Java tutorial
/** * The contents of this file are subject to the Mozilla Public License * Version 1.1 (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.mozilla.org/MPL/ * * Software distributed under the License is distributed on an "AS IS" * basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the * License for the specific language governing rights and limitations under * the License. * * The Original Code is OpenELIS code. * * Copyright (C) CIRG, University of Washington, Seattle WA. All Rights Reserved. * */ package us.mn.state.health.lims.testreflex.action.util; import org.apache.commons.validator.GenericValidator; import us.mn.state.health.lims.analysis.valueholder.Analysis; import us.mn.state.health.lims.analyte.dao.AnalyteDAO; import us.mn.state.health.lims.analyte.daoimpl.AnalyteDAOImpl; import us.mn.state.health.lims.analyte.valueholder.Analyte; import us.mn.state.health.lims.dictionary.dao.DictionaryDAO; import us.mn.state.health.lims.dictionary.daoimpl.DictionaryDAOImpl; import us.mn.state.health.lims.dictionary.valueholder.Dictionary; import us.mn.state.health.lims.observationhistory.valueholder.ObservationHistory; import us.mn.state.health.lims.observationhistory.valueholder.ObservationHistory.ValueType; import us.mn.state.health.lims.observationhistorytype.dao.ObservationHistoryTypeDAO; import us.mn.state.health.lims.observationhistorytype.daoImpl.ObservationHistoryTypeDAOImpl; import us.mn.state.health.lims.observationhistorytype.valueholder.ObservationHistoryType; import us.mn.state.health.lims.result.dao.ResultDAO; import us.mn.state.health.lims.result.daoimpl.ResultDAOImpl; import us.mn.state.health.lims.result.valueholder.Result; import us.mn.state.health.lims.sample.valueholder.Sample; import us.mn.state.health.lims.scriptlet.valueholder.Scriptlet; import us.mn.state.health.lims.test.dao.TestDAO; import us.mn.state.health.lims.test.daoimpl.TestDAOImpl; import us.mn.state.health.lims.test.valueholder.Test; import us.mn.state.health.lims.testresult.dao.TestResultDAO; import us.mn.state.health.lims.testresult.daoimpl.TestResultDAOImpl; import us.mn.state.health.lims.testresult.valueholder.TestResult; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; public class RetroCIReflexActions extends ReflexAction { private static final String HIV_D = "HIV D"; private static final String HIV_2 = "HIV 2"; private static final String HIV_1 = "HIV 1"; private static final String HIV_N = "HIV N"; private static final String HIV_INDETERMINATE = "HIV Indeterminate"; private static final String HIV_INVALID = "HIV Invalid"; private static final String HIV_NAME = "hivStatus"; private static String OBSERVATION_HIV_STATUS_ID; private static Analyte ANALYTE_CONCLUSION; private static Analyte ANALYTE_CD4_CT_GENERATED; private static Analyte ANALYTE_GB_RESULT; private static Analyte ANALYTE_LYMPH_PER_RESULT; private static Analyte ANALYTE_CD4_PER_RESULT; private static TestResult TEST_RESULT_CD4_CALCULATED; private static List<Integer> CD4_RESULT_TEST_DEPENDANCIES; private static Map<String, String> hivStatusToDictonaryIDMap; static { ObservationHistoryTypeDAO typeDAO = new ObservationHistoryTypeDAOImpl(); ObservationHistoryType observationHistoryType = typeDAO.getByName(HIV_NAME); OBSERVATION_HIV_STATUS_ID = observationHistoryType == null ? null : observationHistoryType.getId(); hivStatusToDictonaryIDMap = new HashMap<String, String>(); DictionaryDAO dictionaryDAO = new DictionaryDAOImpl(); List<Dictionary> dictionaryList = dictionaryDAO.getDictionaryEntrysByCategoryName("HIVResult"); for (Dictionary dictionary : dictionaryList) { if (dictionary.getDictEntry().equals("HIV1")) { hivStatusToDictonaryIDMap.put(HIV_1, dictionary.getId()); } else if (dictionary.getDictEntry().equals("HIV2")) { hivStatusToDictonaryIDMap.put(HIV_2, dictionary.getId()); } else if (dictionary.getDictEntry().equals("HIVD")) { hivStatusToDictonaryIDMap.put(HIV_D, dictionary.getId()); } else if (dictionary.getDictEntry().equals("Negative")) { hivStatusToDictonaryIDMap.put(HIV_N, dictionary.getId()); } else if (dictionary.getDictEntry().equals("Indeterminate")) { hivStatusToDictonaryIDMap.put(HIV_INDETERMINATE, dictionary.getId()); } else if (dictionary.getDictEntry().equals("Invalid")) { hivStatusToDictonaryIDMap.put(HIV_INVALID, dictionary.getId()); } } AnalyteDAO