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) The Minnesota Department of Health. All Rights Reserved. */ package us.mn.state.health.lims.reports.send.sample.action; import org.apache.commons.beanutils.PropertyUtils; import org.apache.struts.Globals; import org.apache.struts.action.ActionForm; import org.apache.struts.action.ActionForward; import org.apache.struts.action.ActionMapping; import org.apache.struts.action.ActionMessages; import org.exolab.castor.mapping.Mapping; import org.exolab.castor.xml.Marshaller; import org.xml.sax.InputSource; import us.mn.state.health.lims.analysis.dao.AnalysisDAO; import us.mn.state.health.lims.analysis.daoimpl.AnalysisDAOImpl; import us.mn.state.health.lims.analysis.valueholder.Analysis; import us.mn.state.health.lims.analyte.valueholder.Analyte; import us.mn.state.health.lims.common.action.BaseAction; import us.mn.state.health.lims.common.action.BaseActionForm; import us.mn.state.health.lims.common.exception.LIMSRuntimeException; import us.mn.state.health.lims.common.log.LogEvent; import us.mn.state.health.lims.common.security.IAuthorizationActionConstants; import us.mn.state.health.lims.common.services.TestService; import us.mn.state.health.lims.common.util.StringUtil; import us.mn.state.health.lims.common.util.SystemConfiguration; import us.mn.state.health.lims.common.util.resources.ResourceLocator; import us.mn.state.health.lims.common.util.validator.ActionError; 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.login.dao.UserTestSectionDAO; import us.mn.state.health.lims.login.daoimpl.UserTestSectionDAOImpl; import us.mn.state.health.lims.method.dao.MethodDAO; import us.mn.state.health.lims.method.daoimpl.MethodDAOImpl; import us.mn.state.health.lims.organization.dao.OrganizationDAO; import us.mn.state.health.lims.organization.daoimpl.OrganizationDAOImpl; import us.mn.state.health.lims.organization.valueholder.Organization; import us.mn.state.health.lims.patient.dao.PatientDAO; import us.mn.state.health.lims.patient.daoimpl.PatientDAOImpl; import us.mn.state.health.lims.person.dao.PersonDAO; import us.mn.state.health.lims.person.daoimpl.PersonDAOImpl; import us.mn.state.health.lims.person.valueholder.Person; import us.mn.state.health.lims.provider.dao.ProviderDAO; import us.mn.state.health.lims.provider.daoimpl.ProviderDAOImpl; import us.mn.state.health.lims.reports.send.sample.valueholder.*; 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.dao.SampleDAO; import us.mn.state.health.lims.sample.daoimpl.SampleDAOImpl; import us.mn.state.health.lims.samplehuman.dao.SampleHumanDAO; import us.mn.state.health.lims.samplehuman.daoimpl.SampleHumanDAOImpl; import us.mn.state.health.lims.samplehuman.valueholder.SampleHuman; import us.mn.state.health.lims.sampleitem.dao.SampleItemDAO; import us.mn.state.health.lims.sampleitem.daoimpl.SampleItemDAOImpl; import us.mn.state.health.lims.sampleitem.valueholder.SampleItem; import us.mn.state.health.lims.sampleorganization.dao.SampleOrganizationDAO; import us.mn.state.health.lims.sampleorganization.daoimpl.SampleOrganizationDAOImpl; import us.mn.state.health.lims.sampleorganization.valueholder.SampleOrganization; import us.mn.state.health.lims.sourceofsample.dao.SourceOfSampleDAO; import us.mn.state.health.lims.sourceofsample.daoimpl.SourceOfSampleDAOImpl; import us.mn.state.health.lims.sourceofsample.valueholder.SourceOfSample; 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.testanalyte.dao.TestAnalyteDAO; import us.mn.state.health.lims.testanalyte.daoimpl.TestAnalyteDAOImpl; import us.mn.state.health.lims.testanalyte.valueholder.TestAnalyte; 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 us.mn.state.health.lims.testtrailer.dao.TestTrailerDAO; import us.mn.state.health.lims.testtrailer.daoimpl.TestTrailerDAOImpl; import us.mn.state.health.lims.testtrailer.valueholder.TestTrailer; import us.mn.state.health.lims.typeofsample.dao.TypeOfSampleDAO; import us.mn.state.health.lims.typeofsample.daoimpl.TypeOfSampleDAOImpl; import us.mn.state.health.lims.typeofsample.valueholder.TypeOfSample; import us.mn.state.health.lims.typeoftestresult.dao.TypeOfTestResultDAO; import us.mn.state.health.lims.typeoftestresult.daoimpl.TypeOfTestResultDAOImpl; import