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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 gov.nih.nci.firebird.common.RichTextUtil; import gov.nih.nci.firebird.common.ValidationFailure; import gov.nih.nci.firebird.common.ValidationResult; import gov.nih.nci.firebird.exception.ValidationException; import java.text.MessageFormat; import java.util.Date; import java.util.EnumSet; import java.util.Locale; import java.util.ResourceBundle; import java.util.Set; import javax.persistence.Basic; import javax.persistence.CascadeType; import javax.persistence.Column; 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.Lob; import javax.persistence.ManyToOne; import javax.persistence.MappedSuperclass; import javax.persistence.Transient; import org.apache.commons.lang.StringUtils; import org.hibernate.annotations.Cascade; import org.hibernate.annotations.ForeignKey; import org.hibernate.validator.NotNull; import com.fiveamsolutions.nci.commons.data.persistent.PersistentObject; import com.google.common.collect.Sets; /** * Base class for forms filled out by users (typically registration forms). */ @MappedSuperclass @SuppressWarnings({ "PMD.TooManyMethods", "PMD.ExcessiveClassLength" }) // Mainly getters and setters public abstract class AbstractRegistrationForm implements PersistentObject { private static final long serialVersionUID = 1L; private static final String PDF_EXTENSION = ".pdf"; static final EnumSet<FormStatus> SUBMITTABLE_STATUSES = EnumSet.of(FormStatus.SUBMITTED, FormStatus.COMPLETED, FormStatus.ACCEPTED, FormStatus.REJECTED, FormStatus.REVISED); static final EnumSet<FormStatus> CURRENTLY_REVIEWABLE_STATUSES = EnumSet.of(FormStatus.IN_REVIEW, FormStatus.ACCEPTED, FormStatus.REJECTED); static final EnumSet<FormStatus> REVIEWED_STATUSES = EnumSet.of(FormStatus.ACCEPTED, FormStatus.REJECTED); static final Set<FormTypeEnum> FORMS_WITH_COLLECTION_OF_DOCUMENTS = EnumSet .of(FormTypeEnum.HUMAN_RESEARCH_CERTIFICATE); private Long id; private FormStatus formStatus = FormStatus.NOT_STARTED; private Date formStatusDate = new Date(); private FormType formType; private FirebirdFile signedPdf; private FirebirdFile flattenedPdf; private String comments; private final Set<Long> invalidEntityIds = Sets.newHashSet(); AbstractRegistrationForm() { // no-arg constructor required by Hibernate } AbstractRegistrationForm(FormType formType) { setFormType(formType); } AbstractRegistrationForm(FormType formType, FormStatus formStatus) { setFormType(formType); this.formStatus = formStatus; } /** * @return all organizations referenced in this form. */ @Transient public Set<Organization> getOrganizations() { Set<Organization> organizations = Sets.newHashSet(); if (getRegistration().getProfile().getPrimaryOrganization() != null) { organizations.add(getRegistration().getProfile().getPrimaryOrganization().getOrganization()); } return organizations; } /** * @return all organizations referenced in this form. */ @Transient public abstract Set<Person> getPersons(); @Id @GeneratedValue(strategy = GenerationType.AUTO) @Override public Long getId() { return id; } /** * @param id db id to set */ public void setId(Long id) { this.id = id; } /** * @return whether or not this form has additional documents. */ @Transient @SuppressWarnings("PMD.EmptyMethodInAbstractClassShouldBeAbstract") // As a team we decided this should be here public boolean isAdditionalDocumentsUploaded() { return false; } /** * @return the number of additional documents added to this form. */ @Transient @SuppressWarnings("PMD.EmptyMethodInAbstractClassShouldBeAbstract") // As a team we decided this should be here public int getNumberOfAdditionalDocuments() { return 0; } /** * @return form status */ @Enumerated(EnumType.STRING) @Column(name = "form_status") public FormStatus getFormStatus() { return formStatus; } /** * @param formStatus how the form status will show. */ public void setFormStatus(FormStatus formStatus) { if (formStatus != this.formStatus) { setFormStatusDate(new Date()); this.formStatus = formStatus; } } /** * @return the status date. */ @NotNull @Column(name = "status_date") public Date getFormStatusDate() { return formStatusDate; } /** * @param formStatusDate formStatusDate to set */ protected void setFormStatusDate(Date formStatusDate) { this.formStatusDate = formStatusDate; } /** * @param formType the formType to set */ private void setFormType(FormType formType) { this.formType = formType; } /** * @return the formType */ @ManyToOne(optional = false, cascade = { CascadeType.PERSIST, CascadeType.MERGE, CascadeType.REFRESH }, fetch = FetchType.EAGER) @Cascade(org.hibernate.annotations.CascadeType.SAVE_UPDATE) @ForeignKey(name = "form_form_type_fkey") @JoinColumn(name = "form_type_id") public FormType getFormType() { return formType; } /** * @return the registration to the protocol */ @Transient public abstract AbstractRegistration getRegistration(); /** * @return the investigator associated with the form. */ @Transient public Person getInvestigator() { return getRegistration().getProfile().getPerson(); } /** * @return the signedPdf */ @ManyToOne @Cascade(org.hibernate.annotations.CascadeType.ALL) @JoinColumn(name = "signed_pdf_id") @ForeignKey(name = "registration_form_signed_pdf_fkey") public