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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.data; import java.util.ArrayList; import java.util.Collections; import java.util.Date; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; import javax.persistence.CascadeType; import javax.persistence.Column; import javax.persistence.Embedded; import javax.persistence.Entity; import javax.persistence.EnumType; import javax.persistence.Enumerated; import javax.persistence.FetchType; import javax.persistence.GeneratedValue; import javax.persistence.GenerationType; import javax.persistence.Id; import javax.persistence.JoinColumn; import javax.persistence.JoinTable; import javax.persistence.ManyToMany; import javax.persistence.ManyToOne; import javax.persistence.OneToMany; import javax.persistence.OrderBy; import javax.persistence.Table; import javax.persistence.Temporal; import javax.persistence.TemporalType; import javax.persistence.Transient; import javax.persistence.UniqueConstraint; import com.google.common.base.Preconditions; import com.google.common.base.Predicate; import org.apache.commons.lang.text.StrBuilder; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.ForeignKey; import org.hibernate.annotations.Sort; import org.hibernate.annotations.SortType; import org.hibernate.validator.Length; import org.hibernate.validator.NotEmpty; import org.hibernate.validator.NotNull; import com.fiveamsolutions.nci.commons.data.persistent.PersistentObject; import com.google.common.base.Predicates; import com.google.common.collect.FluentIterable; import com.google.common.collect.ImmutableSet; import com.google.common.collect.Iterables; import com.google.common.collect.Sets; /** * Investigation Protocol. */ @Entity @Table(name = Protocol.PROTOCOL_STRING, uniqueConstraints = { @UniqueConstraint(columnNames = { "protocol_number", "sponsor_id" }) }) @SuppressWarnings({ "PMD.AvoidDuplicateLiterals", "PMD.TooManyMethods" }) // literals appear in warning suppressions, class exposes mostly getters and setters public final class Protocol implements PersistentObject, Cloneable { private static final long serialVersionUID = 1L; static final String PROTOCOL_STRING = "protocol"; // for PMD /** * Maximum allowable length for protocol number field. */ public static final int MAX_PROTOCOL_NUM_SIZE = 200; /** * Maximum allowable length for protocol title field. */ public static final int MAX_TITLE_LENGTH = 4000; private Long id; private String protocolNumber; private String protocolTitle; private Organization sponsor; private Set<ProtocolLeadOrganization> leadOrganizations = Sets.newHashSet(); private ProtocolPhase phase; private SortedSet<ProtocolAgent> agents = new TreeSet<ProtocolAgent>(); private Set<FirebirdFile> documents = new HashSet<FirebirdFile>(); private ProtocolRegistrationConfiguration registrationConfiguration = new ProtocolRegistrationConfiguration(); private Set<AbstractProtocolRegistration> registrations = new HashSet<AbstractProtocolRegistration>(); private List<ProtocolRevision> revisionHistory = new ArrayList<ProtocolRevision>(); private Date lastUpdate; /** * Instantiates a new Protocol. This constructor should only be used by Struts and * Hibernate frameworks -- client code should use the <code>create</code> method * below. */ public Protocol() { // empty constructor body } @Id @GeneratedValue(strategy = GenerationType.AUTO) @Override public Long getId() { return id; } /** * @param id the id to set */ public void setId(Long id) { this.id = id; } /** * @return investigational agents used in this protocol. */ @ManyToMany(fetch = FetchType.LAZY) @JoinTable(name = "protocol_protocolagent", joinColumns = @JoinColumn(name = "protocol_id"), inverseJoinColumns = @JoinColumn(name = "protocolagent_id")) @ForeignKey(name = "protocol_fkey", inverseName = "protocolagent_fkey") @Cascade({ org.hibernate.annotations.CascadeType.ALL }) @Sort(type = SortType.NATURAL) public SortedSet<ProtocolAgent> getAgents() { return agents; } @SuppressWarnings("unused") // required by Hibernate private void setAgents(SortedSet<ProtocolAgent> agents) { this.agents = agents; } /** * @return a comma-separated list of the protocol's agents */ @Transient public String getAgentListForDisplay() { StrBuilder builder = new StrBuilder(); for (ProtocolAgent agent : getAgents()) { builder.appendSeparator(", "); builder.append(agent.getName()); } return builder.toString(); } /** * @return files documenting this protocol. */ @ManyToMany(fetch = FetchType.LAZY) @JoinTable(name = "protocol_firebirdfile", joinColumns = @JoinColumn(name = PROTOCOL_STRING), inverseJoinColumns = @JoinColumn(name = "firebirdfile")) @ForeignKey(name = "protocol_fkey", inverseName = "firebirdfile_fkey") @Cascade({ org.hibernate.annotations.CascadeType.ALL, org.hibernate.annotations.CascadeType.DELETE_ORPHAN }) public Set<FirebirdFile> getDocuments() { return documents; } @SuppressWarnings("unused") // required by Hibernate private void setDocuments(Set<FirebirdFile> documents) { this.documents = documents; } /** * @return the trial phase. */ @Enumerated(EnumType.STRING) @Column(length = ProtocolPhase.MAX_LENGTH) @NotNull public ProtocolPhase getPhase() { return phase; } /** * @param phase trial phase. */ public void setPhase(ProtocolPhase phase) { this.phase = phase; } /** * @return protocol number. */ @NotEmpty @Column(name = "protocol_number") @Length(min = 1, max = MAX_PROTOCOL_NUM_SIZE) public String getProtocolNumber() { return protocolNumber; } /** * @param protocolNumber protocol number. */ public void setProtocolNumber(String protocolNumber) { this.protocolNumber = protocolNumber; } /** * @return protocol title. */ @NotNull @Column(name = "protocol_title") @Length(min = 1, max = MAX_TITLE_LENGTH) public String getProtocolTitle() { return protocolTitle; } /** * @param protocolTitle protocol title. */ public void setProtocolTitle(String protocolTitle) { this.protocolTitle = protocolTitle; } /** * @return sponsor organization. */ @ManyToOne(cascade = { CascadeType.PERSIST, CascadeType.MERGE, CascadeType.REFRESH }) @Cascade(org.hibernate.annotations.CascadeType.SAVE_UPDATE) @JoinColumn(name = "sponsor_id") @ForeignKey(name = "protocol_sponsor_fkey") @NotNull public Organization getSponsor() { return sponsor; } /** * @param sponsor sponsor org. */ public void setSponsor(Organization sponsor) { this.sponsor = sponsor; } /** * @return the Set of Lead Organizations. */ @OneToMany(mappedBy = "protocol", fetch = FetchType.LAZY) @Cascade({ org.hibernate.annotations.CascadeType.ALL, org.hibernate.annotations.CascadeType.DELETE_ORPHAN }) public Set<ProtocolLeadOrganization> getLeadOrganizations() { return leadOrganizations; } /** * @param leadOrganizations the Lead Organizations to set. */ public void setLeadOrganizations(Set<ProtocolLeadOrganization> leadOrganizations) { this.leadOrganizations = leadOrganizations; } /** * Add a new Lead Organization to the Protocol. * * @param organization The Organization. * @param principalInvestigator The Principal Investigator person. * @return The new LeadOrganization object. */ public ProtocolLeadOrganization addLeadOrganization(Organization organization, Person principalInvestigator) { Preconditions.checkArgument(!hasExistingLeadOrganization(organization, principalInvestigator), "Lead Organization organizations must be unique!"); ProtocolLeadOrganization leadOrganization = new ProtocolLeadOrganization(this, organization, principalInvestigator); getLeadOrganizations().add(leadOrganization); return leadOrganization; } /** * Checks to see if this protocol already contains an equivalent Lead organization. * * * @param organization The Organization * @param principalInvestigator The Principal Investigator * @return if there is already a Lead organization in this protocol that matches. */ public boolean hasExistingLeadOrganization(Organization organization, Person principalInvestigator) { return getLeadOrganizations() .contains(new ProtocolLeadOrganization(this, organization, principalInvestigator)); } /** * @return the registrationConfiguration */ @Embedded public ProtocolRegistrationConfiguration getRegistrationConfiguration() { return registrationConfiguration; } @SuppressWarnings("unused") // setter required by hibernate private void setRegistrationConfiguration(ProtocolRegistrationConfiguration registrationConfiguration) { this.registrationConfiguration = registrationConfiguration; } /** * Updates the set of <code>ProtocolAgents</code> associated with this protocol. Any new agents will be added and * any existing agents not in the list of names will be removed. * * @param agentNames contains the complete set of agent names for agents to be associated to this protocol. */ public void updateAgents(Set<String> agentNames) { Set<String> newAgentNames = Sets.newHashSet(agentNames); Set<ProtocolAgent> removedAgents = Sets.newHashSet(); for (ProtocolAgent agent : getAgents()) { if (agentNames.contains(agent.getName())) { newAgentNames.remove(agent.getName()); } else { removedAgents.add(agent); } } addAgents(newAgentNames); getAgents().removeAll(removedAgents); } private void addAgents(Set<String> newAgentNames) { for (String agentName : newAgentNames) { getAgents().add(new ProtocolAgent(agentName)); } } @OneToMany(mappedBy = PROTOCOL_STRING, fetch = FetchType.LAZY) @Cascade({ org.hibernate.annotations.CascadeType.ALL, org.hibernate.annotations.CascadeType.DELETE_ORPHAN }) private Set<AbstractProtocolRegistration> getRegistrationsInternal() { return registrations; } @SuppressWarnings("unused") // required by Hibernate private void setRegistrationsInternal(Set<AbstractProtocolRegistration> investigatorRegistrationsInternal) { this.registrations = investigatorRegistrationsInternal; } /** * @param registration the registration to add to this protocol. */ public void addRegistration(AbstractProtocolRegistration registration) { registration.setProtocol(this); registration.configureForms(); getRegistrationsInternal().add(registration); } /** * @return current investigator registrations (aren't revised). */ @Transient public Set<InvestigatorRegistration> getCurrentInvestigatorRegistrations() { return ImmutableSet.copyOf( Iterables.filter(getAllInvestigatorRegistrations(), new Predicate<InvestigatorRegistration>() { @Override public boolean apply(InvestigatorRegistration registration) { return !