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.sample.action; import java.sql.Timestamp; import java.util.ArrayList; import java.util.Calendar; import java.util.Date; import java.util.HashMap; import java.util.List; import java.util.Locale; import javax.servlet.http.HttpServletRequest; import javax.servlet.http.HttpServletResponse; 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 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.analysisqaevent.dao.AnalysisQaEventDAO; import us.mn.state.health.lims.analysisqaevent.daoimpl.AnalysisQaEventDAOImpl; import us.mn.state.health.lims.analysisqaevent.valueholder.AnalysisQaEvent; import us.mn.state.health.lims.citystatezip.dao.CityStateZipDAO; import us.mn.state.health.lims.citystatezip.daoimpl.CityStateZipDAOImpl; import us.mn.state.health.lims.citystatezip.valueholder.CityStateZip; 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.provider.validation.CityStateZipComboValidationProvider; import us.mn.state.health.lims.common.provider.validation.CityValidationProvider; import us.mn.state.health.lims.common.provider.validation.HumanSampleSourceValidationProvider; import us.mn.state.health.lims.common.provider.validation.HumanSampleTypeValidationProvider; import us.mn.state.health.lims.common.provider.validation.OrganizationLocalAbbreviationValidationProvider; import us.mn.state.health.lims.common.provider.validation.ProjectIdOrNameValidationProvider; import us.mn.state.health.lims.common.provider.validation.StateValidationProvider; import us.mn.state.health.lims.common.provider.validation.ZipValidationProvider; import us.mn.state.health.lims.common.services.StatusService; import us.mn.state.health.lims.common.services.StatusService.SampleStatus; import us.mn.state.health.lims.common.util.DateUtil; 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.validator.ActionError; import us.mn.state.health.lims.hibernate.HibernateUtil; import us.mn.state.health.lims.login.valueholder.UserSessionData; 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.patient.valueholder.Patient; 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.project.dao.ProjectDAO; import us.mn.state.health.lims.project.daoimpl.ProjectDAOImpl; import us.mn.state.health.lims.project.valueholder.Project; import us.mn.state.health.lims.provider.dao.ProviderDAO; import us.mn.state.health.lims.provider.daoimpl.ProviderDAOImpl; import us.mn.state.health.lims.provider.valueholder.Provider; import us.mn.state.health.lims.qaevent.dao.QaEventDAO; import us.mn.state.health.lims.qaevent.daoimpl.QaEventDAOImpl; import us.mn.state.health.lims.qaevent.valueholder.QaEvent; import us.mn.state.health.lims.sample.dao.SampleDAO; import us.mn.state.health.lims.sample.daoimpl.SampleDAOImpl; import us.mn.state.health.lims.sample.valueholder.Sample; 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.sampleproject.dao.SampleProjectDAO; import us.mn.state.health.lims.sampleproject.daoimpl.SampleProjectDAOImpl; import us.mn.state.health.lims.sampleproject.valueholder.SampleProject; import us.mn.state.health.lims.sourceofsample.dao.SourceOfSampleDAO; import us.mn.state.health.lims.sourceofsample.daoimpl.SourceOfSampleDAOImpl; 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; /** * @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 HumanSampleTwoUpdateAction extends BaseAction { private boolean isNew = false; protected ActionForward performAction(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { // The first job is to determine if we are coming to this action with an // ID parameter in the request. If there is no parameter, we are // creating a new Sample. // If there is a parameter present, we should bring up an existing // Sample to edit. String forward = FWD_SUCCESS; request.setAttribute(ALLOW_EDITS_KEY, "true"); String id = request.getParameter(ID); if (StringUtil.isNullorNill(id) || "0".equals(id)) { isNew = true; } else { isNew = false; } BaseActionForm dynaForm = (BaseActionForm) form; // first get the accessionNumber and whether we are on blank page or not String accessionNumber = (String) dynaForm.get("accessionNumber"); String