us.mn.state.health.lims.typeoftestresult.valueholder.TypeOfTestResult; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; import java.io.IOException; import java.io.InputStream; import java.io.StringWriter; import java.io.Writer; import java.sql.Timestamp; import java.util.ArrayList; import java.util.List; import java.util.Properties; /** * @author diane benz * * To change this generated comment edit the template variable "typecomment": * Window>Preferences>Java>Templates. To enable and disable the creation of type * comments go to Window>Preferences>Java>Code Generation. */ public class SampleXMLByTestProcessAction extends BaseAction { InputStream propertyStream = null; Properties transmissionMap = null; protected ActionForward performAction(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { String forward = FWD_SUCCESS; BaseActionForm dynaForm = (BaseActionForm) form; ActionMessages errors = null; request.setAttribute(ALLOW_EDITS_KEY, "false"); request.setAttribute(PREVIOUS_DISABLED, "true"); request.setAttribute(NEXT_DISABLED, "true"); request.setAttribute(IAuthorizationActionConstants.UPDATE_TESTCOMPONENT_TESTRESULT, "true"); // CHANGED // String selectedTestId = (String) request.getParameter("Test"); String xmlString = null; // get transmission resources properties ResourceLocator rl = ResourceLocator.getInstance(); // Now load a java.util.Properties object with the // properties transmissionMap = new Properties(); try { propertyStream = rl.getNamedResourceAsInputStream(ResourceLocator.XMIT_PROPERTIES); transmissionMap.load(propertyStream); } catch (IOException e) { //bugzilla 2154 LogEvent.logError("SampleXMLByTestProcessAction", "performAction()", e.toString()); throw new LIMSRuntimeException("Unable to load transmission resource mappings.", e); } finally { if (null != propertyStream) { try { propertyStream.close(); propertyStream = null; } catch (Exception e) { //bugzilla 2154 LogEvent.logError("SampleXMLByTestProcessAction", "performAction()", e.toString()); } } } List methods = new ArrayList(); MethodDAO methodDAO = new MethodDAOImpl(); methods = methodDAO.getAllMethods(); //Get tests/testsections by user system id //bugzilla 2160 UserTestSectionDAO userTestSectionDAO = new UserTestSectionDAOImpl(); List testSections = userTestSectionDAO.getAllUserTestSections(request); //bugzilla 2291 List tests = userTestSectionDAO.getAllUserTests(request, true); // get 3 drop down selections so we can repopulate String selectedTestSectionId = (String) dynaForm.get("selectedTestSectionId"); String selectedMethodId = (String) dynaForm.get("selectedMethodId"); String selectedTestId = (String) dynaForm.get("selectedTestId"); // PROCESS String humanDomain = SystemConfiguration.getInstance().getHumanDomain(); String animalDomain = SystemConfiguration.getInstance().getAnimalDomain(); if (!StringUtil.isNullorNill(selectedTestId)) { Test test = new Test(); test.setId(selectedTestId); TestDAO testDAO = new TestDAOImpl(); testDAO.getData(test); try { List analyses = new ArrayList(); AnalysisDAO analysisDAO = new AnalysisDAOImpl(); //bugzilla 2227 analyses = analysisDAO.getAllMaxRevisionAnalysesPerTest(test); SampleDAO sampleDAO = new SampleDAOImpl(); ResultDAO resultDAO = new ResultDAOImpl(); PatientDAO patientDAO = new PatientDAOImpl(); PersonDAO personDAO = new PersonDAOImpl(); ProviderDAO providerDAO = new ProviderDAOImpl(); SampleItemDAO sampleItemDAO = new SampleItemDAOImpl(); TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl(); SourceOfSampleDAO sourceOfSampleDAO = new SourceOfSampleDAOImpl(); SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl(); SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl(); OrganizationDAO organizationDAO = new OrganizationDAOImpl(); TestTrailerDAO testTrailerDAO = new TestTrailerDAOImpl(); TypeOfTestResultDAO typeOfTestResultDAO = new TypeOfTestResultDAOImpl(); // for overall message portion of message MessageXmit message = new MessageXmit(); // for UHL portion of message UHLXmit uhl = new UHLXmit(); Organization organization = new Organization(); TestingFacilityXmit uhlFacility = new TestingFacilityXmit(); //bugzilla 2069 organization.setOrganizationLocalAbbreviation( SystemConfiguration.getInstance().getMdhOrganizationIdForXMLTransmission()); organization = organizationDAO.getOrganizationByLocalAbbreviation(organization, true); StringBuffer orgName = new StringBuffer(); orgName.append(organization.getOrganizationName()); orgName.append(SystemConfiguration.getInstance().getDefaultTransmissionTextSeparator()); orgName.append(organization.getStreetAddress()); orgName.append(SystemConfiguration.getInstance().getDefaultTransmissionTextSeparator()); orgName.append(organization.getCity()); orgName.append(SystemConfiguration.getInstance().getDefaultTransmissionTextSeparator()); orgName.append(organization.getState()); orgName.append(SystemConfiguration.getInstance().getDefaultTransmissionTextSeparator()); orgName.append(organization.getZipCode()); orgName.append(SystemConfiguration.getInstance().getDefaultTransmissionTextSeparator()); orgName.append(SystemConfiguration.getInstance().getMdhPhoneNumberForXMLTransmission()); uhl.setId(SystemConfiguration.getInstance().getMdhUhlIdForXMLTransmission()); uhlFacility.setOrganizationName(orgName.toString()); uhlFacility.setUniversalId(SystemConfiguration.getInstance().getMdhUniversalIdForXMLTransmission()); uhlFacility.setUniversalIdType( SystemConfiguration.getInstance().getMdhUniversalIdTypeForXMLTransmission()); uhl.setFacility(uhlFacility); uhl.setApplicationName(SystemConfiguration.getInstance().getDefaultApplicationName()); uhl.setMessageTime((new Timestamp(System.currentTimeMillis())).toString()); uhl.setProcessingId(SystemConfiguration.getInstance().getDefaultProcessingIdForXMLTransmission()); uhl.setTransportMethod( SystemConfiguration.getInstance().getDefaultTransportMethodForXMLTransmission()); PatientXmit patient = new PatientXmit(); Person person = new Person(); ProviderXmit provider = new ProviderXmit(); FacilityXmit facility = new FacilityXmit(); Person providerPerson = new Person(); SampleHuman sampleHuman = new SampleHuman(); SampleOrganization sampleOrganization = new SampleOrganization(); List analysesBySample = null; SourceOfSample sourceOfSample = new SourceOfSample(); TypeOfSample typeOfSample = new TypeOfSample(); for (int i = 0; i < analyses.size(); i++) { Analysis analysis = (Analysis) analyses.get(i); SampleItem sampleItem = (SampleItem) analysis.getSampleItem(); sampleItemDAO.getData(sampleItem); sourceOfSample.setId(sampleItem.getSourceOfSampleId()); if (!StringUtil.isNullorNill(sourceOfSample.getId())) { sourceOfSampleDAO.getData(sourceOfSample); } typeOfSample.setId(sampleItem.getTypeOfSampleId()); if (!StringUtil.isNullorNill(typeOfSample.getId())) { typeOfSampleDAO.getData(typeOfSample); } // System.out.println("This is sampleItem " + sampleItem); if (sampleItem != null) { //bugzilla 1773 need to store sample not sampleId for use in sorting String sampleId = sampleItem.getSample().getId(); SampleXmit sample = new SampleXmit(); sample.setId(sampleId); sampleDAO.getData(sample); // marshall to XML Mapping castorMapping = new Mapping(); String castorMappingName = transmissionMap.getProperty("SampleToXmlMapping"); InputSource source = getSource(castorMappingName); // bugzilla #1346 add ability to hover over accession // number and // view patient/person information (first and last name // and external id) String domain = sample.getDomain(); if (domain != null && domain.equals(humanDomain)) { // go to human view // bugzilla #1346 add ability to hover over // accession number and // view patient/person information (first and last // name and external id) if (!StringUtil.isNullorNill(sample.getId())) { sampleHuman.setSampleId(sample.getId()); sampleHumanDAO.getDataBySample(sampleHuman); sampleOrganization.setSampleId(sample.getId()); sampleOrganizationDAO.getDataBySample(sampleOrganization); patient.setId(sampleHuman.getPatientId()); patientDAO.getData(patient); person.setId(patient.getPerson().getId()); personDAO.getData(person); //do we need to set id on patient to be externalId? patient.setLastName(person.getLastName()); patient.setFirstName(person.getFirstName()); patient.setStreetAddress(person.getState()); patient.setCity(person.getCity()); patient.setState(person.getState()); patient.setZipCode(person.getZipCode()); patient.setHomePhone(person.getHomePhone()); provider.setId(sampleHuman.getProviderId()); providerDAO.getData(provider); providerPerson = provider.getPerson(); personDAO.getData(providerPerson); Organization