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/** * 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.investigatorprofile; import com.google.common.base.Preconditions; import com.google.inject.Inject; import gov.nih.nci.firebird.data.AbstractCredential; import gov.nih.nci.firebird.data.AbstractPersonAssociation; import gov.nih.nci.firebird.data.CertifiedSpecialtyBoard; import gov.nih.nci.firebird.data.CertifiedSpecialtyType; import gov.nih.nci.firebird.data.FirebirdFile; import gov.nih.nci.firebird.data.FormTypeEnum; import gov.nih.nci.firebird.data.InvestigatorProfile; import gov.nih.nci.firebird.data.OrderingDesignee; import gov.nih.nci.firebird.data.Organization; import gov.nih.nci.firebird.data.OrganizationAssociation; import gov.nih.nci.firebird.data.OrganizationRoleType; import gov.nih.nci.firebird.data.PersistentObjectUtil; import gov.nih.nci.firebird.data.Person; import gov.nih.nci.firebird.data.PracticeSite; import gov.nih.nci.firebird.data.PracticeSiteType; import gov.nih.nci.firebird.data.PrimaryOrganization; import gov.nih.nci.firebird.data.ShippingDesignee; import gov.nih.nci.firebird.data.SubInvestigator; import gov.nih.nci.firebird.data.TrainingCertificate; import gov.nih.nci.firebird.exception.AssociationAlreadyExistsException; import gov.nih.nci.firebird.exception.CredentialAlreadyExistsException; import gov.nih.nci.firebird.exception.ValidationException; import gov.nih.nci.firebird.service.AbstractGenericServiceBean; import gov.nih.nci.firebird.service.file.FileMetadata; import gov.nih.nci.firebird.service.file.FileService; import gov.nih.nci.firebird.service.organization.OrganizationAssociationService; import gov.nih.nci.firebird.service.organization.OrganizationService; import gov.nih.nci.firebird.service.person.PersonAssociationService; import gov.nih.nci.firebird.service.registration.ProtocolRegistrationService; import org.apache.commons.lang.StringUtils; import org.hibernate.Query; import javax.annotation.Resource; import javax.ejb.Stateless; import javax.ejb.TransactionAttribute; import javax.ejb.TransactionAttributeType; import java.io.File; import java.io.IOException; import java.util.Collections; import java.util.Comparator; import java.util.List; /** * Implementation of the investigator profile service. */ @Stateless @TransactionAttribute(TransactionAttributeType.REQUIRED) @SuppressWarnings({ "PMD.TooManyMethods" }) // facade service expected to expose many methods public class InvestigatorProfileServiceBean extends AbstractGenericServiceBean<InvestigatorProfile> implements InvestigatorProfileService { private static final String PROFILE_BY_PERSON_QUERY = "from " + InvestigatorProfile.class.getName() + " where person = :person"; private static final String SPECIALTIES_BY_BOARD = "from " + CertifiedSpecialtyType.class.getName() + " where board = :board"; private OrganizationService organizationService; private OrganizationAssociationService organizationAssociationService; private PersonAssociationService personAssociationService; private FileService fileService; private ProtocolRegistrationService registrationService; private InvestigatorProfileHelper investigatorProfileHelper; private InvestigatorRegistrationHelper investigatorRegistrationHelper; @Override public void setPrimaryOrganization(InvestigatorProfile profile, PrimaryOrganization primaryOrganization) throws ValidationException { Preconditions.checkNotNull(profile.getPerson()); Preconditions.checkNotNull(primaryOrganization); investigatorProfileHelper.associatePrimaryOrganization(profile, primaryOrganization); save(profile, FormTypeEnum.CV, FormTypeEnum.FINANCIAL_DISCLOSURE_FORM); } @Override public void createPrimaryOrganization(InvestigatorProfile profile) throws ValidationException { Preconditions.checkNotNull(profile.getPerson()); Preconditions.checkNotNull(profile.getPrimaryOrganization()); Preconditions.checkNotNull(profile.getPrimaryOrganization().getType(), "Primary organization type can't be null"); Preconditions.checkArgument(PersistentObjectUtil.isNew(profile.getPrimaryOrganization().getOrganization()), "Profile primary organization is not new"); organizationAssociationService.createNewPrimaryOrganization(profile.getPrimaryOrganization()); investigatorProfileHelper.checkCorrelation(profile); save(profile, FormTypeEnum.CV, FormTypeEnum.FINANCIAL_DISCLOSURE_FORM); } @Override public OrganizationAssociation addAssociatedPracticeSite(InvestigatorProfile profile, Organization organization, String dataField, PracticeSiteType practiceSiteType) throws AssociationAlreadyExistsException, ValidationException { OrganizationAssociation association = profile.addOrganizationAssociation(organization, OrganizationRoleType.PRACTICE_SITE); association.getOrganizationRole().setDataField(dataField); ((PracticeSite) association.getOrganizationRole()).setType(practiceSiteType); saveNewAssociation(profile, association); return association; } private void saveNewAssociation(InvestigatorProfile profile, OrganizationAssociation association) throws ValidationException { organizationAssociationService.handleNew(association); save(profile); } @Override public OrganizationAssociation addAssociatedInstitutionalReviewBoard(InvestigatorProfile profile, Organization organization) throws AssociationAlreadyExistsException, ValidationException { OrganizationAssociation association = profile.addOrganizationAssociation(organization, OrganizationRoleType.IRB); saveNewAssociation(profile, association); return association; } @Override public OrganizationAssociation addAssociatedClinicalLab(InvestigatorProfile profile, Organization organization) throws AssociationAlreadyExistsException, ValidationException { OrganizationAssociation association = profile.addOrganizationAssociation(organization, OrganizationRoleType.CLINICAL_LABORATORY); saveNewAssociation(profile, association); return association; } @Override public void deleteAssociatedOrganization(InvestigatorProfile profile, OrganizationAssociation association) { profile.getOrganizationAssociations().remove(association); investigatorRegistrationHelper.deleteAssociatedOrganizationFromUnlockedRegistrations(profile, association); save(profile); } @Override public void updateAssociationOhrp(OrganizationAssociation association, String ohrp) { investigatorProfileHelper.validateAssociationOhrp(association, ohrp); association.getOrganizationRole().setDataField(ohrp); save(association.getProfile()); } @Override public SubInvestigator addSubInvestigator(InvestigatorProfile profile, Person person) throws AssociationAlreadyExistsException, ValidationException { SubInvestigator subInvestigator = profile.addSubInvestigator(person); personAssociationService.handleNew(subInvestigator); save(profile); return subInvestigator; } @Override public void deleteAssociatedSubInvestigator(InvestigatorProfile profile, SubInvestigator subInvestigator) { profile.removeSubInvestigator(subInvestigator); personAssociationService.delete(subInvestigator); investigatorRegistrationHelper.deleteSubInvestigatorRegistrations(profile, subInvestigator); save(profile); } @Override public OrderingDesignee addOrderingDesignee(InvestigatorProfile profile, Person person) throws AssociationAlreadyExistsException, ValidationException { OrderingDesignee orderingDesignee = profile.addOrderingDesignee(person); personAssociationService.handleNew(orderingDesignee); save(profile); return orderingDesignee; } @Override public void setShippingDesignee(InvestigatorProfile profile, ShippingDesignee shippingDesignee) throws ValidationException { shippingDesignee.setProfile(profile); if (shippingDesignee.getOrganization() != null && StringUtils.isEmpty(shippingDesignee.getOrganization().getExternalId())) { organizationService.create(shippingDesignee.getOrganization(), OrganizationRoleType.GENERIC_ORGANIZATION); } profile.setShippingDesignee(shippingDesignee); personAssociationService.handleNew(shippingDesignee); save(profile); } @Override public void deleteAssociatedOrderingDesignee(InvestigatorProfile profile, OrderingDesignee orderingDesignee) { profile.removeOrderingDesignee(orderingDesignee); removePersonAssociation(profile, orderingDesignee); } @Override public void deleteAssociatedShippingDesignee(InvestigatorProfile profile, ShippingDesignee shippingDesignee) { profile.setShippingDesignee(null); removePersonAssociation(profile, shippingDesignee); } private void removePersonAssociation(InvestigatorProfile profile, AbstractPersonAssociation personAssociation) { personAssociationService.delete(personAssociation); save(profile); } @Override public void saveCredential(InvestigatorProfile profile, AbstractCredential<?