blankscreen = (String) dynaForm.get("blankscreen"); String start = (String) request.getParameter("startingRecNo"); String typeOfSample = (String) dynaForm.get("typeOfSampleDesc"); //bugzilla 2470, unused //String sourceOfSample = (String) dynaForm.get("sourceOfSampleDesc"); List typeOfSamples = new ArrayList(); List sourceOfSamples = new ArrayList(); if (dynaForm.get("typeOfSamples") != null) { typeOfSamples = (List) dynaForm.get("typeOfSamples"); } else { TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl(); typeOfSamples = typeOfSampleDAO.getAllTypeOfSamples(); } if (dynaForm.get("sourceOfSamples") != null) { sourceOfSamples = (List) dynaForm.get("sourceOfSamples"); } else { SourceOfSampleDAO sourceOfSampleDAO = new SourceOfSampleDAOImpl(); sourceOfSamples = sourceOfSampleDAO.getAllSourceOfSamples(); } HashMap humanSampleOneMap = new HashMap(); if (dynaForm.get("humanSampleOneMap") != null) { humanSampleOneMap = (HashMap) dynaForm.get("humanSampleOneMap"); } String projectIdOrName = (String) dynaForm.get("projectIdOrName"); String project2IdOrName = (String) dynaForm.get("project2IdOrName"); String projectNameOrId = (String) dynaForm.get("projectNameOrId"); String project2NameOrId = (String) dynaForm.get("project2NameOrId"); String projectId = null; String project2Id = null; if (projectIdOrName != null && projectNameOrId != null) { try { Integer i = Integer.valueOf(projectIdOrName); projectId = projectIdOrName; } catch (NumberFormatException nfe) { //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "performAction()", nfe.toString()); projectId = projectNameOrId; } } if (project2IdOrName != null && project2NameOrId != null) { try { Integer i = Integer.valueOf(project2IdOrName); project2Id = project2IdOrName; } catch (NumberFormatException nfe) { //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "performAction()", nfe.toString()); project2Id = project2NameOrId; } } //bugzilla 2028 //bugzilla 2069 String submitterNumber = (String) dynaForm.get("organizationLocalAbbreviation"); // set current date for validation of dates Date today = Calendar.getInstance().getTime(); Locale locale = (Locale) request.getSession().getAttribute("org.apache.struts.action.LOCALE"); String dateAsText = DateUtil.formatDateAsText(today, locale); PersonDAO personDAO = new PersonDAOImpl(); PatientDAO patientDAO = new PatientDAOImpl(); ProviderDAO providerDAO = new ProviderDAOImpl(); SampleDAO sampleDAO = new SampleDAOImpl(); SampleItemDAO sampleItemDAO = new SampleItemDAOImpl(); SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl(); SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl(); AnalysisDAO analysisDAO = new AnalysisDAOImpl(); SampleProjectDAO sampleProjectDAO = new SampleProjectDAOImpl(); ProjectDAO projectDAO = new ProjectDAOImpl(); AnalysisQaEventDAO analysisQaEventDAO = new AnalysisQaEventDAOImpl(); QaEventDAO qaEventDAO = new QaEventDAOImpl(); Patient patient = new Patient(); Person person = new Person(); Provider provider = new Provider(); Person providerPerson = new Person(); Sample sample = new Sample(); SampleHuman sampleHuman = new SampleHuman(); SampleOrganization sampleOrganization = new SampleOrganization(); List oldSampleProjects = new ArrayList(); List newSampleProjects = new ArrayList(); SampleItem sampleItem = new SampleItem(); sampleItem.setStatusId(StatusService.getInstance().getStatusID(SampleStatus.Entered)); // TODO need to populate this with tests entered in HSE I List analyses = new ArrayList(); ActionMessages errors = null; // validate on server-side sample accession number try { errors = new ActionMessages(); errors = validateAccessionNumber(request, errors, dynaForm); // System.out.println("Just validated accessionNumber"); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "performAction()", e.toString()); ActionError error = new ActionError("errors.ValidationException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } // System.out.println("This is errors after validation of accn Number " // + errors); if (errors != null && errors.size() > 0) { saveErrors(request, errors); // initialize the form