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Posted to commits@ctakes.apache.org by se...@apache.org on 2019/07/18 16:03:43 UTC
svn commit: r1863323 - in
/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc:
db/DefaultJdbcDb.java i2b2/I2b2Db.java i2b2/I2b2JdbcWriter.java
i2b2/ObservationFactRow.java i2b2/ObservationFactTable.java
row/EmptyInitializer.java
Author: seanfinan
Date: Thu Jul 18 16:03:42 2019
New Revision: 1863323
URL: http://svn.apache.org/viewvc?rev=1863323&view=rev
Log:
DefaultJdbcDb Simple implementation of AbstractJdbcDb.
i2b2 package with simple default writer for i2b2 observation_fact tables.
EmptyInitializer can be passed as Corpus Initializer that does nothing.
Added:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java
Modified:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java?rev=1863323&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/db/DefaultJdbcDb.java Thu Jul 18 16:03:42 2019
@@ -0,0 +1,21 @@
+package org.apache.ctakes.core.cc.jdbc.db;
+
+
+import org.apache.uima.resource.ResourceInitializationException;
+
+/**
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 7/18/2019
+ */
+final public class DefaultJdbcDb extends AbstractJdbcDb {
+
+ public DefaultJdbcDb( final String driver,
+ final String url,
+ final String user,
+ final String pass,
+ final String keepAlive ) throws ResourceInitializationException {
+ super( driver, url, user, pass, keepAlive );
+ }
+
+}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java?rev=1863323&r1=1863322&r2=1863323&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2Db.java Thu Jul 18 16:03:42 2019
@@ -31,19 +31,18 @@ public class I2b2Db extends AbstractJdbc
* @return observation fact table with only negation marked by a negative (-) sign before concept codes.
* @throws SQLException -
*/
- protected ObservationFactTable addObservationFact( final String tableName, final boolean repeatCuis )
+ public ObservationFactTable addObservationFact( final String tableName, final boolean repeatCuis )
throws SQLException {
- final CorpusSettings settings = new CorpusSettings( CorpusSettings.Marker.MARK_NEGATED );
+ final ObservationFactTable.CorpusSettings settings
+ = new ObservationFactTable.CorpusSettings( ObservationFactTable.CorpusSettings.Marker.MARK_NEGATED );
return addObservationFact( tableName, repeatCuis, settings );
}
/**
- * @param tableName name of the output observation fact table.
- * @param corpusSettings settings for marking negation, uncertainty and generics.
- * @return observation fact table.
- * @throws SQLException -
+ * {@inheritDoc}
*/
- protected ObservationFactTable addObservationFact( final String tableName,
+// @Override
+ public ObservationFactTable addObservationFact( final String tableName,
final boolean repeatCuis,
final CorpusSettings corpusSettings ) throws SQLException {
final ObservationFactTable table
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java?rev=1863323&r1=1863322&r2=1863323&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/I2b2JdbcWriter.java Thu Jul 18 16:03:42 2019
@@ -51,7 +51,15 @@ public class I2b2JdbcWriter extends Abst
super.process( jcas );
}
- final protected JdbcDb createJdbcDb( final String driver,
+ final protected String getTableName() {
+ return _tableName;
+ }
+
+ final protected boolean isRepeatCuis() {
+ return _repeatCuis;
+ }
+
+ protected JdbcDb createJdbcDb( final String driver,
final String url,
final String user,
final String pass,
@@ -59,7 +67,7 @@ public class I2b2JdbcWriter extends Abst
LOGGER.info( "Initializing connection to " + url + " ..." );
final I2b2Db db = new I2b2Db( driver, url, user, pass, keepAlive );
try {
- db.addObservationFact( _tableName, _repeatCuis );
+ db.addObservationFact( getTableName(), isRepeatCuis() );
} catch ( SQLException sqlE ) {
throw new ResourceInitializationException( sqlE );
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java?rev=1863323&r1=1863322&r2=1863323&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactRow.java Thu Jul 18 16:03:42 2019
@@ -28,7 +28,7 @@ import static org.apache.ctakes.core.cc.
* @version %I%
* @since 3/14/2019
*/
-final public class ObservationFactRow
+public class ObservationFactRow
implements JdbcRow<CorpusSettings, JCas, JCas, IdentifiedAnnotation, UmlsConcept> {
static private final Logger LOGGER = Logger.getLogger( "ObservationFactRow" );
@@ -177,7 +177,7 @@ final public class ObservationFactRow
/**
* Set document information as empty.
*/
- private void setEmptyDocInfo() {
+ protected void setEmptyDocInfo() {
_encounter = -1;
_provider = "";
_start = Timestamp.valueOf( LocalDateTime.now() );
@@ -199,7 +199,7 @@ final public class ObservationFactRow
return concept.getPreferredText();
}
- private String getObservationBlob( final UmlsConcept concept ) {
+ protected String getObservationBlob( final UmlsConcept concept ) {
return "";
}
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java?rev=1863323&r1=1863322&r2=1863323&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/i2b2/ObservationFactTable.java Thu Jul 18 16:03:42 2019
@@ -23,7 +23,7 @@ import static org.apache.ctakes.core.cc.
* @version %I%
* @since 3/12/2019
*/
-final public class ObservationFactTable extends AbstractUmlsTable<CorpusSettings> {
+public class ObservationFactTable extends AbstractUmlsTable<CorpusSettings> {
private final CorpusSettings _corpusSettings;
Added: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java?rev=1863323&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java (added)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/jdbc/row/EmptyInitializer.java Thu Jul 18 16:03:42 2019
@@ -0,0 +1,17 @@
+package org.apache.ctakes.core.cc.jdbc.row;
+
+
+import org.apache.log4j.Logger;
+
+/**
+ * Does nothing. Can be passed to JdbcRow to do nothing for patient, document initialization.
+ *
+ * @author SPF , chip-nlp
+ * @version %I%
+ * @since 7/18/2019
+ */
+final public class EmptyInitializer {
+
+ static private final Logger LOGGER = Logger.getLogger( "EmptyInitializer" );
+
+}