Java tutorial
/* * This file is part of i2b2-Java-API. * * The i2b2-Java-API is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation, either version 3 of the License, or * (at your option) any later version. * * i2b2-Java-API is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with i2b2-Java-API. If not, see <http://www.gnu.org/licenses/>. */ package edu.harvard.hms.dbmi.i2b2.api.samples; import java.io.IOException; import java.util.List; import javax.xml.bind.JAXBException; import org.apache.http.client.ClientProtocolException; import org.apache.http.client.HttpClient; import org.apache.http.impl.client.HttpClients; import edu.harvard.hms.dbmi.i2b2.api.crc.CRCCell; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.pdo.OutputOptionSelectType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.pdo.ParamType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.pdo.PatientDataResponseType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.pdo.PatientSet; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.pdo.PatientType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.ItemType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.MasterInstanceResultResponseType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.PanelType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.QueryResultInstanceType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.ResultOutputOptionListType; import edu.harvard.hms.dbmi.i2b2.api.crc.xml.psm.ResultOutputOptionType; import edu.harvard.hms.dbmi.i2b2.api.exception.I2B2InterfaceException; /** * Provides an example of performing a simple query using the i2b2-Java-API * * A simple example would be the following: * * java SimpleQuery i2b2demo demo demouser http://192.168.56.101:9090/i2b2/services/QueryToolService Demo \\\\i2b2_DEMO\\i2b2\\Demographics\\Gender\\ * @author Jeremy R. Easton-Marks * */ public class SimpleQuery { private CRCCell crcCell = new CRCCell(); /** * Runs the simple query example * * Requires 6 parameters: * domain userName password ontologyCellURL project path * * @param args * arguments */ public static void main(String[] args) { if (args.length != 6) { System.out.println("Invalid number of arguments."); System.out.println("java SimpleQuery domain userName password ontologyCellURL project path"); } String domain = args[0]; String userName = args[1]; String password = args[2]; String crcCellURL = args[3]; String project = args[4]; String path = args[5]; SimpleQuery simpleQuery = new SimpleQuery(); try { simpleQuery.setup(userName, domain, password, crcCellURL, project); HttpClient httpClient = HttpClients.createDefault(); String queryMasterId = simpleQuery.runQuery(httpClient, path); simpleQuery.printResults(httpClient, queryMasterId); } catch (JAXBException | IOException | I2B2InterfaceException e) { System.out.println("An error occurred running the simple query"); e.printStackTrace(); } } /** * Runs the query * * @param httpClient HTTP client * @param path Path to query on * @return The query master id * @throws ClientProtocolException * A client protocol exception occurred * @throws JAXBException * An XML exception occurred * @throws IOException * An IO exception occurred * @throws I2B2InterfaceException * An exception occurred on the I2B2 server */ private String runQuery(HttpClient httpClient, String path) throws ClientProtocolException, JAXBException, I2B2InterfaceException, IOException { PanelType panel = new PanelType(); panel.setPanelNumber(1); panel.setPanelAccuracyScale(100); panel.setInvert(0); panel.setPanelTiming("ANY"); PanelType.TotalItemOccurrences tio = new PanelType.TotalItemOccurrences(); tio.setValue(1); panel.setTotalItemOccurrences(tio); ItemType itemType = new ItemType(); itemType.setItemKey(path); panel.getItem().add(itemType); //Set up the result option to return a patient set ResultOutputOptionListType roolt = new ResultOutputOptionListType(); ResultOutputOptionType root = new ResultOutputOptionType(); root.setPriorityIndex(9); root.setName("patientset"); roolt.getResultOutput().add(root); MasterInstanceResultResponseType mirrt = crcCell.runQueryInstanceFromQueryDefinition(httpClient, null, null, "Simple Query", null, "ANY", 0, roolt, panel); return mirrt.getQueryInstance().getQueryMasterId(); } /** * Prints the results of the query * * @param httpClient HTTP Client * @param queryMasterId Master Query Id * @throws ClientProtocolException * A client protocol exception occurred * @throws JAXBException * An XML exception occurred * @throws IOException * An IO exception occurred * @throws I2B2InterfaceException * An exception occurred on the I2B2 server */ private void printResults(HttpClient httpClient, String queryMasterId) throws ClientProtocolException, JAXBException, I2B2InterfaceException, IOException { List<QueryResultInstanceType> response = crcCell.getQueryResultInstanceListFromQueryInstanceId(httpClient, queryMasterId); String resultInstanceId = response.get(0).getResultInstanceId(); PatientDataResponseType pdrt = crcCell.getPDOfromInputList(httpClient, resultInstanceId, 0, 100000, false, false, false, OutputOptionSelectType.USING_INPUT_LIST); PatientSet patientSet = pdrt.getPatientData().getPatientSet(); if (patientSet.getPatient().size() == 0) { System.out.println("No results returned"); return; } System.out.print("Patient Id\t|"); PatientType columnPatientType = patientSet.getPatient().get(0); String[] columns = new String[columnPatientType.getParam().size()]; for (int i = 0; i < columnPatientType.getParam().size(); i++) { String columnName = columnPatientType.getParam().get(i).getColumn(); columns[i] = columnName; System.out.print("\t|\t" + columnName); } System.out.println("\t|\n"); for (PatientType patientType : patientSet.getPatient()) { System.out.println(patientType.getPatientId().getValue() + "\t|"); List<ParamType> patientParams = patientType.getParam(); for (String column : columns) { for (ParamType patientParam : patientParams) { if (patientParam.getColumn().equalsIgnoreCase(column)) { System.out.print("\t|\t" + patientParam.getValue()); } } } System.out.println("\t|"); } System.out.println("\nResults: " + patientSet.getPatient().size()); } private void setup(String userName, String domain, String password, String crcCellURL, String project) throws JAXBException { crcCell.setup(crcCellURL, domain, userName, password, project, false, null); } }