Java tutorial
/** * The software subject to this notice and license includes both human readable * source code form and machine readable, binary, object code form. The NCI OCR * Software was developed in conjunction with the National Cancer Institute * (NCI) by NCI employees and 5AM Solutions, Inc. (5AM). To the extent * government employees are authors, any rights in such works shall be subject * to Title 17 of the United States Code, section 105. * * This NCI OCR Software License (the License) is between NCI and You. You (or * Your) shall mean a person or an entity, and all other entities that control, * are controlled by, or are under common control with the entity. Control for * purposes of this definition means (i) the direct or indirect power to cause * the direction or management of such entity, whether by contract or otherwise, * or (ii) ownership of fifty percent (50%) or more of the outstanding shares, * or (iii) beneficial ownership of such entity. * * This License is granted provided that You agree to the conditions described * below. NCI grants You a non-exclusive, worldwide, perpetual, fully-paid-up, * no-charge, irrevocable, transferable and royalty-free right and license in * its rights in the NCI OCR Software to (i) use, install, access, operate, * execute, copy, modify, translate, market, publicly display, publicly perform, * and prepare derivative works of the NCI OCR Software; (ii) distribute and * have distributed to and by third parties the NCI OCR Software and any * modifications and derivative works thereof; and (iii) sublicense the * foregoing rights set out in (i) and (ii) to third parties, including the * right to license such rights to further third parties. For sake of clarity, * and not by way of limitation, NCI shall have no right of accounting or right * of payment from You or Your sub-licensees for the rights granted under this * License. This License is granted at no charge to You. * * Your redistributions of the source code for the Software must retain the * above copyright notice, this list of conditions and the disclaimer and * limitation of liability of Article 6, below. Your redistributions in object * code form must reproduce the above copyright notice, this list of conditions * and the disclaimer of Article 6 in the documentation and/or other materials * provided with the distribution, if any. * * Your end-user documentation included with the redistribution, if any, must * include the following acknowledgment: This product includes software * developed by 5AM and the National Cancer Institute. If You do not include * such end-user documentation, You shall include this acknowledgment in the * Software itself, wherever such third-party acknowledgments normally appear. * * You may not use the names "The National Cancer Institute", "NCI", or "5AM" * to endorse or promote products derived from this Software. This License does * not authorize You to use any trademarks, service marks, trade names, logos or * product names of either NCI or 5AM, except as required to comply with the * terms of this License. * * For sake of clarity, and not by way of limitation, You may incorporate this * Software into Your proprietary programs and into any third party proprietary * programs. However, if You incorporate the Software into third party * proprietary programs, You agree that You are solely responsible for obtaining * any permission from such third parties required to incorporate the Software * into such third party proprietary programs and for informing Your * sub-licensees, including without limitation Your end-users, of their * obligation to secure any required permissions from such third parties before * incorporating the Software into such third party proprietary software * programs. In the event that You fail to obtain such permissions, You agree * to indemnify NCI for any claims against NCI by such third parties, except to * the extent prohibited by law, resulting from Your failure to obtain such * permissions. * * For sake of clarity, and not by way of limitation, You may add Your own * copyright statement to Your modifications and to the derivative works, and * You may provide additional or different license terms and conditions in Your * sublicenses of modifications of the Software, or any derivative works of the * Software as a whole, provided Your use, reproduction, and distribution of the * Work otherwise complies with the conditions stated in this License. * * THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED WARRANTIES, * (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, * NON-INFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN NO * EVENT SHALL THE NATIONAL CANCER INSTITUTE, 5AM SOLUTIONS, INC. OR THEIR * AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; * OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR * OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ package gov.nih.nci.firebird.service.protocol; import gov.nih.nci.firebird.data.Organization; import gov.nih.nci.firebird.data.OrganizationRoleType; import