but retain the invalid accessionNumber dynaForm.initialize(mapping); dynaForm.set("accessionNumber", accessionNumber); // repopulate lists PropertyUtils.setProperty(dynaForm, "typeOfSamples", typeOfSamples); PropertyUtils.setProperty(dynaForm, "sourceOfSamples", sourceOfSamples); PropertyUtils.setProperty(dynaForm, "blankscreen", "true"); request.setAttribute(ALLOW_EDITS_KEY, "false"); return mapping.findForward(FWD_FAIL); } // System.out.println("Now try to get data for accession number "); errors = dynaForm.validate(mapping, request); try { errors = validateAll(request, errors, dynaForm, humanSampleOneMap); } catch (Exception e) { //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "performAction()", e.toString()); ActionError error = new ActionError("errors.ValidationException", null, null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } // end of zip/city combination check if (errors != null && errors.size() > 0) { saveErrors(request, errors); // since we forward to jsp - not Action we don't need to // repopulate // the lists here return mapping.findForward(FWD_FAIL); } // GET ORIGINAL DATA try { sample.setAccessionNumber(accessionNumber); sampleDAO.getSampleByAccessionNumber(sample); if (!StringUtil.isNullorNill(sample.getId())) { sampleHuman.setSampleId(sample.getId()); sampleHumanDAO.getDataBySample(sampleHuman); sampleOrganization.setSampleId(sample.getId()); sampleOrganizationDAO.getDataBySample(sampleOrganization); //bugzilla 1773 need to store sample not sampleId for use in sorting sampleItem.setSample(sample); sampleItemDAO.getDataBySample(sampleItem); patient.setId(sampleHuman.getPatientId()); patientDAO.getData(patient); person = patient.getPerson(); personDAO.getData(person); provider.setId(sampleHuman.getProviderId()); providerDAO.getData(provider); providerPerson = provider.getPerson(); personDAO.getData(providerPerson); //bugzilla 2227 analyses = analysisDAO.getMaxRevisionAnalysesBySample(sampleItem); oldSampleProjects = sample.getSampleProjects(); } } catch (LIMSRuntimeException lre) { // if error then forward to fail and don't update to blank page // = false //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "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); } TypeOfSample typeOfSamp = null; // get the right typeOfSamp to update sampleitem with for (int i = 0; i < typeOfSamples.size(); i++) { TypeOfSample s = (TypeOfSample) typeOfSamples.get(i); // if (s.getId().equals(typeOfSampleId)) { if (s.getDescription().equalsIgnoreCase(typeOfSample)) { typeOfSamp = s; break; } } // fixed in bugzilla 2470, unused //SourceOfSample sourceOfSamp = null; /* // get the right sourceOfSamp to update sampleitem with for (int i = 0; i < sourceOfSamples.size(); i++) { SourceOfSample s = (SourceOfSample) sourceOfSamples.get(i); // if (s.getId().equals(sourceOfSampleId)) { if (s.getDescription().equalsIgnoreCase(sourceOfSample)) { sourceOfSamp = s; break; } } */ // System.out.println("This is entered date before update from form // " // + sample.getEnteredDate() // + sample.getEnteredDateForDisplay()); // UPDATE DATA FROM FORM // populate valueholder from form PropertyUtils.copyProperties(sample, dynaForm); PropertyUtils.copyProperties(person, dynaForm); PropertyUtils.copyProperties(patient, dynaForm); PropertyUtils.copyProperties(provider, dynaForm); PropertyUtils.copyProperties(sampleHuman, dynaForm); PropertyUtils.copyProperties(sampleOrganization, dynaForm); PropertyUtils.copyProperties(sampleItem, dynaForm); Organization org = new Organization(); org.setOrganizationLocalAbbreviation((String) dynaForm.get("organizationLocalAbbreviation")); OrganizationDAO organizationDAO = new OrganizationDAOImpl(); org = organizationDAO.getOrganizationByLocalAbbreviation(org, true); sampleOrganization.setOrganization(org); // if there was a first sampleProject id entered // if there was a first sampleProject id entered if (!StringUtil.isNullorNill(projectId)) { SampleProject sampleProject = new SampleProject(); Project p = new Project(); //bugzilla 2438 p.setLocalAbbreviation(projectId); p = projectDAO.getProjectByLocalAbbreviation(p, true); sampleProject.setProject(p); sampleProject.setSample(sample); sampleProject.setIsPermanent(NO); newSampleProjects.add(sampleProject); } // in case there was a second sampleProject id entered if (!StringUtil.isNullorNill(project2Id)) { SampleProject sampleProject2 = new SampleProject(); Project p2 = new Project(); //bugzilla 2438 p2.setLocalAbbreviation(project2Id); p2 = projectDAO.getProjectByLocalAbbreviation(p2, true); sampleProject2.setProject(p2); sampleProject2.setSample(sample); sampleProject2.setIsPermanent(NO); newSampleProjects.add(sampleProject2); } // set the provider person manually as we have two Person // valueholders // to populate and copyProperties() can only handle one per form providerPerson.setFirstName((String) dynaForm.get("providerFirstName")); providerPerson.setLastName((String) dynaForm.get("providerLastName")); // format workPhone for storage String workPhone = (String) dynaForm.get("providerWorkPhone"); String ext = (String) dynaForm.get("providerWorkPhoneExtension"); String formattedPhone = StringUtil.formatPhone(workPhone, ext); // phone is stored as 999/999-9999.9999 // area code/phone - number.extension providerPerson.setWorkPhone(formattedPhone); //bugzilla 1701 blank out provider.externalId - this is copied from patient //externalId which is not related...and we currently don't enter an externalId for //provider on this screen provider.setExternalId(BLANK); // set collection time String time = (String) dynaForm.get("collectionTimeForDisplay"); if (StringUtil.isNullorNill(time)) { time = "00:00"; } sample.setCollectionTimeForDisplay(time); Timestamp d = sample.getCollectionDate(); //bgm - bugzilla 1586 check for null date if (null != d) { if (time.indexOf(":") > 0) { //bugzilla 1857 deprecated stuff Calendar cal = Calendar.getInstance(); cal.setTime(d); cal.set(Calendar.HOUR_OF_DAY, Integer.valueOf(time.substring(0, 2)).intValue()); cal.set(Calendar.MINUTE, Integer.valueOf(time.substring(3, 5)).intValue()); //d.setHours(Integer.valueOf(time.substring(0, 2)).intValue()); //d.setMinutes(Integer.valueOf(time.substring(3, 5)).intValue()); d = new Timestamp(cal.getTimeInMillis()); sample.setCollectionDate(d); } } // sampleItem sampleItem.setSortOrder("1"); // set the typeOfSample sampleItem.setTypeOfSample(typeOfSamp); // set the sourceOfSample // fixed in bugzilla 2470 unused //sampleItem.setSourceOfSample(sourceOfSamp); sample.setSampleProjects(newSampleProjects); // get entered by through system (when we have login functionality) // removed per Christina 3/03/2006 // sample.setEnteredBy("diane"); //get sysUserId from login module UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA); String sysUserId = String.valueOf(usd.getSystemUserId()); org.hibernate.Transaction tx = HibernateUtil.getSession().beginTransaction(); List newIds = new ArrayList(); List oldIds = new ArrayList(); if (newSampleProjects != null) { for (int i = 0; i < newSampleProjects.size(); i++) { SampleProject sp = (SampleProject) newSampleProjects.get(i); newIds.add(sp.getId()); } } if (oldSampleProjects != null) { List listOfOldOnesToRemove = new ArrayList(); for (int i = 0; i < oldSampleProjects.size(); i++) { SampleProject sp = (SampleProject) oldSampleProjects.get(i); oldIds.add(sp.getId()); if (!newIds.contains(sp.getId())) { // remove ones that are to be deleted listOfOldOnesToRemove.add(new Integer(i)); } } int decreaseOSPIndexBy = 0; int decreaseOIIndexBy = 0; List listOfSampleProjectObjectsToDelete = new ArrayList(); for (int i = 0; i < listOfOldOnesToRemove.size(); i++) { SampleProject sp = (SampleProject) oldSampleProjects .remove(((Integer) listOfOldOnesToRemove.get(i)).intValue() - decreaseOSPIndexBy++); //bugzilla 1926 sp.setSysUserId(sysUserId); listOfSampleProjectObjectsToDelete.add(sp); oldIds.remove(((Integer) listOfOldOnesToRemove.get(i)).intValue() - decreaseOIIndexBy++); } sampleProjectDAO.deleteData(listOfSampleProjectObjectsToDelete); } if (newSampleProjects != null) { for (int j = 0; j < newSampleProjects.size(); j++) { SampleProject saPr = (SampleProject) newSampleProjects.get(j); int index = oldIds.indexOf(saPr.getId()); if (index >= 0) { SampleProject sampleProjectClone = (SampleProject) oldSampleProjects.get(index); PropertyUtils.copyProperties(sampleProjectClone, saPr); Sample smplClone = (Sample) sampleProjectClone.getSample(); sampleProjectClone.setSample(smplClone); Project pClone = (Project) sampleProjectClone.getProject(); sampleProjectClone.setProject(pClone); PropertyUtils.setProperty(sampleProjectClone, "lastupdated", (Timestamp) dynaForm.get("sampleProject1Lastupdated")); sampleProjectClone.setSysUserId(sysUserId); sampleProjectDAO.updateData(sampleProjectClone); oldSampleProjects.set(index, sampleProjectClone); } else { SampleProject sampleProjectClone = new SampleProject(); PropertyUtils.copyProperties(sampleProjectClone, saPr); Sample smplClone = (Sample) sampleProjectClone.getSample(); sampleProjectClone.setSample(smplClone); Project pClone = (Project) sampleProjectClone.getProject(); sampleProjectClone.setProject(pClone); PropertyUtils.setProperty(sampleProjectClone, "lastupdated", (Timestamp) dynaForm.get("sampleProject2Lastupdated")); //bugzilla 1926 sampleProjectClone.setSysUserId(sysUserId); sampleProjectDAO.insertData(sampleProjectClone); oldSampleProjects.add(sampleProjectClone); } } } sample.setSampleProjects(oldSampleProjects); // END DIANE try { // set last updated from form PropertyUtils.setProperty(person, "lastupdated", (Timestamp) dynaForm.get("personLastupdated")); PropertyUtils.setProperty(patient, "lastupdated", (Timestamp) dynaForm.get("patientLastupdated")); PropertyUtils.setProperty(sample, "lastupdated", (Timestamp) dynaForm.get("lastupdated")); PropertyUtils.setProperty(providerPerson, "lastupdated", (Timestamp) dynaForm.get("providerPersonLastupdated")); PropertyUtils.setProperty(provider, "lastupdated", (Timestamp) dynaForm.get("providerLastupdated")); PropertyUtils.setProperty(sampleItem, "lastupdated", (Timestamp) dynaForm.get("sampleItemLastupdated")); PropertyUtils.setProperty(sampleHuman, "lastupdated", (Timestamp) dynaForm.get("sampleHumanLastupdated")); PropertyUtils.setProperty(sampleOrganization, "lastupdated", (Timestamp) dynaForm.get("sampleOrganizationLastupdated")); //System.out.println("This is person ts " + person.getLastupdated().toLocaleString()); person.setSysUserId(sysUserId); patient.setSysUserId(sysUserId); providerPerson.setSysUserId(sysUserId); provider.setSysUserId(sysUserId); sample.setSysUserId(sysUserId); sampleHuman.setSysUserId(sysUserId); sampleOrganization.setSysUserId(sysUserId); sampleItem.setSysUserId(sysUserId); personDAO.updateData(person); patient.setPerson(person); //System.out.println("This is patient ts " + patient.getLastupdated().toLocaleString()); patientDAO.updateData(patient); personDAO.updateData(providerPerson); provider.setPerson(providerPerson); providerDAO.updateData(provider); sampleHuman.setSampleId(sample.getId()); sampleHuman.setPatientId(patient.getId()); sampleHuman.setProviderId(provider.getId()); sampleHumanDAO.updateData(sampleHuman); sampleOrganization.setSampleId(sample.getId()); sampleOrganization.setSample(sample); sampleOrganizationDAO.updateData(sampleOrganization); //bugzilla 2470 SampleItem si = new SampleItem(); si.setSample(sample); sampleItemDAO.getDataBySample(si); sampleItem.setId(si.getId()); sampleItem.setSourceOfSampleId(si.getSourceOfSampleId()); sampleItem.setSourceOther(si.getSourceOther()); //bugzilla 1773 need to store sample not sampleId for use in sorting sampleItem.setSample(sample); sampleItemDAO.updateData(sampleItem); boolean allAnalysesReleased = true; //bugzilla 2028 get the possible qa events QaEvent qaEventForNoCollectionDate = new QaEvent(); qaEventForNoCollectionDate .setQaEventName(SystemConfiguration.getInstance().getQaEventCodeForRequestNoCollectionDate()); qaEventForNoCollectionDate = qaEventDAO.getQaEventByName(qaEventForNoCollectionDate); QaEvent qaEventForNoSampleType = new QaEvent(); qaEventForNoSampleType .setQaEventName(SystemConfiguration.getInstance().getQaEventCodeForRequestNoSampleType()); qaEventForNoSampleType = qaEventDAO.getQaEventByName(qaEventForNoSampleType); QaEvent qaEventForUnknownSubmitter = new QaEvent(); qaEventForUnknownSubmitter .setQaEventName(SystemConfiguration.getInstance().getQaEventCodeForRequestUnknownSubmitter()); qaEventForUnknownSubmitter = qaEventDAO.getQaEventByName(qaEventForUnknownSubmitter); //end bugzilla 2028 // Analysis table for (int i = 0; i < analyses.size(); i++) { Analysis analysis = (Analysis) analyses.get(i); //bugzilla 1942: if all analyses for this sample have already gone through results verification and analysis.status is released // then change sample.status to released also if (StringUtil.isNullorNill(analysis.getStatus()) || !analysis.getStatus() .equals(SystemConfiguration.getInstance().getAnalysisStatusReleased())) { allAnalysesReleased = false; } analysis.setSampleItem(sampleItem); analysis.setSysUserId(sysUserId); //bugzilla 2028 QA_EVENT COLLECTIONDATE if (sample.getCollectionDate() == null) { AnalysisQaEvent analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForNoCollectionDate); analysisQaEvent = analysisQaEventDAO.getAnalysisQaEventByAnalysisAndQaEvent(analysisQaEvent); if (analysisQaEvent == null) { analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForNoCollectionDate); analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.insertData(analysisQaEvent); } else { if (analysisQaEvent.getCompletedDate() != null) { analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.updateData(analysisQaEvent); } } } //bugzilla 2028 QA_EVENT SAMPLETYPE if (typeOfSample.equals(SAMPLE_TYPE_NOT_GIVEN)) { AnalysisQaEvent analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForNoSampleType); analysisQaEvent = analysisQaEventDAO.getAnalysisQaEventByAnalysisAndQaEvent(analysisQaEvent); if (analysisQaEvent == null) { analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForNoSampleType); analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.insertData(analysisQaEvent); } else { if (analysisQaEvent.getCompletedDate() != null) { analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.updateData(analysisQaEvent); } } } //bugzilla 2028 QA_EVENT UNKNOWN SUBMITTER if (submitterNumber .equals(SystemConfiguration.getInstance().getUnknownSubmitterNumberForQaEvent())) { AnalysisQaEvent analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForUnknownSubmitter); analysisQaEvent = analysisQaEventDAO.getAnalysisQaEventByAnalysisAndQaEvent(analysisQaEvent); if (analysisQaEvent == null) { analysisQaEvent = new AnalysisQaEvent(); analysisQaEvent.setAnalysis(analysis); analysisQaEvent.setQaEvent(qaEventForUnknownSubmitter); analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.insertData(analysisQaEvent); } else { if (analysisQaEvent.getCompletedDate() != null) { analysisQaEvent.setCompletedDate(null); analysisQaEvent.setSysUserId(sysUserId); analysisQaEventDAO.updateData(analysisQaEvent); } } } analysisDAO.updateData(analysis); } //bugzilla 1942 if (analyses.size() > 0 && allAnalysesReleased) { sample.setStatus(SystemConfiguration.getInstance().getSampleStatusReleased()); sample.setReleasedDateForDisplay(dateAsText); } else { sample.setStatus(SystemConfiguration.getInstance().getSampleStatusEntry2Complete()); } sampleDAO.updateData(sample); tx.commit(); // done updating return to menu blankscreen = "false"; forward = FWD_CLOSE; } catch (LIMSRuntimeException lre) { //bugzilla 2154 LogEvent.logError("HumanSampleTwoUpdateAction", "performAction()", lre.toString()); tx.rollback(); // if error then forward to fail and don't update to blank page // = false errors = new ActionMessages(); ActionError error = null; if (lre.getException() instanceof org.hibernate.StaleObjectStateException) { // how can I get popup instead of struts error at the top of // page? // ActionMessages errors = dynaForm.validate(mapping, // request); error = new ActionError("errors.OptimisticLockException", null, null); } else { error = new ActionError("errors.UpdateException", null, null); } errors.add(ActionMessages.GLOBAL_MESSAGE, error); saveErrors(request, errors); request.setAttribute(Globals.ERROR_KEY, errors); request.setAttribute(ALLOW_EDITS_KEY, "false"); forward = FWD_FAIL; } finally { HibernateUtil.closeSession(); } if (forward.equals(FWD_FAIL)) return mapping.findForward(FWD_FAIL); PropertyUtils.setProperty(dynaForm, "typeOfSamples", typeOfSamples); PropertyUtils.setProperty(dynaForm, "sourceOfSamples", sourceOfSamples); PropertyUtils.setProperty(dynaForm, "humanSampleOneMap", humanSampleOneMap); if ("true".equalsIgnoreCase(request.getParameter("close"))) { forward = FWD_CLOSE; } if (sample.getId() != null && !sample.getId().equals("0")) { request.setAttribute(ID, sample.getId()); } if (forward.equals(FWD_SUCCESS)) { request.setAttribute("menuDefinition", "default"); } // return getForward(mapping.findForward(forward), id, start); return mapping.findForward(forward); } protected String getPageTitleKey() { if (isNew) { return "human.sample.two.add.title"; } else { return "human.sample.two.edit.title"; } } protected String getPageSubtitleKey() { if (isNew) { return "human.sample.two.add.title"; } else { return "human.sample.two.edit.title"; } } protected ActionMessages validateZipCity(ActionMessages errors, String zipCode, String city) throws Exception { //bugzilla 1545 CityStateZipDAO cityStateZipDAO = new CityStateZipDAOImpl(); CityStateZip cityStateZip = new CityStateZip(); // use 5-digit zipcode for validation String zc5Dig = null; zc5Dig = zipCode.substring(0, 5); cityStateZip.setZipCode(zc5Dig); cityStateZip.setCity(city); cityStateZip = cityStateZipDAO.getCityStateZipByCityAndZipCode(cityStateZip); if (cityStateZip == null) { errors.add(ActionMessages.GLOBAL_MESSAGE, new ActionError("humansampleone.validation.zipCity", null, null)); } return errors; } // compares values against HashMap of HSE1 values before going to dbase to // revalidate submitted values //bugzilla 1765 changes to city state zip validation protected ActionMessages validateAll(HttpServletRequest request, ActionMessages errors, BaseActionForm dynaForm, HashMap humanSampleOneMap) throws Exception { String result; String messageKey; ProjectIdOrNameValidationProvider projIdValidator = new ProjectIdOrNameValidationProvider(); String projNum = (String) dynaForm.get("projectIdOrName"); if (!StringUtil.isNullorNill(projNum)) { // project ID validation against database (reusing ajax // validation logic) result = compareAgainstHSE1HashMap(humanSampleOneMap, projNum, "projectId"); if (result.equals(INVALID)) { result = projIdValidator.validate(projNum); messageKey = "humansampleone.projectNumber"; if (result.equals(INVALID)) { String projName = (String) dynaForm.get("projectNameOrId"); result = compareAgainstHSE1HashMap(humanSampleOneMap, projName, "projectName"); if (result.equals(INVALID)) { result = projIdValidator.validate(projName); if (result.equals(INVALID)) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } } } String proj2Num = (String) dynaForm.get("project2IdOrName"); if (!StringUtil.isNullorNill(proj2Num)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, proj2Num, "projectId2"); if (result.equals(INVALID)) { result = projIdValidator.validate(proj2Num); messageKey = "humansampleone.project2Number"; if (result.equals(INVALID)) { String proj2Name = (String) dynaForm.get("project2NameOrId"); result = compareAgainstHSE1HashMap(humanSampleOneMap, proj2Name, "projectName2"); if (result.equals(INVALID)) { result = projIdValidator.validate(proj2Name); if (result.equals(INVALID)) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } } } // accession number validation against database (reusing ajax // validation logic) String accnNum = (String) dynaForm.get("accessionNumber"); if (!StringUtil.isNullorNill(accnNum)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, accnNum, "accessionNumber"); if (result.equals(INVALID)) { errors = validateAccessionNumber(request, errors, dynaForm); } } // organization ID (submitter) validation against database (reusing ajax // validation logic) //bugzilla 2069 String orgLocalAbbreviation = (String) dynaForm.get("organizationLocalAbbreviation"); if (!StringUtil.isNullorNill(orgLocalAbbreviation)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, orgLocalAbbreviation, "organizationLocalAbbreviation"); if (result.equals(INVALID)) { //bugzilla 