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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. 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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.google.common.collect.Sets; import com.google.inject.Inject; import gov.nih.nci.firebird.data.AbstractProtocolRegistration; import gov.nih.nci.firebird.data.FormOptionality; import gov.nih.nci.firebird.data.FormType; import gov.nih.nci.firebird.data.FormTypeEnum; import gov.nih.nci.firebird.data.InvestigatorProfile; import gov.nih.nci.firebird.data.Organization; import gov.nih.nci.firebird.data.Person; import gov.nih.nci.firebird.data.Protocol; import gov.nih.nci.firebird.data.ProtocolAgent; import gov.nih.nci.firebird.data.ProtocolForm1572; import gov.nih.nci.firebird.data.ProtocolPhase; import gov.nih.nci.firebird.data.ProtocolRevision; import gov.nih.nci.firebird.data.RegistrationStatus; import gov.nih.nci.firebird.data.user.FirebirdUser; import gov.nih.nci.firebird.data.user.SponsorRole; import gov.nih.nci.firebird.exception.ValidationException; import gov.nih.nci.firebird.service.registration.ProtocolRegistrationService; import gov.nih.nci.firebird.service.sponsor.SponsorNotificationService; import gov.nih.nci.firebird.test.AbstractHibernateTestCase; import gov.nih.nci.firebird.test.FirebirdFileFactory; import gov.nih.nci.firebird.test.FirebirdUserFactory; import gov.nih.nci.firebird.test.FormTypeFactory; import gov.nih.nci.firebird.test.InvestigatorProfileFactory; import gov.nih.nci.firebird.test.OrganizationFactory; import gov.nih.nci.firebird.test.PersonFactory; import gov.nih.nci.firebird.test.ProtocolFactory; import gov.nih.nci.firebird.test.RegistrationFactory; import org.apache.commons.io.FileUtils; import org.junit.BeforeClass; import org.junit.Test; import javax.ejb.SessionContext; import java.io.File; import java.io.IOException; import java.util.Iterator; import java.util.List; import java.util.Set; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertSame; import static org.junit.Assert.assertTrue; import static org.mockito.Mockito.mock; public class ProtocolServiceBeanHibernateTest extends AbstractHibernateTestCase { @Inject private ProtocolServiceBean bean; @Inject private FormTypeService formTypeService; @Inject private ProtocolRegistrationService registrationService; @Inject private ProtocolValidationService protocolValidationService; @Inject private ProtocolAgentService protocolAgentService; private Organization sponsor = OrganizationFactory.getInstance().create(); private Organization leadOrganization = OrganizationFactory.getInstance().create(); private Person principalInvestigator = PersonFactory.getInstance().create(); private FormType form1572Type = FormTypeFactory.getInstance().create(FormTypeEnum.FORM_1572); private FormType financialDisclosureType = FormTypeFactory.getInstance() .create(FormTypeEnum.FINANCIAL_DISCLOSURE_FORM); private FormType additionalAttachmentsType = FormTypeFactory.getInstance() .create(FormTypeEnum.ADDITIONAL_ATTACHMENTS); private static File dataFile; @BeforeClass public static void setupFile() throws IOException { byte[] data = "123".getBytes(); dataFile = File.createTempFile("test", ".blob"); FileUtils.writeByteArrayToFile(dataFile, data); } @Override public void setUp() throws Exception { super.setUp(); bean.setFormTypeService(formTypeService); bean.setRegistrationService(registrationService); bean.setProtocolValidationService(protocolValidationService); bean.setProtocolAgentService(protocolAgentService); } @Test public void testValidateAndSave() throws ValidationException { Protocol protocol = ProtocolFactory.getInstance().createWithForms(); protocol.getAgents().clear(); ProtocolAgent existingAgent = new ProtocolAgent("existing"); protocol.getAgents().add(existingAgent); ProtocolAgent removedAgent = new ProtocolAgent("removed"); protocol.getAgents().add(removedAgent); bean.validateAndSave(protocol); Protocol retrievedProtocol = bean.getById(protocol.getId()); ProtocolFactory.getInstance().compare(protocol, retrievedProtocol); ProtocolAgent previouslyExistingAgent = new ProtocolAgent("previously existing"); save(previouslyExistingAgent); Set<String> agentNames = Sets.newHashSet("existing", "new", "previously existing"); protocol.updateAgents(agentNames); ProtocolFactory.getInstance().populateValues(protocol); saveAll(protocol.getRegistrationConfiguration().getAssociatedFormTypes()); bean.validateAndSave(protocol); Iterator<ProtocolAgent> iterator = protocol.getAgents().iterator(); assertEquals(existingAgent.getId(), iterator.next().getId()); assertNotNull(iterator.next().getId()); assertEquals(previouslyExistingAgent.getId(), iterator.next().getId()); retrievedProtocol = bean.getById(protocol.getId()); ProtocolFactory.getInstance().compare(protocol, retrievedProtocol); } @Test(expected = ValidationException.class) public void testSave_DuplicateProtocolNumber() throws ValidationException { SessionContext mockContext = mock(SessionContext.class); bean.setSessionContext(mockContext); Protocol protocol1 = ProtocolFactory.getInstance().create(); saveAndFlush(protocol1); Protocol protocol2 = ProtocolFactory.getInstance().create(); protocol2.setProtocolNumber(protocol1.getProtocolNumber()); protocol2.setSponsor(protocol1.getSponsor()); bean.validateAndSave(protocol2); } @Test(expected = ValidationException.class) public void testUpdate_ToDuplicateProtocolNumber() throws ValidationException { SessionContext mockContext = mock(SessionContext.class); bean.setSessionContext(mockContext); Protocol protocol1 = ProtocolFactory.getInstance().create(); Protocol protocol2 = ProtocolFactory.getInstance().create(); saveAll(protocol2.getRegistrationConfiguration().getAssociatedFormTypes()); protocol2.setSponsor(protocol1.getSponsor()); saveAndFlush(protocol1, protocol2); protocol2.setProtocolNumber(protocol1.getProtocolNumber()); bean.validateAndSave(protocol2); } @Test public void testCreate() { saveAndFlush(form1572Type, financialDisclosureType, additionalAttachmentsType); Protocol protocol = bean.create(); assertNotNull(protocol); assertEquals(FormOptionality.REQUIRED, protocol.getRegistrationConfiguration().getInvestigatorOptionality(form1572Type)); assertEquals(FormOptionality.REQUIRED, protocol.getRegistrationConfiguration().getInvestigatorOptionality(financialDisclosureType)); assertEquals(FormOptionality.SUPPLEMENTARY, protocol.getRegistrationConfiguration().getInvestigatorOptionality(additionalAttachmentsType)); assertEquals(FormOptionality.REQUIRED, protocol.getRegistrationConfiguration().getSubinvestigatorOptionality(form1572Type)); assertEquals(FormOptionality.REQUIRED, protocol.getRegistrationConfiguration().getSubinvestigatorOptionality(financialDisclosureType)); assertEquals(FormOptionality.SUPPLEMENTARY, protocol.getRegistrationConfiguration().getSubinvestigatorOptionality(additionalAttachmentsType)); } @Test public void testGetAll() { saveAndFlush(form1572Type, financialDisclosureType); Protocol protocol = bean.create(); ProtocolFactory.getInstance().populateValues(protocol); save(protocol); assertEquals(1, bean.getAll().size()); assertEquals(protocol, bean.getAll().get(0)); } @Test public void testGetProtocolsBySponsor() { Organization organization1 = OrganizationFactory.getInstance().create(); Organization organization2 = OrganizationFactory.getInstance().create(); Organization organization3 = OrganizationFactory.getInstance().create(); Protocol protocol1 = ProtocolFactory.getInstance().create(organization1); Protocol protocol2 = ProtocolFactory.getInstance().create(organization2); Protocol protocol3 = ProtocolFactory.getInstance().create(organization3); FirebirdUser user = FirebirdUserFactory.getInstance().create(); SponsorRole role1 = user.addSponsorRepresentativeRole(organization1); save(organization1, organization2, organization3, protocol1, protocol2, protocol3, user); List<Protocol> protocols = bean.getProtocols(user, Sets.newHashSet(role1.getVerifiedSponsorGroupName())); assertEquals(1, protocols.size()); assertSamePersistentObjects(protocol1, protocols.get(0)); } @Test public void testUpdateProtocol() throws ValidationException { bean.setSponsorNotificationService(mock(SponsorNotificationService.class)); InvestigatorProfile profile1 = InvestigatorProfileFactory.getInstance().create(); InvestigatorProfile profile2 = InvestigatorProfileFactory.getInstance().create(); save(sponsor, form1572Type, financialDisclosureType, profile1, profile2); Protocol protocol = makeProtocol(); AbstractProtocolRegistration registrationSubmitted = RegistrationFactory.getInstance() .createInvestigatorRegistration(profile1, protocol); registrationSubmitted.setStatus(RegistrationStatus.SUBMITTED); protocol.addRegistration(registrationSubmitted); AbstractProtocolRegistration registrationNotStarted = RegistrationFactory.getInstance() .createInvestigatorRegistration(profile2, protocol); registrationNotStarted.setStatus(RegistrationStatus.NOT_STARTED); protocol.addRegistration(registrationNotStarted); save(protocol); Protocol snapshot = protocol.createCopy(); protocol.getRegistrationConfiguration().setInvestigatorOptionality(form1572Type, FormOptionality.OPTIONAL); protocol.getRegistrationConfiguration().setInvestigatorOptionality(financialDisclosureType, FormOptionality.REQUIRED); protocol.getRegistrationConfiguration().setSubinvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); protocol.setProtocolTitle("some