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.FirebirdFile; import gov.nih.nci.firebird.data.FormOptionality; import gov.nih.nci.firebird.data.FormType; import gov.nih.nci.firebird.data.ProtocolLeadOrganization; import gov.nih.nci.firebird.data.Protocol; import gov.nih.nci.firebird.data.ProtocolAgent; import gov.nih.nci.firebird.data.ProtocolRevision; import gov.nih.nci.firebird.data.ProtocolModification; import java.text.MessageFormat; import java.util.ArrayList; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.ResourceBundle; import java.util.Set; import org.apache.commons.lang.ObjectUtils; import com.google.common.base.Predicate; import com.google.common.collect.Iterables; /** * Detect changes made to a protocol since the base snapshot was taken. */ @SuppressWarnings("PMD.TooManyMethods") // modification check methods split out for readability class ProtocolModificationDetector { private static final String INVESTIGATOR_MESSAGE_PREFIX = ".investigator.message"; private static final String SPONSOR_MESSAGE_PREFIX = ".sponsor.message"; private final Protocol original; private final Protocol revised; private final ResourceBundle resources; private final List<ProtocolModification> modifications = new ArrayList<ProtocolModification>(); ProtocolModificationDetector(Protocol original, Protocol revised, ResourceBundle resources) { this.original = original; this.revised = revised; this.resources = resources; loadModifications(); } void addModifications(ProtocolRevision revision) { for (ProtocolModification modification : modifications) { revision.addModification(modification); } } boolean isModificationDetected() { return !modifications.isEmpty(); } private void loadModifications() { checkProtocolNumber(); checkProtocolTitle(); checkSponsor(); checkLeadOrganizations(); checkPhase(); checkAgents(); checkDocuments(); checkRegistrationConfiguration(); } private void checkProtocolNumber() { checkPropertyChange("protocol.change.number", original.getProtocolNumber(), revised.getProtocolNumber()); } private void checkPropertyChange(String messageKey, Object oldValue, Object newValue) { if (!ObjectUtils.equals(oldValue, newValue)) { addModification(messageKey, oldValue, newValue); } } private void addModification(String descriptionKeyPrefix, Object... args) { String investigatorDescription = MessageFormat .format(resources.getString(descriptionKeyPrefix + INVESTIGATOR_MESSAGE_PREFIX), args); String sponsorDescription = MessageFormat .format(resources.getString(descriptionKeyPrefix + SPONSOR_MESSAGE_PREFIX), args); ProtocolModification modification = new ProtocolModification(investigatorDescription, sponsorDescription); modifications.add(modification); } private void checkProtocolTitle() { checkPropertyChange("protocol.change.title", original.getProtocolTitle(), revised.getProtocolTitle()); } private void checkSponsor() { checkPropertyChange("protocol.change.sponsor", original.getSponsor().getName(), revised.getSponsor().getName()); } private void checkLeadOrganizations() { Set<ProtocolLeadOrganization> previousLeadOrganizations = original.getLeadOrganizations(); Set<ProtocolLeadOrganization> newLeadOrganizations = revised.getLeadOrganizations(); addRemovedLeadOrganizationMessages(previousLeadOrganizations, newLeadOrganizations); addNewLeadOrganizationsMessages(previousLeadOrganizations, newLeadOrganizations); } private void addRemovedLeadOrganizationMessages(Set<ProtocolLeadOrganization> previousLeadOrganizations, Set<ProtocolLeadOrganization> newLeadOrganizations) { checkForOrganizationsNotPresent(previousLeadOrganizations, newLeadOrganizations, "protocol.change.lead.organization.removed"); } private void checkForOrganizationsNotPresent(Set<ProtocolLeadOrganization> previousLeadOrganizations, Set<ProtocolLeadOrganization> newLeadOrganizations, String messageKey) { for (ProtocolLeadOrganization leadOrganization : previousLeadOrganizations) { if (!containsLeadOrganization(newLeadOrganizations, leadOrganization)) { addModification(messageKey, leadOrganization.getOrganization().getName(), leadOrganization.getPrincipalInvestigator().getDisplayName()); } } } private boolean containsLeadOrganization(Set<ProtocolLeadOrganization> leadOrganizations, final ProtocolLeadOrganization leadOrganization) { return Iterables.any(leadOrganizations, new Predicate<ProtocolLeadOrganization>() { @Override public boolean apply(ProtocolLeadOrganization input) { return input.equals(leadOrganization); } }); } private void addNewLeadOrganizationsMessages(Set<ProtocolLeadOrganization> previousLeadOrganizations, Set<ProtocolLeadOrganization> newLeadOrganizations) { checkForOrganizationsNotPresent(newLeadOrganizations, previousLeadOrganizations, "protocol.change.lead.organization.added"); } private void checkPhase() { checkPropertyChange("protocol.change.phase", original.getPhase().getDisplay(), revised.getPhase().getDisplay()); } private void checkAgents() { checkAgentCollection("protocol.change.agent.removed", original.getAgents(), revised.getAgents()); checkAgentCollection("protocol.change.agent.added", revised.getAgents(), original.getAgents()); } private void checkAgentCollection(String messageKey, Set<ProtocolAgent> actual, Set<ProtocolAgent> expected) { for (ProtocolAgent agent : actual) { if (!expected.contains(agent)) { addModification(messageKey, agent.getName()); } } } private void checkDocuments() { checkDocumentCollection("protocol.change.document.removed", original.getDocuments(), revised.getDocuments()); checkDocumentCollection("protocol.change.document.added", revised.getDocuments(), original.getDocuments()); } private void checkDocumentCollection(String messageKey, Set<FirebirdFile> actual, Set<FirebirdFile> expected) { for (FirebirdFile file : actual) { if (!expected.contains(file)) { addModification(messageKey, file.getName()); } } } private void checkRegistrationConfiguration() { checkForOptionalityChanges("protocol.change.form.optionality.investigator", original.getRegistrationConfiguration().getInvestigatorConfiguration().getFormOptionalities(), revised.getRegistrationConfiguration().getInvestigatorConfiguration().getFormOptionalities()); checkForOptionalityChanges("protocol.change.form.optionality.subinvestigator", original.getRegistrationConfiguration().getSubinvestigatorConfiguration().getFormOptionalities(), revised.getRegistrationConfiguration().getSubinvestigatorConfiguration().getFormOptionalities()); } private void checkForOptionalityChanges(String messageKey, Map<FormType, FormOptionality> baseOptionality, Map<FormType, FormOptionality> modifiedOptionality) { Set<FormType> addedFormTypes = new HashSet<FormType>(modifiedOptionality.keySet()); for (FormType formType : baseOptionality.keySet()) { FormOptionality optionality = baseOptionality.get(formType); if (!addedFormTypes.remove(formType)) { addModification(messageKey, formType.getDescription(), optionality.getDisplay(), FormOptionality.NONE.getDisplay()); } else if (optionality != modifiedOptionality.get(formType)) { addModification(messageKey, formType.getDescription(), optionality.getDisplay(), modifiedOptionality.get(formType).getDisplay()); } } for (FormType type : addedFormTypes) { addModification(messageKey, type.getDescription(), FormOptionality.NONE.getDisplay(), modifiedOptionality.get(type).getDisplay()); } } }