gov.nih.nci.firebird.data.Person; import gov.nih.nci.firebird.data.Protocol; import gov.nih.nci.firebird.exception.ValidationException; import gov.nih.nci.firebird.service.organization.OrganizationService; import gov.nih.nci.firebird.service.person.PersonService; import gov.nih.nci.firebird.service.person.external.InvalidatedPersonException; import java.util.List; import java.util.Map; import java.util.ResourceBundle; import java.util.Set; import javax.annotation.Resource; import javax.ejb.SessionContext; import javax.ejb.Stateless; import javax.ejb.TransactionAttribute; import javax.ejb.TransactionAttributeType; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.math.NumberUtils; import org.hibernate.Session; import com.google.common.collect.Lists; import com.google.common.collect.Maps; import com.google.common.collect.Sets; import com.google.inject.Inject; import com.google.inject.Provider; /** * Bean that implements validation and import of individual protocols. */ @Stateless @TransactionAttribute(TransactionAttributeType.REQUIRES_NEW) @SuppressWarnings("PMD.TooManyMethods") // methods broken down for clarity public class ProtocolImportDetailServiceBean implements ProtocolImportDetailService { private PersonService personService; private ProtocolService protocolService; private OrganizationService organizationService; private ResourceBundle resources; private Provider<Session> sessionProvider; private SessionContext sessionContext; private final Map<String, Person> lookedUpPersons = Maps.newHashMap(); @Resource(mappedName = "firebird/PersonServiceBean/local") void setPersonService(PersonService personService) { this.personService = personService; } @Resource(mappedName = "firebird/ProtocolServiceBean/local") void setProtocolService(ProtocolService protocolService) { this.protocolService = protocolService; } @Resource(mappedName = "firebird/OrganizationServiceBean/local") void setOrganizationService(OrganizationService organizationService) { this.organizationService = organizationService; } @Inject void setResources(ResourceBundle resources) { this.resources = resources; } @Resource void setSessionContext(SessionContext sessionContext) { this.sessionContext = sessionContext; } @Inject void setSessionProvider(Provider<Session> sessionProvider) { this.sessionProvider = sessionProvider; } @Override public void validate(ProtocolImportDetail detail) { lookedUpPersons.clear(); detail.setStatus(ProtocolImportDetailStatus.VALIDATING); checkForDuplicateProtocolNumber(detail); handleLeadOrganizations(detail); checkInvestigators(detail); setFinalValidationStatus(detail); } private void checkForDuplicateProtocolNumber(ProtocolImportDetail detail) { if (protocolService.hasDuplicateProtocolNumber(detail.getProtocol())) { detail.addFailure(resources, "validation.failure.protocol.import.duplicate.number", ProtocolImportJob.PROTOCOL_NUMBER_COLUMN_INDEX, detail.getProtocol().getProtocolNumber()); } } private void handleLeadOrganizations(ProtocolImportDetail detail) { if (!detail.getLeadOrganizationMappings().isEmpty()) { Map<String, Organization> organizations = lookupMappedOrganizations(detail); Map<String, Person> principalInvestigators = lookupMappedInvestigators(detail); for (Map.Entry<String, String> mapping : detail.getLeadOrganizationMappings().entrySet()) { if (validateMapping(mapping, detail)) { Organization leadOrganization = organizations.get(mapping.getKey()); Person principalInvestigator = principalInvestigators.get(mapping.getValue()); addLeadOrganization(detail, leadOrganization, principalInvestigator); } } } } private void addLeadOrganization(ProtocolImportDetail detail, Organization leadOrganization, Person principalInvestigator) { if (leadOrganization != null && principalInvestigator != null) { detail.getProtocol().addLeadOrganization(leadOrganization, principalInvestigator); } } private boolean validateMapping(Map.Entry<String, String> mapping, ProtocolImportDetail detail) { if (StringUtils.isBlank(mapping.getKey()) || StringUtils.isBlank(mapping.getValue())) { detail.addFailure(resources, "validation.failure.protocol.import.invalid.lead.organization.key", ProtocolImportJob.PROTOCOL_LEAD_ORGANIZATION_COLUMN_INDEX, mapping); return false; } return true; } private Map<String, Person> lookupMappedInvestigators(ProtocolImportDetail detail) { Set<String> principalInvestigatorIds = Sets.newHashSet(detail.getLeadOrganizationMappings().values()); Map<String, Person> lookedUpInvestigators = Maps.newHashMap(); for (String externalId : principalInvestigatorIds) { if (StringUtils.isNotBlank(externalId)) { Person person = retrievePrincipalInvestigator(detail, externalId); lookedUpInvestigators.put(externalId, person); } } return lookedUpInvestigators; } private Person retrievePrincipalInvestigator(ProtocolImportDetail detail, String investigatorExternalId) { return retrieveInvestigator(detail, investigatorExternalId, ProtocolImportJob.PROTOCOL_LEAD_ORGANIZATION_COLUMN_INDEX); } private Person retrieveInvestigator(ProtocolImportDetail detail, String