FirebirdFile getSignedPdf() { return signedPdf; } /** * @param signedPdf the signedPdf to set */ public void setSignedPdf(FirebirdFile signedPdf) { this.signedPdf = signedPdf; } /** * @return the flattenedPdf */ @ManyToOne @Cascade(org.hibernate.annotations.CascadeType.ALL) @JoinColumn(name = "flattened_pdf_id") @ForeignKey(name = "registration_form_flattened_pdf_fkey") public FirebirdFile getFlattenedPdf() { return flattenedPdf; } /** * @param flattenedPdf the flattenedPdf to set */ public void setFlattenedPdf(FirebirdFile flattenedPdf) { this.flattenedPdf = flattenedPdf; } /** * @return the plain text Comments. */ @Transient public String getPlainTextComments() { return RichTextUtil.convertToPlainText(getComments()); } /** * @return user entered free-form text. */ @Lob @Basic(fetch = FetchType.LAZY) @Column(name = "comments") public String getComments() { return comments; } /** * @return the base name (i.e. no extension) to be used for files generated from this form. */ @Transient public String getFormFileBaseName() { StringBuilder sb = new StringBuilder(); sb.append(getInvestigator().getLastName()); sb.append('_'); sb.append(getInvestigator().getFirstName()); sb.append('_'); sb.append(getFormType().getFormTypeEnum().name()); return sb.toString().toLowerCase(Locale.getDefault()); } /** * @return the name of the file in progress. */ @Transient public String getInProgressFileName() { return getFormFileBaseName() + PDF_EXTENSION; } /** * @param comments user entered free-form text. */ public void setComments(String comments) { this.comments = comments; } /** * @return the Optionality of the form in the current registration. */ @Transient public final FormOptionality getFormOptionality() { FormOptionality optionality = getRegistration().getFormConfiguration().get(getFormType()); if (optionality != null) { return optionality; } else { return FormOptionality.NONE; } } /** * Validates the current form content and updates its status. If Subclasses require further validation they should * override the validate method and call super.validate(). * * @param resources resource bundle with validation messages included * @throws ValidationException if there are validation problems. */ public final void checkSubmissionReadiness(ResourceBundle resources) throws ValidationException { ValidationResult result = new ValidationResult(); validate(result, resources); updateFormStatus(result); } private void updateFormStatus(ValidationResult result) throws ValidationException { if (!getRegistration().isLockedForInvestigator()) { if (result.isValid()) { if (shouldUpdateStatus()) { setFormStatus(FormStatus.COMPLETED); } } else { downgradeCompleted(); throw new ValidationException(result); } } } private boolean shouldUpdateStatus() { return getRegistration().getLastSubmissionDate() == null || (!isReviewed() && getFormStatus() != FormStatus.REVISED); } private void downgradeCompleted() { if (getRegistration().getStatus() == RegistrationStatus.INCOMPLETE && shouldUpdateStatus()) { setFormStatus(FormStatus.INCOMPLETE); } else if (getFormStatus() == FormStatus.COMPLETED || getFormStatus() == FormStatus.SUBMITTED) { setFormStatus(FormStatus.IN_PROGRESS); } } /** * Performs the validation checks. Subclasses should override if necessary and call super.validate(). * * @param result result to add validation failures to * @param resources resource bundle with validation messages included */ protected void validate(ValidationResult result, ResourceBundle resources) { if (requiresActiveCurationStatus()) { validateNesCurationStatus(result, resources); } } /** * Checks whether entities and roles should be status ACTIVE in NES to be valid for signing. * * @return true if entities and roles must be ACTIVE */ public boolean requiresActiveCurationStatus() { return Boolean.valueOf(System.getProperty("registration.validation.require.nes.status.active")); } /** * Create a Validation Failure object using the provided values. * * @param resources the Resource bundle to retrieve messages from. * @param key the Message key of the error. * @param arguments any optional argument replacements. * @return the Validation Failure object */ public ValidationFailure createValidationFailure(ResourceBundle resources, String key, Object... arguments) { String messageTemplate = resources.getString(key); return new ValidationFailure(MessageFormat.format(messageTemplate, arguments)); } private void validateNesCurationStatus(ValidationResult result, ResourceBundle resources) { for (Organization organization : getOrganizations()) { validateCurationStatus(organization, result, resources); } for (Person person : getPersons()) { validateCurationStatus(person, result, resources); } } private void validateCurationStatus(Organization organization, ValidationResult result, ResourceBundle resources) { if (CurationStatus.NULLIFIED.equals(organization.getCurationStatus())) { ValidationFailure failure = createValidationFailure(resources, "validation.failures.organization.nullified", organization.getName(), getFormType().getName()); addValidationFailure(result, failure, organization.getId()); } else if (!CurationStatus.ACTIVE.equals(organization.getCurationStatus())) { ValidationFailure failure = createValidationFailure(resources, "validation.failure.uncurated", organization.getName(), getFormType().getName(), organization.getCurationStatus().getDisplay()); addValidationFailure(result, failure, organization.getId()); } } /** * Adds the validation error to the validation result object and adds the entity id to the list of invalid entities. * * @param result validation result * @param failure validation failure * @param entityId invalid entity's ID */ public void addValidationFailure(ValidationResult result, ValidationFailure failure, Long entityId) { result.addFailure(failure); getInvalidEntityIds().add(entityId); } private void validateCurationStatus(Person person, ValidationResult result, ResourceBundle resources) { if (CurationStatus.NULLIFIED.equals(person.getCurationStatus())) { result.addFailure(createValidationFailure(resources, "validation.failures.person.nullified", person.getDisplayName(), getFormType().getName())); getInvalidEntityIds().add(person.getId()); } else if (!CurationStatus.ACTIVE.equals(person.getCurationStatus())) { result.addFailure(createValidationFailure(resources, "validation.failure.uncurated", person.getDisplayName(), getFormType().getName(), person.getCurationStatus().getDisplay())); getInvalidEntityIds().add(person.getId()); } else if (person.isUpdatePending()) { result.addFailure(createValidationFailure(resources, "validation.failure.pending.nes.updates", person.getDisplayName(), getFormType().getName())); getInvalidEntityIds().add(person.getId()); } } /** * @return the file the sponsor will review. */ @Transient public FirebirdFile getFileToReview() { return getFlattenedPdf(); } /** * @return whether or not this form requires validation. */ public boolean requiresValidation() { return !FormOptionality.NONE.equals(getFormOptionality()); } /** * @return true if this form can be digitally signed. */ @Transient public boolean isSignable() { return StringUtils.isNotEmpty(getFormType().getSigningField()); } /** * @return true if this form has been digitally signed. */ @Transient public boolean isSigned() { return getSignedPdf() != null; } /** * Default functionality for when this form is submitted. Forms can override functionality to provide for additional * actions that need to be performed when a submit occurs. Ex. Archiving data */ public void submitForm() { if (shouldUpdateStatus()) { setFormStatus(FormStatus.SUBMITTED); } } /** * Default functionality for when this form is returned. Forms can override functionality to provide for additional * actions that need to be performed when a form is returned occurs. Ex. Removing archived data * * @return objects that should be removed from the database */ Set<PersistentObject> returnForm() { Set<PersistentObject> objectsToDelete = Sets.newHashSet(); FirebirdFile removedFlattenedPdf = getFlattenedPdf(); FirebirdFile removedSignedPdf = getSignedPdf(); setFlattenedPdf(null); setSignedPdf(null); if (shouldDeleteFile(removedFlattenedPdf)) { objectsToDelete.add(removedFlattenedPdf); } if (shouldDeleteFile(removedSignedPdf)) { objectsToDelete.add(removedSignedPdf); } return objectsToDelete; } boolean shouldDeleteFile(FirebirdFile file) { return file != null && getRegistration().getProfile().isOrphan(file); } /** * @return whether or not this form has a submittable status */ @Transient public boolean isSubmittable() { return SUBMITTABLE_STATUSES.contains(getFormStatus()); } /** * @return whether or not this form is currently reviewable by the sponsor */ @Transient public boolean isCurrentlyReviewable() { return getRegistration().getStatus() == RegistrationStatus.IN_REVIEW && CURRENTLY_REVIEWABLE_STATUSES.contains(getFormStatus()); } /** * @return whether or not this form is reviewed by the sponsor */ @Transient public boolean isReviewed() { return REVIEWED_STATUSES.contains(getFormStatus()); } /** * @return whether or not this form required to be reviewed by the sponsor. */ @Transient @SuppressWarnings("PMD.EmptyMethodInAbstractClassShouldBeAbstract") // This should be here public boolean isReviewRequired() { return true; } /** * @return All entity ids which have failed validation */ @Transient public Set<Long> getInvalidEntityIds() { return invalidEntityIds; } void copyCommonData(AbstractRegistrationForm copyTo) { copyTo.setFormStatus(getFormStatus()); copyTo.setFormStatusDate(getFormStatusDate()); copyTo.setSignedPdf(getSignedPdf()); copyTo.setFlattenedPdf(getFlattenedPdf()); copyTo.setComments(getComments()); } /** * Checks if the given file is referenced from this form. Subclasses should * override as appropriate. * * @param file check if this form references this file * @return true if referenced */ boolean isFileReferenced(FirebirdFile file) { return file.equals(getFlattenedPdf()) || file.equals(getSignedPdf()); } /** * @return whether or not to show the comments link for the investigator */ @Transient public boolean isCommentsLinkToInvestigatorToBeDisplayed() { return !getPlainTextComments().isEmpty() && getFormStatus() != FormStatus.ACCEPTED && getFormStatus() != FormStatus.IN_REVIEW; } /** * @return true if this form consists of a collection of documents. */ @Transient public boolean isCollectionOfDocuments() { return FORMS_WITH_COLLECTION_OF_DOCUMENTS.contains(getFormType().getFormTypeEnum()); } }