o = sampleOrganization.getOrganization(); if (o != null) { PropertyUtils.copyProperties(facility, provider); //per Nancy 01/12/2007 // have added null check if (!StringUtil.isNullorNill(o.getCliaNum())) { facility.setId(o.getCliaNum()); } facility.setOrganizationName(o.getOrganizationName()); facility.setDepartment(o.getOrganizationName()); facility.setStreetAddress(o.getStreetAddress()); facility.setCity(o.getCity()); facility.setState(o.getState()); facility.setZipCode(o.getZipCode()); } provider.setWorkPhone(providerPerson.getWorkPhone()); provider.setLastName(providerPerson.getLastName()); provider.setFirstName(providerPerson.getFirstName()); if (StringUtil.isNullorNill(sample.getRevision())) { sample.setRevision("0"); } sample.setExternalId(patient.getExternalId()); if (StringUtil.isNullorNill(sample.getStatus())) { sample.setStatus("THIS IS SAMPLE STATUS - IF BLANK SHOULD WE SEND DEFAULT"); } sample.setPatient(patient); sample.setProvider(provider); sample.setFacility(facility); // get all tests for this sample //bugzilla 2227 analysesBySample = analysisDAO.getMaxRevisionAnalysesBySample(sampleItem); ArrayList sampleTests = new ArrayList(); // assemble Test Elements for (int j = 0; j < analysesBySample.size(); j++) { TestXmit sampleTest = new TestXmit(); Analysis a = (Analysis) analysesBySample.get(j); Test t = a.getTest(); sampleTest.setMethod(t.getMethodName()); sampleTest.setReleasedDate(a.getReleasedDate()); if (sourceOfSample != null && !StringUtil.isNullorNill(sourceOfSample.getDescription())) { sampleTest.setSourceOfSample(sourceOfSample.getDescription()); } if (typeOfSample != null && !StringUtil.isNullorNill(typeOfSample.getDescription())) { sampleTest.setTypeOfSample(typeOfSample.getDescription()); } CodeElementXmit testName = new CodeElementXmit(); // do we need go to receiver_xref to get // their test name? identifier, codesystem // type, testName.setIdentifier(TestService.getLocalizedTestName(a.getTest())); testName.setCodeSystemType("L"); testName.setText("This is some kind of text"); sampleTest.setName(testName); TestTrailer testTrailer = t.getTestTrailer(); CommentXmit testComment = new CommentXmit(); if (testTrailer != null) { testComment.setComment(testTrailer.getText()); testComment.setCommentSource(""); } sampleTest.setComment(testComment); sampleTest.setStatus("This could be analysis status"); // NOW GET THE RESULTS FOR THIS TEST TestResultDAO testResultDAO = new TestResultDAOImpl(); DictionaryDAO dictDAO = new DictionaryDAOImpl(); // load collection of // TestAnalyte_TestResults for the // test TestAnalyteDAO testAnalyteDAO = new TestAnalyteDAOImpl(); List testAnalytes = testAnalyteDAO.getAllTestAnalytesPerTest(t); ArrayList testResults = new ArrayList(); for (int k = 0; k < testAnalytes.size(); k++) { TestAnalyte testAnalyte = (TestAnalyte) testAnalytes.get(k); Result result = new Result(); ResultXmit resultXmit = new ResultXmit(); resultDAO.getResultByAnalysisAndAnalyte(result, analysis, testAnalyte); if (result != null && !StringUtil.isNullorNill(result.getId())) { // we have at least one result so // add this TestResult testResult = result.getTestResult(); String value = null; if (testResult.getTestResultType().equals( SystemConfiguration.getInstance().getDictionaryType())) { // get from dictionary Dictionary dictionary = new Dictionary(); dictionary.setId(testResult.getValue()); dictDAO.getData(dictionary); // System.out.println("setting // dictEntry " // + dictionary.getDictEntry()); value = dictionary.getDictEntry(); } else { value = testResult.getValue(); } // now create other objects // within the result ObservationXmit observationXmit = new ObservationXmit(); CodeElementXmit observationIdentifier = new CodeElementXmit(); Analyte analyte = testAnalyte.getAnalyte(); if (!StringUtil.isNullorNill(analyte.getExternalId())) { observationIdentifier.setIdentifier(analyte.getExternalId()); } else { observationIdentifier.setIdentifier(analyte.getId()); } observationIdentifier.setText(analyte.getAnalyteName()); observationIdentifier.setCodeSystemType(SystemConfiguration .getInstance().getDefaultTransmissionCodeSystemType()); observationXmit.setIdentifier(observationIdentifier); observationXmit.setValue(value); //bugzilla 1866 