COLUMN );
- _cliTable.getColumnModel().getColumn( 0 ).setPreferredWidth( 100 );
- _cliTable.getColumnModel().getColumn( 0 ).setMaxWidth( 100 );
- _cliTable.getColumnModel().getColumn( 1 ).setMaxWidth( 50 );
+ _cliTable.getColumnModel().getColumn( 0 ).setPreferredWidth( 200 );
+ _cliTable.getColumnModel().getColumn( 0 ).setMaxWidth( 200 );
+ _cliTable.getColumnModel().getColumn( 1 ).setMaxWidth( 100 );
_cliTable.getColumnModel().getColumn( 3 ).setMaxWidth( 25 );
_cliTable.setRowSelectionAllowed( true );
_cliTable.setCellSelectionEnabled( true );
Modified: ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/pom.xml?rev=1846041&r1=1846040&r2=1846041&view=diff
==============================================================================
--- ctakes/trunk/pom.xml (original)
+++ ctakes/trunk/pom.xml Wed Nov 7 15:08:00 2018
@@ -153,6 +153,7 @@
<modules>
<module>ctakes-gui</module>
<module>ctakes-gui-res</module>
+ <module>ctakes-fhir</module>
<module>ctakes-utils</module>
<module>ctakes-core</module>
<module>ctakes-type-system</module>
@@ -515,6 +516,11 @@
<version>${project.version}</version>
</dependency>
<dependency>
+ <groupId>org.apache.ctakes</groupId>
+ <artifactId>ctakes-fhir</artifactId>
+ <version>${project.version}</version>
+ </dependency>
+ <dependency>
<groupId>org.apache.ctakes</groupId>
<artifactId>ctakes-examples</artifactId>
<version>${project.version}</version>