2531 OrganizationLocalAbbreviationValidationProvider organiationLocalAbbreviationValidator = new OrganizationLocalAbbreviationValidationProvider(); result = organiationLocalAbbreviationValidator .validate((String) dynaForm.get("organizationLocalAbbreviation"), null); messageKey = "humansampleone.provider.organization.localAbbreviation"; if (result.equals(INVALID)) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } boolean stateValid = true; String state = (String) dynaForm.get("state"); if (!StringUtil.isNullorNill(state)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, state, "state"); if (result.equals(INVALID)) { // state validation against database (reusing ajax validation // logic StateValidationProvider stateValidator = new StateValidationProvider(); result = stateValidator.validate(state); messageKey = "person.state"; if (result.equals(INVALID)) { stateValid = false; ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } boolean cityValid = true; String city = (String) dynaForm.get("city"); if (!StringUtil.isNullorNill(city)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, city, "city"); if (result.equals(INVALID)) { // city validation against database (reusing ajax validation // logic CityValidationProvider cityValidator = new CityValidationProvider(); result = cityValidator.validate(city); messageKey = "person.city"; if (result.equals(INVALID)) { cityValid = false; ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } boolean zipValid = true; String zip = (String) dynaForm.get("zipCode"); if (!StringUtil.isNullorNill(zip)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, zip, "zipCode"); if (result.equals(INVALID)) { // zip validation against database (reusing ajax validation // logic ZipValidationProvider zipValidator = new ZipValidationProvider(); result = zipValidator.validate((String) dynaForm.get("zipCode")); messageKey = "person.zipCode"; if (result.equals(INVALID)) { zipValid = false; ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } if (cityValid && stateValid && zipValid) { String messageKey1 = "person.city"; String messageKey2 = "person.zipCode"; String messageKey3 = "person.state"; CityStateZipComboValidationProvider cityStateZipComboValidator = new CityStateZipComboValidationProvider(); result = cityStateZipComboValidator.validate((String) dynaForm.get("city"), (String) dynaForm.get("state"), (String) dynaForm.get("zipCode")); // combination is invalid if result is invalid if ("invalid".equals(result)) { ActionError error = new ActionError("errors.combo.3.invalid", getMessageForKey(messageKey1), getMessageForKey(messageKey2), getMessageForKey(messageKey3), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } // sample type validation against database (reusing ajax validation // logic String sampleType = (String) dynaForm.get("typeOfSampleDesc"); if (!StringUtil.isNullorNill(sampleType)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, sampleType, "typeOfSampleDesc"); if (result.equals(INVALID)) { HumanSampleTypeValidationProvider typeValidator = new HumanSampleTypeValidationProvider(); result = typeValidator.validate(sampleType); messageKey = "sampleitem.typeOfSample"; if (result.equals(INVALID)) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } String sampleSource = (String) dynaForm.get("sourceOfSampleDesc"); if (!StringUtil.isNullorNill(sampleSource)) { result = compareAgainstHSE1HashMap(humanSampleOneMap, sampleSource, "sourceOfSampleDesc"); // sample source validation against database (reusing ajax // validation // logic if (result.equals(INVALID)) { HumanSampleSourceValidationProvider sourceValidator = new HumanSampleSourceValidationProvider(); result = sourceValidator.validate(sampleSource); messageKey = "sampleitem.sourceOfSample"; if (result.equals(INVALID)) { ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null); errors.add(ActionMessages.GLOBAL_MESSAGE, error); } } } return errors; } private String compareAgainstHSE1HashMap(HashMap humanSampleOneMap, String value, String key) { if (humanSampleOneMap.get(key).equals(value)) { return VALID; } else { return INVALID; } } }