> credential, FormTypeEnum... formTypesToSetToRevised) throws CredentialAlreadyExistsException, ValidationException { if (credential.getIssuer() != null && StringUtils.isEmpty(credential.getIssuer().getExternalId())) { organizationService.create(credential.getIssuer(), OrganizationRoleType.GENERIC_ORGANIZATION); } if (PersistentObjectUtil.isNew(credential)) { profile.addCredential(credential); } save(profile, formTypesToSetToRevised); } @Override public void saveCertificate(InvestigatorProfile profile, TrainingCertificate cert, File certificateFile, FileMetadata fileMetadata) throws CredentialAlreadyExistsException, IOException, ValidationException { if (fileMetadata != null) { FirebirdFile file = fileService.createFile(certificateFile, fileMetadata); cert.setFile(file); } else if (cert.getFile() == null) { throw new IllegalArgumentException("File information is required to add this certificate!"); } if (!PersistentObjectUtil.isNew(cert)) { registrationService.setRegistrationFormStatusesToRevisedIfReviewed( investigatorRegistrationHelper.getAffectedRegistrationsByCertificateModification(profile, cert), FormTypeEnum.HUMAN_RESEARCH_CERTIFICATE); } saveCredential(profile, cert, FormTypeEnum.CV); } @Override public InvestigatorProfile getByPerson(Person person) { if (person == null) { throw new IllegalArgumentException("Person was null"); } if (person.getId() == null) { return null; } Query q = getSession().createQuery(PROFILE_BY_PERSON_QUERY); q.setEntity("person", person); return (InvestigatorProfile) q.uniqueResult(); } @SuppressWarnings("unchecked") // hibernate does not provide typed arguments @Override public List<CertifiedSpecialtyType> getSpecialtiesByBoard(CertifiedSpecialtyBoard board) { if (board == null) { throw new IllegalArgumentException("Certification Board was null"); } List<CertifiedSpecialtyType> types = null; Query q = getSession().createQuery(SPECIALTIES_BY_BOARD); q.setEntity("board", board); types = q.list(); Collections.sort(types, new Comparator<CertifiedSpecialtyType>() { @Override public int compare(CertifiedSpecialtyType o1, CertifiedSpecialtyType o2) { int ret = o1.getDesignation().name().compareTo(o2.getDesignation().name()); if (ret == 0) { ret = o1.getName().compareTo(o2.getName()); } return ret; } }); return types; } @Override public List<InvestigatorProfile> search(String searchTerm) { return investigatorProfileHelper.search(searchTerm); } @Override public List<InvestigatorProfile> searchForCtepProfiles(String searchTerm) { return investigatorProfileHelper.getOnlyCtepInvestigators(search(searchTerm)); } @Override public Long save(InvestigatorProfile profile, FormTypeEnum... formTypesToSetToRevised) { registrationService.setReturnedOrRevisedRegistrationsFormStatusesToRevised(profile, formTypesToSetToRevised); return save(profile); } @Override public void deleteCertificate(InvestigatorProfile profile, TrainingCertificate certificate) { investigatorRegistrationHelper.breakCertificateLinks(profile, certificate); profile.getCredentials().remove(certificate); if (profile.isOrphan(certificate.getFile())) { getSession().delete(certificate.getFile()); } save(profile, FormTypeEnum.CV); } @Override public FirebirdFile addFile(InvestigatorProfile profile, File contents, FileMetadata fileMetadata) throws IOException { FirebirdFile file = fileService.createFile(contents, fileMetadata); profile.getUploadedFiles().add(file); save(profile); return file; } @Override public void removeFile(InvestigatorProfile aProfile, FirebirdFile aFile) { FirebirdFile file = fileService.getById(aFile.getId()); InvestigatorProfile profile = getById(aProfile.getId()); profile.getUploadedFiles().remove(file); investigatorProfileHelper.removeFileFromUnLockedRegistrations(profile, file); save(profile); if (profile.isOrphan(file)) { fileService.delete(file); } } @Resource(mappedName = "firebird/OrganizationServiceBean/local") void setOrganizationService(OrganizationService organizationService) { this.organizationService = organizationService; } @Resource(mappedName = "firebird/OrganizationAssociationServiceBean/local") void setOrganizationAssociationService(OrganizationAssociationService organizationAssociationService) { this.organizationAssociationService = organizationAssociationService; } @Resource(mappedName = "firebird/PersonAssociationServiceBean/local") void setPersonAssociationService(PersonAssociationService personAssociationService) { this.personAssociationService = personAssociationService; } @Resource(mappedName = "firebird/FileServiceBean/local") void setFileService(FileService fileService) { this.fileService = fileService; } @Resource(mappedName = "firebird/ProtocolRegistrationServiceBean/local") void setRegistrationService(ProtocolRegistrationService registrationService) { this.registrationService = registrationService; } @Inject void setInvestigatorProfileHelper(InvestigatorProfileHelper investigatorProfileHelper) { this.investigatorProfileHelper = investigatorProfileHelper; } @Inject public void setInvestigatorRegistrationHelper(InvestigatorRegistrationHelper investigatorRegistrationHelper) { this.investigatorRegistrationHelper = investigatorRegistrationHelper; } }