TypeOfTestResult totr = new TypeOfTestResult(); totr.setTestResultType(testResult.getTestResultType()); totr = typeOfTestResultDAO.getTypeOfTestResultByType(totr); observationXmit.setValueType(totr.getHl7Value()); //end bugzilla 1866 resultXmit.setObservation(observationXmit); //bugzilla 1867 remove empty tags //resultXmit.setReferenceRange("UNKNOWN"); resultXmit.setReferenceRange(null); /*CodeElementXmit unitCodeElement = new CodeElementXmit(); unitCodeElement .setIdentifier("UNKNOWN"); unitCodeElement.setText("UNKNOWN"); unitCodeElement .setCodeSystemType(SystemConfiguration .getInstance() .getDefaultTransmissionCodeSystemType());*/ //resultXmit.setUnit(unitCodeElement); resultXmit.setUnit(null); //end bugzilla 1867 } testResults.add(resultXmit); } // END RESULTS FOR TEST sampleTest.setResults(testResults); sampleTest.setReleasedDate(analysis.getReleasedDate()); //there is a requirement that there is at least one result for a test if (testResults.size() > 0) { sampleTests.add(sampleTest); } } sample.setTests(sampleTests); message.setSample(sample); message.setUhl(uhl); try { // castorMapping.loadMapping(url); castorMapping.loadMapping(source); // Marshaller marshaller = new Marshaller( // new OutputStreamWriter(System.out)); Marshaller marshaller = new Marshaller(); marshaller.setMapping(castorMapping); Writer writer = new StringWriter(); marshaller.setWriter(writer); marshaller.marshal(message); xmlString = writer.toString(); xmlString = convertToDisplayableXML(xmlString); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("SampleXMLByTestProcessAction", "performAction()", e.toString()); } // this writes a default mapping to oc4j's // j2ee/home directory /* * try { MappingTool tool = new MappingTool(); * tool.setForceIntrospection(false); * tool.addClass("us.mn.state.health.lims.patient.valueholder.Patient"); * tool.write(new * FileWriter("XMLTestMapping.xml")); } * catch(MappingException ex){ * System.out.println("Error" + * ex.getLocalizedMessage());} catch(IOException * ex){ System.out.println("Error" + * ex.getLocalizedMessage());} */ } } else if (domain != null && domain.equals(animalDomain)) { // go to animal view // System.out.println("Going to animal view"); } else { // go toother view } } } } catch (LIMSRuntimeException lre) { // if error then forward to fail and don't update to blank // page // = false //bugzilla 2154 LogEvent.logError("SampleXMLByTestProcessAction", "performAction()", lre.toString()); errors = new ActionMessages(); ActionError error = null; error = new ActionError("errors.GetException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); request.setAttribute(ALLOW_EDITS_KEY, "false"); return mapping.findForward(FWD_FAIL); } } // END PROCESS // initialize the form dynaForm.initialize(mapping); PropertyUtils.setProperty(dynaForm, "testSections", testSections); PropertyUtils.setProperty(dynaForm, "methods", methods); PropertyUtils.setProperty(dynaForm, "tests", tests); PropertyUtils.setProperty(dynaForm, "selectedTestSectionId", selectedTestSectionId); PropertyUtils.setProperty(dynaForm, "selectedMethodId", selectedMethodId); PropertyUtils.setProperty(dynaForm, "selectedTestId", selectedTestId); // PropertyUtils.setProperty(dynaForm, "xmlString", // "<ajdf>asdfasdf</ajdf>"); PropertyUtils.setProperty(dynaForm, "xmlString", xmlString); return mapping.findForward(forward); } protected String getPageTitleKey() { return "report.sample.xml.by.test.title"; } protected String getPageSubtitleKey() { return "report.sample.xml.by.test.subtitle"; } protected String convertToDisplayableXML(String xml) { if (!StringUtil.isNullorNill(xml)) { xml = xml.replaceAll("<", "<"); xml = xml.replaceAll(">", ">"); // the following 2 lines are for display on page (not for system // out) xml = xml.replaceAll("\n", "<br>"); xml = xml.replaceAll(" ", " "); } return xml; } protected InputSource getSource(String castorMappingName) { InputStream mappingStream = null; // System.out.println("This is classpath " + // System.getProperty("java.class.path")); InputStream mappingXml = Thread.currentThread().getContextClassLoader() .getResourceAsStream(castorMappingName); // System.out.println("this is mappingXml " + mappingXml); InputSource source = new InputSource(mappingXml); return source; } }