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From tm...@apache.org
Subject svn commit: r1850060 - in /ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest: service/CtakesRestController.java service/CuiResponse.java util/JCasParser.java
Date Mon, 31 Dec 2018 17:16:59 GMT
Author: tmill
Date: Mon Dec 31 17:16:59 2018
New Revision: 1850060

URL: http://svn.apache.org/viewvc?rev=1850060&view=rev
Log:
Merge branch 'fix-rest'

Added:
    ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
    ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java
Modified:
    ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java

Modified: ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java?rev=1850060&r1=1850059&r2=1850060&view=diff
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java
(original)
+++ ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CtakesRestController.java
Mon Dec 31 17:16:59 2018
@@ -18,24 +18,19 @@
  */
 package org.apache.ctakes.rest.service;
 
-import org.apache.commons.io.output.ByteArrayOutputStream;
 import org.apache.ctakes.core.pipeline.PipelineBuilder;
 import org.apache.ctakes.core.pipeline.PiperFileReader;
-import org.apache.ctakes.rest.util.XMLParser;
+import org.apache.ctakes.rest.util.JCasParser;
 import org.apache.log4j.Logger;
 import org.apache.uima.UIMAFramework;
 import org.apache.uima.analysis_engine.AnalysisEngine;
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
-import org.apache.uima.cas.impl.XmiCasSerializer;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.util.JCasPool;
 import org.springframework.web.bind.annotation.*;
 
 import javax.annotation.PostConstruct;
 import javax.servlet.ServletException;
-import java.io.ByteArrayInputStream;
-import java.nio.file.Files;
-import java.nio.file.Paths;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -60,12 +55,12 @@ public class CtakesRestController {
     public void init() throws ServletException {
         LOGGER.info("Initializing analysis engines and jcas pools");
         _pipelineRunners.put(DEFAULT_PIPELINE, new PipelineRunner(DEFAULT_PIPER_FILE_PATH));
-        _pipelineRunners.put(FULL_PIPELINE, new PipelineRunner(FULL_PIPER_FILE_PATH));
+//        _pipelineRunners.put(FULL_PIPELINE, new PipelineRunner(FULL_PIPER_FILE_PATH));
     }
 
     @RequestMapping(value = "/analyze", method = RequestMethod.POST)
     @ResponseBody
-    public Map<String, Map<String, List<String>>> getAnalyzedJSON(@RequestBody
String analysisText,
+    public Map<String, List<CuiResponse>> getAnalyzedJSON(@RequestBody String
analysisText,
                                                                   @RequestParam("pipeline")
Optional<String> pipelineOptParam)
             throws Exception {
         String pipeline = DEFAULT_PIPELINE;
@@ -79,13 +74,9 @@ public class CtakesRestController {
 
     }
 
-    static private Map<String, Map<String, List<String>>> formatResults(JCas
jcas) throws Exception {
-        ByteArrayOutputStream output = new ByteArrayOutputStream();
-        XmiCasSerializer.serialize(jcas.getCas(), output);
-        String outputStr = output.toString();
-        // For debugging: Files.write(Paths.get("Result.xml"), outputStr.getBytes());
-        XMLParser parser = new XMLParser();
-        return parser.parse(new ByteArrayInputStream(outputStr.getBytes()));
+    static private Map<String, List<CuiResponse>> formatResults(JCas jcas) throws
Exception {
+        JCasParser parser = new JCasParser();
+        return parser.parse(jcas);
     }
 
     static private final class PipelineRunner {
@@ -105,9 +96,9 @@ public class CtakesRestController {
             }
         }
 
-        public Map<String, Map<String, List<String>>> process(final String
text) throws ServletException {
+        public Map<String, List<CuiResponse>> process(final String text) throws
ServletException {
             JCas jcas = null;
-            Map<String, Map<String, List<String>>> resultMap = null;
+            Map<String, List<CuiResponse>> resultMap = null;
             if (text != null) {
                 try {
                     jcas = _pool.getJCas(-1);

Added: ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java?rev=1850060&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
(added)
+++ ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/service/CuiResponse.java
Mon Dec 31 17:16:59 2018
@@ -0,0 +1,61 @@
+/**
+ * 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
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
+ * 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.rest.service;
+
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by tmill on 12/20/18.
+ */
+public class CuiResponse {
+    public int begin;
+    public int end;
+    public String text;
+    public int polarity;
+    public List<Map<String,String>> conceptAttributes = new ArrayList<>();
+
+    public CuiResponse(Annotation annotation){
+        begin = annotation.getBegin();
+        end = annotation.getEnd();
+        text = annotation.getCoveredText();
+
+        if(annotation instanceof IdentifiedAnnotation) {
+            IdentifiedAnnotation ia = (IdentifiedAnnotation) annotation;
+            polarity = ia.getPolarity();
+            if(ia.getOntologyConceptArr() != null) {
+                for (UmlsConcept concept : JCasUtil.select(ia.getOntologyConceptArr(), UmlsConcept.class))
{
+                    Map<String, String> atts = new HashMap<>();
+                    atts.put("codingScheme", concept.getCodingScheme());
+                    atts.put("cui", concept.getCui());
+                    atts.put("code", concept.getCode());
+                    atts.put("tui", concept.getTui());
+                    conceptAttributes.add(atts);
+                }
+            }
+        }
+    }
+}

Added: ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java?rev=1850060&view=auto
==============================================================================
--- ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java
(added)
+++ ctakes/trunk/ctakes-web-rest/src/main/java/org/apache/ctakes/rest/util/JCasParser.java
Mon Dec 31 17:16:59 2018
@@ -0,0 +1,74 @@
+/**
+ * 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
+ * <p>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p>
+ * 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.rest.util;
+
+import org.apache.ctakes.drugner.type.*;
+import org.apache.ctakes.rest.service.CuiResponse;
+import org.apache.ctakes.typesystem.type.textsem.*;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Created by tmill on 12/20/18.
+ */
+public class JCasParser {
+    List<Class<? extends Annotation>> semClasses = new ArrayList<>();
+
+    public JCasParser(){
+        // CUI types:
+        semClasses.add(DiseaseDisorderMention.class);
+        semClasses.add(SignSymptomMention.class);
+        semClasses.add(ProcedureMention.class);
+        semClasses.add(AnatomicalSiteMention.class);
+        semClasses.add(MedicationMention.class);
+
+        // Temporal types:
+        semClasses.add(TimeMention.class);
+        semClasses.add(DateAnnotation.class);
+
+        // Drug-related types:
+        semClasses.add(FractionStrengthAnnotation.class);
+        semClasses.add(DrugChangeStatusAnnotation.class);
+        semClasses.add(StrengthUnitAnnotation.class);
+        semClasses.add(StrengthAnnotation.class);
+        semClasses.add(RouteAnnotation.class);
+        semClasses.add(FrequencyUnitAnnotation.class);
+        semClasses.add(MeasurementAnnotation.class);
+    }
+
+    public Map<String, List<CuiResponse>> parse(JCas jcas) throws Exception {
+
+        Map<String, List<CuiResponse>> responseMap = new HashMap<>();
+        for(Class<? extends Annotation> semClass : semClasses){
+            List<CuiResponse> annotations = new ArrayList<>();
+            for(Annotation annot : JCasUtil.select(jcas, semClass)){
+                CuiResponse response = new CuiResponse(annot);
+                annotations.add(response);
+            }
+            responseMap.put(semClass.getSimpleName(), annotations);
+        }
+        return responseMap;
+    }
+}



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