You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by dl...@apache.org on 2015/08/06 21:32:57 UTC
svn commit: r1694560 - in
/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes: consumers/
pipelines/
Author: dligach
Date: Thu Aug 6 19:32:57 2015
New Revision: 1694560
URL: http://svn.apache.org/r1694560
Log:
refactoring + added a sentence printer consumer (for indexing sentences later)
Added:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/ClinicalConceptViewer.java
- copied, changed from r1693617, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/ClinicalConceptViewer.java
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/PolysemyAnalysis.java
- copied, changed from r1693615, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/PolysemyAnalysis.java
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SemanticTypePrinter.java
- copied, changed from r1693617, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/SemanticTypePrinter.java
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java (with props)
Removed:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/ClinicalConceptViewer.java
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/PolysemyAnalysis.java
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/SemanticTypePrinter.java
Modified:
ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java
Copied: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/ClinicalConceptViewer.java (from r1693617, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/ClinicalConceptViewer.java)
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/ClinicalConceptViewer.java?p2=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/ClinicalConceptViewer.java&p1=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/ClinicalConceptViewer.java&r1=1693617&r2=1694560&rev=1694560&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/ClinicalConceptViewer.java (original)
+++ ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/ClinicalConceptViewer.java Thu Aug 6 19:32:57 2015
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package org.apache.ctakes.pipelines;
+package org.apache.ctakes.consumers;
import java.io.File;
Copied: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/PolysemyAnalysis.java (from r1693615, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/PolysemyAnalysis.java)
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/PolysemyAnalysis.java?p2=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/PolysemyAnalysis.java&p1=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/PolysemyAnalysis.java&r1=1693615&r2=1694560&rev=1694560&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/PolysemyAnalysis.java (original)
+++ ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/PolysemyAnalysis.java Thu Aug 6 19:32:57 2015
@@ -1,4 +1,4 @@
-package org.apache.ctakes.pipelines;
+package org.apache.ctakes.consumers;
import java.io.File;
import java.util.Arrays;
Copied: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SemanticTypePrinter.java (from r1693617, ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/SemanticTypePrinter.java)
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SemanticTypePrinter.java?p2=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SemanticTypePrinter.java&p1=ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/SemanticTypePrinter.java&r1=1693617&r2=1694560&rev=1694560&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/SemanticTypePrinter.java (original)
+++ ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SemanticTypePrinter.java Thu Aug 6 19:32:57 2015
@@ -16,7 +16,7 @@
* specific language governing permissions and limitations
* under the License.
*/
-package org.apache.ctakes.pipelines;
+package org.apache.ctakes.consumers;
import java.io.File;
import java.util.ArrayList;
Added: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java?rev=1694560&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java (added)
+++ ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java Thu Aug 6 19:32:57 2015
@@ -0,0 +1,77 @@
+/**
+ * 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.
+ */
+package org.apache.ctakes.consumers;
+
+import java.io.File;
+
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.ctakes.utils.Utils;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Read cTAKES annotations from XMI files.
+ *
+ * @author dmitriy dligach
+ */
+public class SentencePrinter {
+
+ static interface Options {
+
+ @Option(
+ longName = "xmi-dir",
+ description = "path to xmi files")
+ public File getInputDirectory();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+ CollectionReader collectionReader = Utils.getCollectionReader(options.getInputDirectory());
+ AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(RelationContextPrinter.class);
+ SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+ }
+
+ /**
+ * Print events and entities.
+ *
+ * @author dmitriy dligach
+ */
+ public static class RelationContextPrinter extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ for(Sentence sentence : JCasUtil.select(jCas, Sentence.class)) {
+ System.out.println(sentence.getCoveredText());
+ }
+ }
+ }
+}
+
+
\ No newline at end of file
Propchange: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/consumers/SentencePrinter.java
------------------------------------------------------------------------------
svn:mime-type = text/plain
Modified: ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java?rev=1694560&r1=1694559&r2=1694560&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java (original)
+++ ctakes/sandbox/ctakes-wsd/src/main/java/org/apache/ctakes/pipelines/BasicPipeline.java Thu Aug 6 19:32:57 2015
@@ -59,8 +59,8 @@ import com.google.common.io.CharStreams;
public class BasicPipeline {
- public static File inputDirectory = new File("/Users/Dima/Boston/Data/Sharp/FromSameer/Text/");
- public static String outputDirectory = "/Users/Dima/Boston/Out/";
+ public static File inputDirectory = new File("/Users/dima/Boston/Data/DeepPhe/Text/");
+ public static String outputDirectory = "/Users/dima/Boston/Data/DeepPhe/Xmi/";
public static void main(String[] args) throws Exception {