Java tutorial
/* * Copyright 2016 King's College London, Richard Jackson <richgjackson@gmail.com>. * * Licensed 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 uk.ac.kcl; import ca.uhn.hl7v2.HL7Exception; import ca.uhn.hl7v2.model.AbstractMessage; import ca.uhn.hl7v2.model.DataTypeException; import ca.uhn.hl7v2.model.Message; import ca.uhn.hl7v2.model.v23.datatype.TS; import ca.uhn.hl7v2.model.v23.segment.MSH; import ca.uhn.hl7v2.parser.CanonicalModelClassFactory; import ca.uhn.hl7v2.parser.DefaultXMLParser; import ca.uhn.hl7v2.util.Hl7InputStreamMessageIterator; import ca.uhn.hl7v2.util.Terser; import java.io.ByteArrayInputStream; import org.apache.hadoop.fs.Path; //import org.apache.hadoop.conf.*; import org.apache.hadoop.io.*; import java.io.IOException; import java.io.InputStream; import java.nio.charset.StandardCharsets; import java.util.*; import java.util.logging.Level; import java.util.logging.Logger; import org.codehaus.jackson.map.ObjectMapper; import com.fasterxml.jackson.dataformat.xml.XmlMapper; import java.io.StringWriter; import java.text.DateFormat; import java.text.SimpleDateFormat; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerFactory; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.mapreduce.Job; import org.apache.hadoop.mapreduce.Mapper; import org.apache.hadoop.mapreduce.lib.input.FileInputFormat; import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat; import org.elasticsearch.hadoop.mr.EsOutputFormat; import org.w3c.dom.Document; import org.w3c.dom.Element; import org.w3c.dom.Node; import org.w3c.dom.NodeList; public class Transform23 { public static class MapToHL7String extends Mapper { @Override protected void map(Object key, Object value, Context context) throws IOException, InterruptedException { // create the MapWritable object MapWritable doc = new MapWritable(); doc.putAll(Transform23.extractHL7Metadata(value.toString())); if (doc.size() != 0) { context.write(NullWritable.get(), doc); } } } public static Map<Text, Writable> extractHL7Metadata(String messageString) { InputStream is = new ByteArrayInputStream(messageString.getBytes(StandardCharsets.UTF_8)); Hl7InputStreamMessageIterator iter = new Hl7InputStreamMessageIterator(is); Map<Text, Writable> map = new HashMap<>(); while (iter.hasNext()) { Message next = iter.next(); Text fieldName = new Text("body"); try { if (!next.printStructure().startsWith("ACK")) { try { map.put(fieldName, new Text(next.printStructure())); } catch (HL7Exception ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } try { map.put(new Text("message_time_stamp"), Transform23.getIso8601TimeFromMSH(Transform23.getMSH((AbstractMessage) next))); } catch (HL7Exception ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } try { map.put(new Text("pid"), Transform23.getPID((AbstractMessage) next)); } catch (HL7Exception ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } } } catch (HL7Exception ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } } return map; } public static void main(String[] args) throws Exception { Configuration conf = new Configuration(); conf.setBoolean("mapred.map.tasks.speculative.execution", false); conf.setBoolean("mapred.reduce.tasks.speculative.execution", false); //example config // conf.set("es.nodes", "192.168.1.101:9200"); // conf.set("es.resource", "hl7/message"); // conf.set("es.input.json", "yes"); // conf.set("es.net.ssl", "true"); // conf.set("es.net.ssl.keystore.location", "file:///home/rich/junk/node01.jks"); // conf.set("es.net.ssl.keystore.pass", ""); // conf.set("es.net.ssl.truststore.location", "file:///home/rich/junk/node01.jks"); // conf.set("es.net.ssl.truststore.pass", ""); // conf.set("es.net.http.auth.user", "admin"); // conf.set("es.net.http.auth.pass", ""); conf.set("es.nodes", args[2]); conf.set("es.resource", args[10] + args[11]); conf.set("textinputformat.record.delimiter", "\n"); //conf.set("es.input.json", "yes"); if (args[3].equalsIgnoreCase("true")) { conf.set("es.net.ssl", "true"); conf.set("es.net.ssl.keystore.location", args[4]); conf.set("es.net.ssl.keystore.pass", args[5]); conf.set("es.net.ssl.truststore.location", args[6]); conf.set("es.net.ssl.truststore.pass", args[7]); conf.set("es.net.http.auth.user", args[8]); conf.set("es.net.http.auth.pass", args[9]); } Job job = Job.getInstance(conf); FileInputFormat.setInputPaths(job, new Path(args[0])); FileOutputFormat.setOutputPath(job, new Path(args[1])); job.setMapperClass(MapToHL7String.class); job.setMapOutputKeyClass(NullWritable.class); //change if using re-existing json //job.setMapOutputValueClass(BytesWritable.class); job.setMapOutputValueClass(MapWritable.class); job.setOutputFormatClass(EsOutputFormat.class); job.waitForCompletion(true); } public static String convertHL7ToJson(Message message) { try { DefaultXMLParser xmlParser = new DefaultXMLParser(new CanonicalModelClassFactory("2.4")); Document xml = xmlParser.encodeDocument(message); cleanFieldNames(xml.getChildNodes().item(0)); XmlMapper xmlMapper = new XmlMapper(); List entries = null; try { entries = xmlMapper.readValue(getStringFromDocument(xml), List.class); } catch (IOException | TransformerException ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } ObjectMapper jsonMapper = new ObjectMapper(); String json = null; try { json = jsonMapper.writeValueAsString(entries); } catch (IOException ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } //System.out.println(json); json = json.substring(1, (json.length() - 1)); //to do - add code to rename fields, removing periods return json; } catch (HL7Exception ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); } return null; } public static String getStringFromDocument(Document doc) throws TransformerException { DOMSource domSource = new DOMSource(doc); StringWriter writer = new StringWriter(); StreamResult result = new StreamResult(writer); TransformerFactory tf = TransformerFactory.newInstance(); Transformer transformer = tf.newTransformer(); transformer.transform(domSource, result); return writer.toString(); } public static void cleanFieldNames(Node node) { // do something with the current node instead of System.out //System.out.println(node.getNodeName()); NodeList nodeList = node.getChildNodes(); for (int i = 0; i < nodeList.getLength(); i++) { Node currentNode = nodeList.item(i); if (currentNode.getNodeType() == Node.ELEMENT_NODE) { //calls this method for all the children which is Element Element el = (Element) nodeList.item(i); //System.out.println(el.getNodeName()); //System.out.println(nodeList.getLength()); if (el.getNodeName().contains(".")) { el.getOwnerDocument().renameNode(nodeList.item(i), null, el.getNodeName().replace(".", "_")); } cleanFieldNames(currentNode); } } } public static Writable getIso8601TimeFromMSH(MSH msh) { TS ts = msh.getDateTimeOfMessage(); Date date = null; try { date = ts.getTimeOfAnEvent().getValueAsDate(); } catch (DataTypeException ex) { Logger.getLogger(Transform23.class.getName()).log(Level.SEVERE, null, ex); return NullWritable.get(); } DateFormat df = new SimpleDateFormat("yyyy-MM-dd'T'HH:mmZ"); String returnString = null; try { returnString = df.format(date); } catch (NullPointerException ex) { return NullWritable.get(); } System.out.println(returnString); return new Text(returnString); } public static MSH getMSH(AbstractMessage message) throws HL7Exception { return (MSH) message.get("MSH"); } public static Writable getPID(AbstractMessage message) throws HL7Exception { Terser terser = new Terser(message); Text t; t = new Text(terser.get("/PID-3")); if (t != null) { return t; } else { return NullWritable.get(); } } }