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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.protocol; import com.fiveamsolutions.nci.commons.data.persistent.PersistentObject; import gov.nih.nci.firebird.data.AbstractProtocolRegistration; import gov.nih.nci.firebird.data.AbstractRegistrationForm; import gov.nih.nci.firebird.data.FormStatus; import gov.nih.nci.firebird.data.FormType; import gov.nih.nci.firebird.data.InvestigatorRegistration; import gov.nih.nci.firebird.data.InvitationStatus; import gov.nih.nci.firebird.data.Organization; import gov.nih.nci.firebird.data.PersistentObjectUtil; import gov.nih.nci.firebird.data.Person; import gov.nih.nci.firebird.data.Protocol; import gov.nih.nci.firebird.data.ProtocolRegistrationConfiguration; import gov.nih.nci.firebird.data.ProtocolRevision; import gov.nih.nci.firebird.data.RegistrationStatus; import gov.nih.nci.firebird.data.RegistrationType; import gov.nih.nci.firebird.data.SubInvestigatorRegistration; import gov.nih.nci.firebird.data.user.FirebirdUser; import gov.nih.nci.firebird.exception.ValidationException; 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.util.Collections; import java.util.Date; import java.util.List; import java.util.Set; import static com.google.common.base.Preconditions.checkArgument; import static com.google.common.base.Preconditions.checkNotNull; /** * Service for Investigational Protocols. */ @Stateless @TransactionAttribute(TransactionAttributeType.REQUIRED) @SuppressWarnings({ "PMD.TooManyMethods" }) // facade service expected to expose many methods public class ProtocolServiceBean extends AbstractProtocolServiceBean<Protocol> implements ProtocolService { private FormTypeService formTypeService; private ProtocolValidationService protocolValidationService; @Override public Protocol create() { Protocol protocol = new Protocol(); addFormTypes(protocol.getRegistrationConfiguration()); return protocol; } @Override public void addFormTypes(ProtocolRegistrationConfiguration configuration) { List<FormType> configurableFormTypes = formTypeService .getStandardConfigureableForms(RegistrationType.PROTOCOL); configurableFormTypes.addAll(formTypeService.getSupplementalForms(RegistrationType.PROTOCOL)); for (FormType formType : configurableFormTypes) { configuration.setInvestigatorOptionality(formType, formType.getInvestigatorDefault()); configuration.setSubinvestigatorOptionality(formType, formType.getSubinvestigatorDefault()); } } @Override protected void validate(Protocol protocol) throws ValidationException { protocolValidationService.validate(protocol); } @Override public boolean hasDuplicateProtocolNumber(Protocol protocol) { if (!PersistentObjectUtil.isNew(protocol.getSponsor())) { Protocol existingProtocolWithNumber = getProtocol(protocol.getProtocolNumber(), protocol.getSponsor()); return existingProtocolWithNumber != null && !PersistentObjectUtil.areSame(protocol, existingProtocolWithNumber); } else { return false; } } @Override public Long save(Protocol protocol) { getProtocolAgentService().handleAgents(protocol); return super.save(protocol); } @Override public InvestigatorRegistration addInvestigator(Protocol protocol, Person investigator) throws ValidationException { return getRegistrationService().createInvestigatorRegistration(protocol, investigator); } @Override public void invite(InvestigatorRegistration registration) { getRegistrationService().inviteToRegistration(registration); } @Override @SuppressWarnings("unchecked") // Hibernate only returns untyped collections public List<Protocol> getProtocols(FirebirdUser user, Set<String> groupNames) { checkNotNull(user); checkNotNull(groupNames); List<Organization> verifiedSponsorOrganizations = user.getVerifiedSponsorOrganizations(groupNames); if (verifiedSponsorOrganizations.isEmpty()) { return Collections.emptyList(); } else { String protocolQueryHql = HQL_FROM_BASE + Protocol.class.getName() + " where sponsor in (:sponsors)"; Query query = getSession().createQuery(protocolQueryHql); query.setParameterList("sponsors", verifiedSponsorOrganizations); return query.list(); } } @Override public void approvePacket(InvestigatorRegistration registration) { if (!registration.isApprovable()) { throw new IllegalArgumentException("Registration is not in an approvable state"); } ProtocolUtil.markAllApproved(registration); getSponsorNotificationService().notifyInvestigatorsOfApproval(registration); getRegistrationService().save(registration); } @Override public void deactivatePacket(InvestigatorRegistration registration, String comments) { if (StringUtils.isNotEmpty(comments)) { deactivateRegistration(registration, comments); for (SubInvestigatorRegistration subRegistration : registration.getSubinvestigatorRegistrations()) { deactivateRegistration(subRegistration, comments); } } else { throw new IllegalArgumentException("Comments must be entered when deactivating a registration packet!"); } } private void deactivateRegistration(AbstractProtocolRegistration registration, String comments) { registration.setStatus(RegistrationStatus.INACTIVE); for (AbstractRegistrationForm form : registration.getForms()) { form.setFormStatus(FormStatus.INACTIVE); form.setComments(null); } getRegistrationService().save(registration); getSponsorNotificationService().notifyOfDeactivation(registration, comments); } @Override