investigatorExternalId, int column) { if (!NumberUtils.isDigits(investigatorExternalId)) { handleInvalidInvestigatorIdFormat(detail, investigatorExternalId, column); return null; } Person investigator = lookedUpPersons.get(investigatorExternalId); if (investigator == null) { investigator = lookupInvestigator(detail, investigatorExternalId, column); lookedUpPersons.put(investigatorExternalId, investigator); } return investigator; } private Person lookupInvestigator(ProtocolImportDetail detail, String investigatorExternalId, int column) { try { Person investigator = personService.getByExternalId(investigatorExternalId); if (investigator == null) { handleInvalidInvestigatorId(detail, investigatorExternalId, column); } return investigator; } catch (InvalidatedPersonException e) { handleInvalidInvestigatorId(detail, investigatorExternalId, column); } return null; } private void handleInvalidInvestigatorIdFormat(ProtocolImportDetail detail, String investigatorExternalId, int column) { detail.addFailure(resources, "validation.failure.protocol.import.invalid.investigator.id.format", column, investigatorExternalId); } private void handleInvalidInvestigatorId(ProtocolImportDetail detail, String investigatorExternalId, int column) { detail.addFailure(resources, "validation.failure.protocol.import.invalid.investigator.id", column, investigatorExternalId); } private Map<String, Organization> lookupMappedOrganizations(ProtocolImportDetail detail) { Set<String> leadOrganizationIds = detail.getLeadOrganizationMappings().keySet(); Map<String, Organization> lookedUpOrganizations = Maps.newHashMap(); for (String ctepId : leadOrganizationIds) { if (StringUtils.isNotBlank(ctepId)) { lookedUpOrganizations.put(ctepId, retrieveLeadOrganization(detail, ctepId)); } } return lookedUpOrganizations; } private Organization retrieveLeadOrganization(ProtocolImportDetail detail, String ctepId) { List<Organization> leadOrganizations = organizationService.getByAlternateIdentifier(ctepId, OrganizationRoleType.GENERIC_ORGANIZATION); if (leadOrganizations.isEmpty()) { handleInvalidLeadOrganizationCtepId(detail, ctepId); } else if (leadOrganizations.size() > 1) { handleTooManyLeadOrganizationsReturned(detail, ctepId); } else { return leadOrganizations.get(0); } return null; } private void handleInvalidLeadOrganizationCtepId(ProtocolImportDetail detail, String ctepId) { detail.addFailure(resources, "validation.failure.protocol.import.invalid.lead.organization.ctep.id", ProtocolImportJob.PROTOCOL_LEAD_ORGANIZATION_COLUMN_INDEX, ctepId); } private void handleTooManyLeadOrganizationsReturned(ProtocolImportDetail detail, String ctepId) { detail.addFailure(resources, "validation.failure.protocol.import.too.many.lead.organizations.returned", ProtocolImportJob.PROTOCOL_LEAD_ORGANIZATION_COLUMN_INDEX, ctepId); } private void checkInvestigators(ProtocolImportDetail detail) { for (String investigatorExternalId : detail.getInvestigatorExternalIds()) { Person investigator = retrieveInvestigator(detail, investigatorExternalId); if (investigator != null) { detail.getInvestigators().add(investigator); } } } private Person retrieveInvestigator(ProtocolImportDetail detail, String investigatorExternalId) { return retrieveInvestigator(detail, investigatorExternalId, ProtocolImportJob.PROTOCOL_INVESTIGATOR_IDS_COLUMN_INDEX); } private void setFinalValidationStatus(ProtocolImportDetail detail) { if (detail.getValidationResult().isValid()) { detail.setStatus(ProtocolImportDetailStatus.VALID); } else { detail.setStatus(ProtocolImportDetailStatus.INVALID); } } @Override public void importProtocol(ProtocolImportDetail detail) { lookedUpPersons.clear(); detail.setStatus(ProtocolImportDetailStatus.IMPORTING); List<Person> investigators = retrieveInvestigators(detail); if (detail.getValidationResult().isValid()) { Protocol protocolToSave = detail.getProtocol().createCopy(); protocolService.addFormTypes(protocolToSave.getRegistrationConfiguration()); protocolService.save(protocolToSave); addInvestigators(detail, investigators, protocolToSave); sessionProvider.get().flush(); detail.setStatus(ProtocolImportDetailStatus.IMPORT_COMPLETE); } else { detail.setStatus(ProtocolImportDetailStatus.IMPORT_ERROR); } } private void addInvestigators(ProtocolImportDetail detail, List<Person> investigators, Protocol protocol) { for (Person investigator : investigators) { addInvestigator(detail, investigator, protocol); } } private void addInvestigator(ProtocolImportDetail detail, Person investigator, Protocol protocol) { try { protocolService.addInvestigator(protocol, investigator); } catch (ValidationException e) { detail.getValidationResult().addFailures(e.getResult()); detail.setStatus(ProtocolImportDetailStatus.IMPORT_ERROR); sessionContext.setRollbackOnly(); } } private List<Person> retrieveInvestigators(ProtocolImportDetail detail) { List<Person> investigators = Lists.newArrayList(); for (String investigatorExternalId : detail.getInvestigatorExternalIds()) { investigators.add(retrieveInvestigator(detail, investigatorExternalId)); } return investigators; } }