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.web.action.sponsor.protocol; import static org.apache.commons.lang3.StringUtils.*; import gov.nih.nci.firebird.data.Organization; import gov.nih.nci.firebird.data.Person; import gov.nih.nci.firebird.data.ProtocolAgent; import gov.nih.nci.firebird.data.ProtocolLeadOrganization; import gov.nih.nci.firebird.exception.ValidationException; import gov.nih.nci.firebird.service.organization.InvalidatedOrganizationException; import gov.nih.nci.firebird.service.protocol.ProtocolService; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Set; import org.apache.commons.lang.StringUtils; import com.google.common.base.Predicate; import com.google.common.base.Splitter; import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.collect.Maps; /** * Helper action for protocol management. */ @SuppressWarnings("PMD.TooManyMethods") // broken down for easier readability. abstract class AbstractModifyProtocolAction extends AbstractProtocolAction { private static final long serialVersionUID = 1L; private String agentList = ""; private Organization sponsor; private String sponsorExternalId; private final Map<String, List<String>> leadOrganizationIdMappings = Maps.newHashMap(); private final Map<Organization, List<Person>> leadOrganizationMappings = Maps.newHashMap(); /** * @param protocolService the protocol service */ protected AbstractModifyProtocolAction(ProtocolService protocolService) { super(protocolService); } @Override public void prepare() { super.prepare(); if (getId(getProtocol()) == null) { setProtocol(getProtocolService().create()); } setSponsor(lookupSponsor()); configureLeadOrganizationMappings(); agentList = StringUtils.trimToNull(getProtocol().getAgentListForDisplay()); } private void configureLeadOrganizationMappings() { if (!leadOrganizationIdMappings.isEmpty()) { populateFromSubmittedValues(); } } private Organization lookupSponsor() { if (!isEmpty(getSponsorExternalId())) { return getOrganization(getSponsorExternalId()); } else { return null; } } private void populateFromSubmittedValues() { leadOrganizationMappings.clear(); Iterator<Entry<String, List<String>>> mappingIterator = leadOrganizationIdMappings.entrySet().iterator(); while (mappingIterator.hasNext()) { Entry<String, List<String>> mapping = mappingIterator.next(); List<Person> investigators = lookupPrincipalInvestigators(mapping.getValue()); try { this.leadOrganizationMappings.put(getOrganizationService().getByExternalId(mapping.getKey()), investigators); } catch (InvalidatedOrganizationException e) { mappingIterator.remove(); addActionError(getText("sponsor.protocol.lead.organization.unavailable.organization.error")); } } } private List<Person> lookupPrincipalInvestigators(List<String> externalIds) { List<Person> investigators = Lists.newArrayList(); if (!externalIds.isEmpty()) { for (String externalId : externalIds) { Person investigator = getPerson(externalId); if (!investigators.contains(investigator)) { investigators.add(investigator); } } } else { addActionError(getText("sponsor.protocol.lead.organization.principal.investigator.required")); } return investigators; } /** * @return parse agentList into individual agent Names. */ Set<String> getAgentNameSet() { Set<String> agentNameSet = new HashSet<String>(); agentList = StringUtils.trimToEmpty(agentList); for (String agentName : Splitter.on(',').omitEmptyStrings().trimResults().split(agentList)) { if (agentName.length() <= ProtocolAgent.MAX_AGENT_LENGTH) { agentNameSet.add(agentName); } else { addFieldError("agentList", getText("sponsor.protocol.agents.error", agentName)); } } return agentNameSet; } /** * Prepares the Mapping Set when entering into the modification screen for the first time. */ protected void doExistingLeadOrganizationMappingSetup() { for (ProtocolLeadOrganization leadOrganization : getProtocol().getLeadOrganizations()) { Organization organization = leadOrganization.getOrganization(); Person principalInvestigator = leadOrganization.getPrincipalInvestigator(); if (leadOrganizationMappings.containsKey(organization)) { leadOrganizationMappings.get(organization).add(principalInvestigator); } else { leadOrganizationMappings.put(organization, Lists.newArrayList(principalInvestigator)); } } } /** * @return struts forward. */ protected String saveProtocol() { getProtocol().setSponsor(getSponsor()); getProtocol().updateAgents(getAgentNameSet()); updateLeadOrganizations(); if (getFieldErrors().size() > 0) { return INPUT; } try { performSave(); return SUCCESS; } catch (ValidationException e) { return handleValidationException(e); } } private void updateLeadOrganizations() { if (leadOrganizationIdMappings.isEmpty()) { getProtocol().getLeadOrganizations().clear(); } else { removeLeadOrganizationsFromProtocol(); addNewLeadOrganizations(); } } private void removeLeadOrganizationsFromProtocol() { Iterator<ProtocolLeadOrganization> leadOrganizationIterator = getProtocol().getLeadOrganizations() .iterator(); while (leadOrganizationIterator.hasNext()) { if (!checkLeadOrganizationSelected(leadOrganizationIterator.next())) { leadOrganizationIterator.remove(); } } } private boolean checkLeadOrganizationSelected(ProtocolLeadOrganization leadOrganization) { String organizationExternalId = leadOrganization.getOrganization().getExternalId(); String investigatorExternalId = leadOrganization.getPrincipalInvestigator().getExternalId(); return leadOrganizationIdMappings.containsKey(organizationExternalId) && leadOrganizationIdMappings.get(organizationExternalId).contains(investigatorExternalId); } private void addNewLeadOrganizations() { for (Entry<String, List<String>> leadOrganizationIdMapping : leadOrganizationIdMappings.entrySet()) { Organization organization = getOrganizationWithId(leadOrganizationIdMapping.getKey()); for (String personKey : leadOrganizationIdMapping.getValue()) { Person principalInvestigator = getInvestigatorWithId(organization, personKey); if (!getProtocol().hasExistingLeadOrganization(organization, principalInvestigator)) { getProtocol().addLeadOrganization(organization, principalInvestigator); } } } } private Organization getOrganizationWithId(final String id) { return Iterables.find(leadOrganizationMappings.keySet(), new Predicate<Organization>() { public boolean apply(Organization organization) { return id.equals(organization.getExternalId()); } }); } private Person getInvestigatorWithId(Organization organization, final String id) { return Iterables.find(leadOrganizationMappings.get(organization), new Predicate<Person>() { public boolean apply(Person person) { return id.equals(person.getExternalId()); } }); } /** * @throws ValidationException if Validation errors exist. */ protected abstract void performSave() throws ValidationException; public void setAgentList(String agentList) { this.agentList = agentList; } public String getAgentList() { return agentList; } public String getSponsorExternalId() { return sponsorExternalId; } public void setSponsorExternalId(String sponsorExternalId) { this.sponsorExternalId = sponsorExternalId; } public Organization getSponsor() { return sponsor; } void setSponsor(Organization sponsor) { this.sponsor = sponsor; } /** * @return The Map identifying the lead organization's external ID to the principal investigator's external ID. */ public Map<String, List<String>> getLeadOrganizationIdMappings() { return leadOrganizationIdMappings; } /** * @return The mapping of lead organizations to primary investigators */ public Map<Organization, List<Person>> getLeadOrganizationMappings() { return leadOrganizationMappings; } }