new title"); bean.updateProtocol(snapshot, protocol, "change is good"); assertEquals(1, protocol.getRevisionHistory().size()); ProtocolRevision change = protocol.getRevisionHistory().iterator().next(); Set<String> expected = Sets.newHashSet( getPropertyText("protocol.change.title.investigator.message", snapshot.getProtocolTitle(), protocol.getProtocolTitle()), getPropertyText("protocol.change.form.optionality.investigator.investigator.message", FormTypeEnum.FORM_1572.getDisplay(), FormOptionality.REQUIRED.getDisplay(), FormOptionality.OPTIONAL.getDisplay()), getPropertyText("protocol.change.form.optionality.investigator.investigator.message", FormTypeEnum.FINANCIAL_DISCLOSURE_FORM.getDisplay(), FormOptionality.NONE.getDisplay(), FormOptionality.REQUIRED.getDisplay()), getPropertyText("protocol.change.form.optionality.subinvestigator.investigator.message", FormTypeEnum.FORM_1572.getDisplay(), FormOptionality.OPTIONAL.getDisplay(), FormOptionality.REQUIRED.getDisplay())); for (String msg : change.getInvestigatorModificationDescriptions()) { assertTrue("expected " + msg, expected.remove(msg)); } assertTrue(expected.toString(), expected.isEmpty()); assertEquals(RegistrationStatus.PROTOCOL_UPDATED, registrationSubmitted.getStatus()); assertEquals(RegistrationStatus.NOT_STARTED, registrationNotStarted.getStatus()); } @Test public void testUpdateProtocol_NewForm() throws ValidationException { InvestigatorProfile profile = InvestigatorProfileFactory.getInstance().create(); save(sponsor, form1572Type, financialDisclosureType, profile); Protocol protocol = makeProtocol(); protocol.getRegistrationConfiguration().setInvestigatorOptionality(form1572Type, FormOptionality.NONE); AbstractProtocolRegistration registrationNotStarted = RegistrationFactory.getInstance() .createInvestigatorRegistration(profile, protocol); registrationNotStarted.setStatus(RegistrationStatus.NOT_STARTED); protocol.addRegistration(registrationNotStarted); save(protocol); Protocol snapshot = protocol.createCopy(); assertNull(registrationNotStarted.getForm1572()); protocol.getRegistrationConfiguration().setInvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); protocol.getRegistrationConfiguration().setSubinvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); bean.updateProtocol(snapshot, protocol, "change is good"); assertNotNull(registrationNotStarted.getForm1572()); } @Test public void testUpdateProtocol_ExistingForm() throws ValidationException { InvestigatorProfile profile = InvestigatorProfileFactory.getInstance().create(); save(sponsor, form1572Type, financialDisclosureType, profile); Protocol protocol = makeProtocol(); AbstractProtocolRegistration registrationNotStarted = RegistrationFactory.getInstance() .createInvestigatorRegistration(profile, protocol); registrationNotStarted.setStatus(RegistrationStatus.NOT_STARTED); protocol.addRegistration(registrationNotStarted); save(protocol); Protocol snapshot = protocol.createCopy(); ProtocolForm1572 savedProtocolForm = registrationNotStarted.getForm1572(); assertNotNull(savedProtocolForm); protocol.getRegistrationConfiguration().setInvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); protocol.getRegistrationConfiguration().setSubinvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); bean.updateProtocol(snapshot, protocol, "change is good"); assertSame(savedProtocolForm, registrationNotStarted.getForm1572()); } @Test public void testUpdateProtocolUnchanged() throws ValidationException { save(sponsor, form1572Type, financialDisclosureType); Protocol protocol = makeProtocol(); save(protocol); Protocol snapshot = protocol.createCopy(); bean.updateProtocol(snapshot, protocol, "i will never change!"); assertTrue(protocol.getRevisionHistory().isEmpty()); } @Test(expected = ValidationException.class) public void testUpdateProtocolNoComment() throws ValidationException { save(sponsor, form1572Type, financialDisclosureType); Protocol protocol = makeProtocol(); save(protocol); Protocol snapshot = protocol.createCopy(); protocol.setProtocolNumber("new number"); bean.updateProtocol(snapshot, protocol, null); } private Protocol makeProtocol() { Protocol protocol = new Protocol(); protocol.setSponsor(sponsor); protocol.addLeadOrganization(leadOrganization, principalInvestigator); protocol.setPhase(ProtocolPhase.PHASE_0); protocol.setProtocolNumber("PPPPPNNNNN"); protocol.setProtocolTitle("PPPPP TTTTT"); protocol.getDocuments().add(FirebirdFileFactory.getInstance().create()); protocol.getRegistrationConfiguration().setInvestigatorOptionality(form1572Type, FormOptionality.REQUIRED); protocol.getRegistrationConfiguration().setSubinvestigatorOptionality(form1572Type, FormOptionality.OPTIONAL); return protocol; } }