(registration instanceof RevisedInvestigatorRegistration); } })); } /** * @return all investigator registrations (current and revised). */ @Transient public Set<InvestigatorRegistration> getAllInvestigatorRegistrations() { return ImmutableSet.copyOf(Iterables.filter(getRegistrationsInternal(), InvestigatorRegistration.class)); } /** * @return all revised investigator registrations. */ @Transient public Set<RevisedInvestigatorRegistration> getRevisedInvestigatorRegistrations() { return ImmutableSet .copyOf(Iterables.filter(getRegistrationsInternal(), RevisedInvestigatorRegistration.class)); } /** * @return subinvestigator registrations. */ @Transient public Set<SubInvestigatorRegistration> getSubinvestigatorRegistrations() { return FluentIterable.from(getRegistrationsInternal()).filter(SubInvestigatorRegistration.class).toSet(); } /** * @return active subinvestigator registrations. */ @Transient public Set<SubInvestigatorRegistration> getActiveSubinvestigatorRegistrations() { return FluentIterable.from(getSubinvestigatorRegistrations()) .filter(Predicates.and(AbstractProtocolRegistration.IS_INVITED_PREDICATE, SubInvestigatorRegistration.IS_ACTIVE_PREDICATE)) .toSet(); } /** * @return an unmodifiable set of all registrations (both primary and subinvestigators). */ @Transient public Set<AbstractProtocolRegistration> getAllRegistrations() { return Collections.unmodifiableSet(getRegistrationsInternal()); } /** * @return changes made to this protocol. */ @OneToMany(mappedBy = PROTOCOL_STRING, fetch = FetchType.LAZY, cascade = CascadeType.ALL) @Cascade({ org.hibernate.annotations.CascadeType.ALL, org.hibernate.annotations.CascadeType.DELETE_ORPHAN }) @OrderBy("date DESC") private List<ProtocolRevision> getRevisionHistoryInternal() { return revisionHistory; } @SuppressWarnings("unused") // required by Hibernate private void setRevisionHistoryInternal(List<ProtocolRevision> revisionHistoryInternal) { this.revisionHistory = revisionHistoryInternal; } /** * @return changes made to this protocol in descending order by date. */ @Transient public List<ProtocolRevision> getRevisionHistory() { return Collections.unmodifiableList(getRevisionHistoryInternal()); } /** * @return the lastUpdated */ @Column(name = "last_update") @Temporal(TemporalType.TIMESTAMP) public Date getLastUpdate() { if (lastUpdate != null) { return (Date) lastUpdate.clone(); } return null; } /** * @param lastUpdate the lastUpdated to set */ private void setLastUpdate(Date lastUpdate) { this.lastUpdate = lastUpdate; } /** * @return a copy of this protocol */ public Protocol createCopy() { Protocol copy = new Protocol(); copy.getAgents().addAll(getAgents()); copy.getDocuments().addAll(getDocuments()); copy.setId(getId()); copy.setPhase(getPhase()); copy.setProtocolNumber(getProtocolNumber()); copy.setProtocolTitle(getProtocolTitle()); ProtocolRegistrationConfiguration configuration = copy.getRegistrationConfiguration(); configuration.getInvestigatorConfiguration().setFormOptionalities(new HashMap<FormType, FormOptionality>( getRegistrationConfiguration().getInvestigatorConfiguration().getFormOptionalities())); configuration.getSubinvestigatorConfiguration().setFormOptionalities(new HashMap<FormType, FormOptionality>( getRegistrationConfiguration().getSubinvestigatorConfiguration().getFormOptionalities())); copy.setSponsor(getSponsor()); copyLeadOrganizations(copy); return copy; } private void copyLeadOrganizations(Protocol copy) { for (ProtocolLeadOrganization leadOrganization : leadOrganizations) { copy.addLeadOrganization(leadOrganization.getOrganization(), leadOrganization.getPrincipalInvestigator()); } } /** * @param revision add this revision to the history. */ public void addRevision(ProtocolRevision revision) { revision.setProtocol(this); getRevisionHistoryInternal().add(revision); setLastUpdate(revision.getDate()); } /** * Removes a registration association from a protocol. * * @param registration the registration to remove from this protocol */ void removeRegistration(AbstractProtocolRegistration registration) { registration.setProtocol(null); getRegistrationsInternal().remove(registration); } }