analyteDAO = new AnalyteDAOImpl(); Analyte analyte = new Analyte(); analyte.setAnalyteName("Conclusion"); ANALYTE_CONCLUSION = analyteDAO.getAnalyteByName(analyte, false); analyte.setAnalyteName("CD4 percentage count Result"); ANALYTE_CD4_PER_RESULT = analyteDAO.getAnalyteByName(analyte, false); analyte.setAnalyteName("GB Result"); ANALYTE_GB_RESULT = analyteDAO.getAnalyteByName(analyte, false); analyte.setAnalyteName("Lymph % Result"); ANALYTE_LYMPH_PER_RESULT = analyteDAO.getAnalyteByName(analyte, false); analyte.setAnalyteName("generated CD4 Count"); ANALYTE_CD4_CT_GENERATED = analyteDAO.getAnalyteByName(analyte, false); CD4_RESULT_TEST_DEPENDANCIES = new ArrayList<Integer>(); TestDAO testDAO = new TestDAOImpl(); Test test = new Test(); test.setTestName("GB"); test = testDAO.getTestByName(test); CD4_RESULT_TEST_DEPENDANCIES.add(Integer.parseInt(test.getId())); test.setTestName("Lymph %"); test = testDAO.getTestByName(test); CD4_RESULT_TEST_DEPENDANCIES.add(Integer.parseInt(test.getId())); test.setTestName("CD4 percentage count"); test = testDAO.getTestByName(test); CD4_RESULT_TEST_DEPENDANCIES.add(Integer.parseInt(test.getId())); test.setTestName("CD4 absolute count"); test = testDAO.getTestByName(test); TestResultDAO testResultDAO = new TestResultDAOImpl(); @SuppressWarnings("unchecked") List<TestResult> resultList = testResultDAO.getAllActiveTestResultsPerTest(test); TEST_RESULT_CD4_CALCULATED = resultList.get(0); } @Override protected void handleScriptletAction(Scriptlet scriptlet) { if (scriptlet != null && INTERPERET_TYPE.equals(scriptlet.getCodeType())) { String action = scriptlet.getCodeSource(); if (GenericValidator.isBlankOrNull(action)) { return; } if (action.equals(HIV_INDETERMINATE) || action.equals(HIV_N) || action.equals(HIV_1) || action.equals(HIV_2) || action.equals(HIV_D)) { addHIVObservation(action); } else if (action.equals("Calc CD4")) { finalResult = getCD4CalculationResult(result.getAnalysis().getSampleItem().getSample()); } } } /* * This may be dead code */ public void addCD4Calculation(Result result) { this.result = result; finalResult = getCD4CalculationResult(result.getAnalysis().getSampleItem().getSample()); } public Result getCD4CalculationResult(Sample sample) { Result calculatedResult = null; List<Analysis> analysisList = ANALYSIS_DAO.getAnalysisBySampleAndTestIds(sample.getId(), CD4_RESULT_TEST_DEPENDANCIES); List<Integer> analysisIDList = new ArrayList<Integer>(); for (Analysis analysis : analysisList) { analysisIDList.add(Integer.parseInt(analysis.getId())); } ResultDAO resultDAO = new ResultDAOImpl(); Result CD4Result = resultDAO.getResultForAnalyteInAnalysisSet(ANALYTE_CD4_PER_RESULT.getId(), analysisIDList); Result GBResult = resultDAO.getResultForAnalyteInAnalysisSet(ANALYTE_GB_RESULT.getId(), analysisIDList); Result LymphResult = resultDAO.getResultForAnalyteInAnalysisSet(ANALYTE_LYMPH_PER_RESULT.getId(), analysisIDList); if (CD4Result != null && GBResult != null && LymphResult != null) { try { double result = Double.parseDouble(CD4Result.getValue()) * Double.parseDouble(GBResult.getValue()) * Double.parseDouble(LymphResult.getValue()) * 0.1; result = Math.rint(result); calculatedResult = resultDAO.getResultForAnalyteInAnalysisSet(ANALYTE_CD4_CT_GENERATED.getId(), analysisIDList); if (calculatedResult == null) { calculatedResult = new Result(); calculatedResult.setResultType("N"); calculatedResult.setIsReportable("T"); calculatedResult.setTestResult(TEST_RESULT_CD4_CALCULATED); calculatedResult.setAnalyte(ANALYTE_CD4_CT_GENERATED); calculatedResult.setAnalysis(CD4Result.getAnalysis()); } calculatedResult.setValue(String.valueOf(result)); } catch (NumberFormatException e) { //no op final result should be null. Handles the case of "XXXX" } } return calculatedResult; } private void addHIVObservation(String action) { observation = new ObservationHistory(); observation.setValue(hivStatusToDictonaryIDMap.get(action)); observation.setValueType(ValueType.DICTIONARY); observation.setObservationHistoryTypeId(OBSERVATION_HIV_STATUS_ID); finalResult = new Result(); finalResult.setValue(hivStatusToDictonaryIDMap.get(action)); finalResult.setResultType("D"); finalResult.setIsReportable("T"); finalResult.setAnalyte(ANALYTE_CONCLUSION); } }