public void reactivatePacket(InvestigatorRegistration registration, String comments) { checkArgument(registration.getStatus() == RegistrationStatus.INACTIVE, "Failed to re-activate registration packet due to it being " + registration.getStatus() + " instead of INACTIVE."); if (registration.getApprovalDate() != null) { reactivateApprovedPacket(registration, comments); } else { reactivateUnApprovedPacket(registration, comments); } } @Override public void removePacket(InvestigatorRegistration registration) { if (registration.getStatus() != RegistrationStatus.APPROVED) { getRegistrationService().delete(registration); getSponsorNotificationService().sendPacketRemovedEmail(registration); } else { throw new IllegalStateException( "Cannot remove an investigator if the registration status is approved."); } } private void reactivateApprovedPacket(InvestigatorRegistration registration, String comments) { InvestigatorRegistration reactivatedRegistration = (InvestigatorRegistration) reactivateApprovedRegistration( registration, comments); reactivatedRegistration.getSubinvestigatorRegistrations().clear(); for (SubInvestigatorRegistration subRegistration : registration.getSubinvestigatorRegistrations()) { SubInvestigatorRegistration subInvestigatorRegistration = (SubInvestigatorRegistration) reactivateApprovedRegistration( subRegistration, comments); reactivatedRegistration.addSubinvestigatorRegistration(subInvestigatorRegistration); } } private AbstractProtocolRegistration reactivateApprovedRegistration(AbstractProtocolRegistration registration, String comments) { AbstractProtocolRegistration reactivatedRegistration = registration.isInvestigatorRegistration() ? new InvestigatorRegistration() : new SubInvestigatorRegistration(); reactivatedRegistration.copyFrom(registration); reactivatedRegistration.prepareFormsForReturn(); registration.setCurrentRegistration(reactivatedRegistration); reactivatedRegistration.setStatus(RegistrationStatus.IN_PROGRESS); reactivatedRegistration.setFormStatuses(FormStatus.IN_PROGRESS); reactivatedRegistration.getInvitation().setInvitationStatus(InvitationStatus.REACTIVATED); getRegistrationService().save(reactivatedRegistration); getRegistrationService().save(registration); getSponsorNotificationService().notifyOfReactivation(registration, comments); return reactivatedRegistration; } private void reactivateUnApprovedPacket(InvestigatorRegistration registration, String comments) { reactivateUnApprovedRegistration(registration, comments); for (SubInvestigatorRegistration subRegistration : registration.getSubinvestigatorRegistrations()) { reactivateUnApprovedRegistration(subRegistration, comments); } } private void reactivateUnApprovedRegistration(AbstractProtocolRegistration registration, String comments) { if (InvitationStatus.NO_RESPONSE == registration.getInvitation().getInvitationStatus() || InvitationStatus.NOT_INVITED == registration.getInvitation().getInvitationStatus()) { registration.setStatus(RegistrationStatus.NOT_STARTED); registration.setFormStatuses(FormStatus.NOT_STARTED); } else { registration.setStatus(RegistrationStatus.IN_PROGRESS); registration.getInvitation().setInvitationStatus(InvitationStatus.REACTIVATED); registration.getInvitation().setInvitationChangeDate(new Date()); registration.setFormStatuses(FormStatus.IN_PROGRESS); } Set<PersistentObject> objectsToDelete = registration.prepareFormsForReturn(); deleteAll(objectsToDelete); getRegistrationService().save(registration); getSponsorNotificationService().notifyOfReactivation(registration, comments); } @Override public void updateProtocol(Protocol original, Protocol revised, String comment) throws ValidationException { ProtocolModificationDetector detector = new ProtocolModificationDetector(original, revised, getResources()); if (!detector.isModificationDetected()) { return; } protocolValidationService.validateChanges(revised, comment); ProtocolRevision revision = new ProtocolRevision(); revision.setDate(new Date()); revision.setComment(comment); revised.addRevision(revision); detector.addModifications(revision); validateAndSave(revised); getSession().flush(); handleAffectedRegistrations(revised, revision); } private void handleAffectedRegistrations(Protocol protocol, ProtocolRevision revision) { for (AbstractProtocolRegistration registration : protocol.getAllRegistrations()) { Set<AbstractRegistrationForm> removedForms = registration.configureForms(); deleteForms(removedForms); if (registration.isNotificationRequiredForUpdate()) { getSponsorNotificationService().sendProtocolUpdateEmail(registration, revision); } if (registration.isResubmitRequiredForUpdate()) { registration.setStatus(RegistrationStatus.PROTOCOL_UPDATED); ProtocolUtil.setFormsToInProgress(registration); Set<PersistentObject> objectsToDelete = registration.prepareFormsForReturn(); deleteAll(objectsToDelete); getRegistrationService().save(registration); } } } @Resource(mappedName = "firebird/FormTypeServiceBean/local") void setFormTypeService(FormTypeService formTypeService) { this.formTypeService = formTypeService; } @Resource(mappedName = "firebird/ProtocolValidationServiceBean/local") public void setProtocolValidationService(ProtocolValidationService protocolValidationService) { this.protocolValidationService = protocolValidationService; } }