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From james-mas...@apache.org
Subject svn commit: r1502243 - /ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
Date Thu, 11 Jul 2013 15:19:16 GMT
Author: james-masanz
Date: Thu Jul 11 15:19:16 2013
New Revision: 1502243

URL: http://svn.apache.org/r1502243
Log:
wrapper for running plaintext clinical documents pipeline without needing a run configuration,
and that uses directories listed in AssertionConst.java

Added:
    ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
  (with props)

Added: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java?rev=1502243&view=auto
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
(added)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
Thu Jul 11 15:19:16 2013
@@ -0,0 +1,79 @@
+package org.apache.ctakes.clinicalpipeline;
+/**
+ * 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.
+ */
+
+
+import java.io.File;
+import java.util.Date;
+
+import org.apache.ctakes.assertion.util.AssertionConst;
+import org.apache.ctakes.core.util.CtakesFileNamer;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.collection.CollectionReader;
+import org.cleartk.util.cr.FilesCollectionReader;
+import org.uimafit.component.xwriter.XWriter;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.pipeline.SimplePipeline;
+
+/**
+ * Run the plaintext clinical pipeline, using the dictionary of terms from UMLS.
+ * Note you must have the UMLS password supplied in some way - see the 
+ * User or Developer Guide for information on options for doing that.
+ * Also note you need to have the UMLS dictionaries available (they 
+ * are separate download from Apache cTAKES itself due to licensing).
+ * 
+ * Input and output directory names are taken from {@link AssertionConst} 
+ * 
+ */
+public class ClinicalPipelineWithUmls {
+
+	public File inputDirectory;
+
+	public static void main(String[] args) throws Exception {
+
+	    System.out.println("Started " + ClinicalPipelineWithUmls.class.getCanonicalName() +
" at " + new Date());
+
+		//String documentText = "Text of document to test goes here, such as the following. No
edema, some soreness, denies pain.";
+		//InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText);
+		//CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream);
+		
+		CollectionReader collectionReader = FilesCollectionReader.getCollectionReader(AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES);
+
+		System.out.println("Reading from directory: " + AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES);
+		System.out.println("Outputting to directory: " + AssertionConst.evalOutputDir);
+		
+		AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createAnalysisEngineDescription(
+				"desc/analysis_engine/AggregatePlaintextUMLSProcessor");
+
+		AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
+				XWriter.class,
+				XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
+				AssertionConst.evalOutputDir,
+	            XWriter.PARAM_XML_SCHEME_NAME,
+	            XWriter.XMI,
+	            XWriter.PARAM_FILE_NAMER_CLASS_NAME,
+	            CtakesFileNamer.class.getName());
+
+		SimplePipeline.runPipeline(collectionReader, pipelineIncludingUmlsDictionaries, xWriter);
+		
+	    System.out.println("Done at " + new Date());
+	}
+
+
+}

Propchange: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineWithUmls.java
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