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) ITECH, University of Washington, Seattle WA. All Rights Reserved. * */ package us.mn.state.health.lims.common.services; import org.apache.commons.validator.GenericValidator; import org.dom4j.Document; import org.dom4j.DocumentException; import org.dom4j.DocumentHelper; import org.dom4j.Element; import us.mn.state.health.lims.common.formfields.FormFields; import us.mn.state.health.lims.common.formfields.FormFields.Field; 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.observationhistory.valueholder.ObservationHistory; 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.panel.dao.PanelDAO; import us.mn.state.health.lims.panel.daoimpl.PanelDAOImpl; import us.mn.state.health.lims.panel.valueholder.Panel; import us.mn.state.health.lims.panelitem.dao.PanelItemDAO; import us.mn.state.health.lims.panelitem.daoimpl.PanelItemDAOImpl; import us.mn.state.health.lims.panelitem.valueholder.PanelItem; import us.mn.state.health.lims.sample.valueholder.Sample; import us.mn.state.health.lims.sampleitem.valueholder.SampleItem; import us.mn.state.health.lims.test.valueholder.Test; import us.mn.state.health.lims.typeofsample.dao.TypeOfSampleDAO; import us.mn.state.health.lims.typeofsample.daoimpl.TypeOfSampleDAOImpl; import java.util.*; public class SampleAddService { private final String xml; private final String currentUserId; private final Sample sample; private final List<SampleTestCollection> sampleItemsTests = new ArrayList<SampleTestCollection>(); private final String receivedDate; private final Map<String, Panel> panelIdPanelMap = new HashMap<String, Panel>(); private boolean xmlProcessed = false; private int sampleItemIdIndex = 0; private static final boolean USE_INITIAL_SAMPLE_CONDITION = FormFields.getInstance() .useField(Field.InitialSampleCondition); private static final boolean USE_RECEIVE_DATE_FOR_COLLECTION_DATE = !FormFields.getInstance() .useField(Field.CollectionDate); private static final String INITIAL_CONDITION_OBSERVATION_ID; private static final TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl(); private static final PanelDAO panelDAO = new PanelDAOImpl(); private static final PanelItemDAO panelItemDAO = new PanelItemDAOImpl(); static { ObservationHistoryTypeDAO ohtDAO = new ObservationHistoryTypeDAOImpl(); INITIAL_CONDITION_OBSERVATION_ID = getObservationHistoryTypeId(ohtDAO, "initialSampleCondition"); } private static String getObservationHistoryTypeId(ObservationHistoryTypeDAO ohtDAO, String name) { ObservationHistoryType oht; oht = ohtDAO.getByName(name); if (oht != null) { return oht.getId(); } return null; } public SampleAddService(String xml, String currentUserId, Sample sample, String receiveDate) { this.xml = xml; this.currentUserId = currentUserId; this.sample = sample; this.receivedDate = receiveDate; } public List<SampleTestCollection> createSampleTestCollection() { xmlProcessed = true; String collectionDateFromRecieveDate = null; if (USE_RECEIVE_DATE_FOR_COLLECTION_DATE) { collectionDateFromRecieveDate = receivedDate + " 00:00:00"; } try { Document sampleDom = DocumentHelper.parseText(xml); for (@SuppressWarnings("rawtypes") Iterator i = sampleDom.getRootElement().elementIterator("sample"); i.hasNext();) { sampleItemIdIndex++; Element sampleItem = (Element) i.next(); String testIDs = sampleItem.attributeValue("tests"); String panelIDs = sampleItem.attributeValue("panels"); Map<String, String> testIdToUserSectionMap = getTestIdToSelectionMap( sampleItem.attributeValue("testSectionMap")); Map<String, String> testIdToSampleTypeMap = getTestIdToSelectionMap( sampleItem.attributeValue("testSampleTypeMap")); String collectionDate = sampleItem.attributeValue("date").trim(); String collectionTime = sampleItem.attributeValue("time").trim(); String collectionDateTime = null; if (!GenericValidator.isBlankOrNull(collectionDate) && !GenericValidator.isBlankOrNull(collectionTime)) collectionDateTime = collectionDate + " " + collectionTime; else if (!GenericValidator.isBlankOrNull(collectionDate) && GenericValidator.isBlankOrNull(collectionTime)) collectionDateTime = collectionDate + " 00:00"; augmentPanelIdToPanelMap(panelIDs); List<ObservationHistory> initialConditionList = null; if (USE_INITIAL_SAMPLE_CONDITION) { initialConditionList = addInitialSampleConditions(sampleItem, initialConditionList); } SampleItem item = new SampleItem(); item.setSysUserId(currentUserId); item.setSample(sample); item.setTypeOfSample(typeOfSampleDAO.getTypeOfSampleById(sampleItem.attributeValue("sampleID"))); item.setSortOrder(Integer.toString(sampleItemIdIndex)); item.setStatusId(StatusService.getInstance().getStatusID(SampleStatus.Entered)); item.setCollector(sampleItem.attributeValue("collector")); if (!GenericValidator.isBlankOrNull(collectionDateTime)) item.setCollectionDate(DateUtil.convertStringDateToTimestamp(collectionDateTime)); List<Test> tests = new ArrayList<Test>(); addTests(testIDs, tests); sampleItemsTests.add(new SampleTestCollection(item, tests, USE_RECEIVE_DATE_FOR_COLLECTION_DATE ? collectionDateFromRecieveDate : collectionDateTime, initialConditionList, testIdToUserSectionMap, testIdToSampleTypeMap)); } } catch (DocumentException e) { e.printStackTrace(); } return sampleItemsTests; } public Panel getPanelForTest(Test test) throws IllegalThreadStateException { if (!xmlProcessed) { throw new IllegalThreadStateException("createSampleTestCollection must be called first"); } List<PanelItem> panelItems = panelItemDAO.getPanelItemByTestId(test.getId()); for (PanelItem panelItem : panelItems) { Panel panel = panelIdPanelMap.get(panelItem.getPanel().getId()); if (panel != null) { return panel; } } return null; } public void setInitialSampleItemOrderValue(int initialValue) { sampleItemIdIndex = initialValue; } private Map<String, String> getTestIdToSelectionMap(String mapPairs) { Map<String, String> sectionMap = new HashMap<String, String>(); String[] maps = mapPairs.split(","); for (String map : maps) { String[] mapping = map.split(":"); if (mapping.length == 2) { sectionMap.put(mapping[0].trim(), mapping[1].trim()); } } return sectionMap; } private void augmentPanelIdToPanelMap(String panelIDs) { if (panelIDs != null) { String[] ids = panelIDs.split(","); for (String id : ids) { if (!GenericValidator.isBlankOrNull(id)) { panelIdPanelMap.put(id, panelDAO.getPanelById(id)); } } } } private List<ObservationHistory> addInitialSampleConditions(Element sampleItem, List<ObservationHistory> initialConditionList) { String initialSampleConditionIdString = sampleItem.attributeValue("initialConditionIds"); if (!GenericValidator.isBlankOrNull(initialSampleConditionIdString)) { String[] initialSampleConditionIds = initialSampleConditionIdString.split(","); initialConditionList = new ArrayList<ObservationHistory>(); for (int j = 0; j < initialSampleConditionIds.length; ++j) { ObservationHistory initialSampleConditions = new ObservationHistory(); initialSampleConditions.setValue(initialSampleConditionIds[j]); initialSampleConditions.setValueType(ObservationHistory.ValueType.DICTIONARY); initialSampleConditions.setObservationHistoryTypeId(INITIAL_CONDITION_OBSERVATION_ID); initialConditionList.add(initialSampleConditions); } } return initialConditionList; } private void addTests(String testIDs, List<Test> tests) { StringTokenizer tokenizer = new StringTokenizer(testIDs, ","); while (tokenizer.hasMoreTokens()) { Test test = new Test(); test.setId(tokenizer.nextToken().trim()); tests.add(test); } } public final class SampleTestCollection { public SampleItem item; public List<Test> tests; public String collectionDate; public List<ObservationHistory> initialSampleConditionIdList; public Map<String, String> testIdToUserSectionMap; public Map<String, String> testIdToUserSampleTypeMap; public SampleTestCollection(SampleItem item, List<Test> tests, String collectionDate, List<ObservationHistory> initialConditionList, Map<String, String> testIdToUserSectionMap, Map<String, String> testIdToUserSampleTypeMap) { this.item = item; this.tests = tests; this.collectionDate = collectionDate; this.testIdToUserSectionMap = testIdToUserSectionMap; this.testIdToUserSampleTypeMap = testIdToUserSampleTypeMap; initialSampleConditionIdList = initialConditionList; } } }