Examples with Visibility org.orcid.jaxb.model.message.Visibility used on opensource projects

Example 6 with Visibility

use of org.orcid.jaxb.model.message.Visibility in project ORCID-Source by ORCID.

the class OrcidProfileManagerImpl method addOrcidWorks.

@Override
@Transactional
public void addOrcidWorks(OrcidProfile updatedOrcidProfile) {
    String orcid = updatedOrcidProfile.getOrcidIdentifier().getPath();
    OrcidProfile existingProfile = retrieveOrcidProfile(orcid);
    if (existingProfile == null) {
        throw new IllegalArgumentException("No record found for " + orcid);
    }
    OrcidWorks existingOrcidWorks = existingProfile.retrieveOrcidWorks();
    OrcidWorks updatedOrcidWorks = updatedOrcidProfile.retrieveOrcidWorks();
    Visibility workVisibilityDefault = existingProfile.getOrcidInternal().getPreferences().getActivitiesVisibilityDefault().getValue();
    Boolean claimed = existingProfile.getOrcidHistory().isClaimed();
    setWorkPrivacy(updatedOrcidWorks, workVisibilityDefault, claimed == null ? false : claimed);
    String amenderOrcid = sourceManager.retrieveSourceOrcid();
    addSourceToWorks(updatedOrcidWorks, amenderOrcid);
    updatedOrcidWorks = dedupeWorks(updatedOrcidWorks);
    List<OrcidWork> updatedOrcidWorksList = updatedOrcidWorks.getOrcidWork();
    checkUserCanHoldMoreElement(existingProfile.retrieveOrcidWorks(), updatedOrcidProfile.retrieveOrcidWorks());
    if (compareWorksUsingScopusWay) {
        checkForAlreadyExistingWorks(existingOrcidWorks, updatedOrcidWorksList);
        if (existingOrcidWorks != null)
            checkWorkExternalIdentifiersAreNotDuplicated(updatedOrcidWorksList, existingOrcidWorks.getOrcidWork());
        else
            checkWorkExternalIdentifiersAreNotDuplicated(updatedOrcidWorksList, null);
    } else {
        checkForAlreadyExistingWorksLegacyMode(existingOrcidWorks, updatedOrcidWorksList);
    }
    //workDao.increaseDisplayIndexOnAllElements(orcid);
    persistAddedWorks(orcid, updatedOrcidWorksList);
    profileDao.flush();
    boolean notificationsEnabled = existingProfile.getOrcidInternal().getPreferences().getNotificationsEnabled();
    if (notificationsEnabled) {
        List<Item> activities = new ArrayList<>();
        for (OrcidWork updatedWork : updatedOrcidWorksList) {
            Item activity = new Item();
            activity.setItemName(updatedWork.getWorkTitle().getTitle().getContent());
            activity.setItemType(ItemType.WORK);
            activity.setPutCode(updatedWork.getPutCode());
            activities.add(activity);
        }
        notificationManager.sendAmendEmail(existingProfile, AmendedSection.WORK, activities);
    }
}

Example 7 with Visibility

use of org.orcid.jaxb.model.message.Visibility in project ORCID-Source by ORCID.

the class OrcidProfileManagerImpl method updateOrcidProfile.

@Override
@Transactional
public OrcidProfile updateOrcidProfile(OrcidProfile orcidProfile, UpdateOptions updateOptions) {
    String amenderOrcid = sourceManager.retrieveSourceOrcid();
    ProfileEntity existingProfileEntity = profileDao.find(orcidProfile.getOrcidIdentifier().getPath());
    Visibility defaultVisibility = Visibility.fromValue(existingProfileEntity.getActivitiesVisibilityDefault().value());
    if (existingProfileEntity != null) {
        //Dont delete the existing elements anymore
        //profileDao.removeChildrenWithGeneratedIds(existingProfileEntity);
        setWorkPrivacy(orcidProfile, defaultVisibility);
        setAffiliationPrivacy(orcidProfile, defaultVisibility);
        setFundingPrivacy(orcidProfile, defaultVisibility);
    }
    dedupeWorks(orcidProfile);
    dedupeAffiliations(orcidProfile);
    dedupeFundings(orcidProfile);
    addSourceToEmails(orcidProfile, existingProfileEntity, amenderOrcid);
    Boolean claimed = orcidProfile.getOrcidHistory() != null ? orcidProfile.getOrcidHistory().isClaimed() : existingProfileEntity.getClaimed();
    if (orcidProfile.getOrcidInternal() != null && orcidProfile.getOrcidInternal().getPreferences() != null && orcidProfile.getOrcidInternal().getPreferences().getActivitiesVisibilityDefault() != null) {
        defaultVisibility = orcidProfile.getOrcidInternal().getPreferences().getActivitiesVisibilityDefault().getValue();
    }
    addDefaultVisibilityToBioItems(orcidProfile, defaultVisibility, claimed);
    ProfileEntity profileEntity = adapter.toProfileEntity(orcidProfile, existingProfileEntity, updateOptions);
    profileEntity.setLastModified(new Date());
    profileEntity.setIndexingStatus(IndexingStatus.PENDING);
    profileDao.flush();
    ProfileEntity updatedProfileEntity = profileDao.merge(profileEntity);
    profileDao.refresh(updatedProfileEntity);
    OrcidProfile updatedOrcidProfile = convertToOrcidProfile(updatedProfileEntity, LoadOptions.ALL);
    orcidProfileCacheManager.put(updatedOrcidProfile);
    return updatedOrcidProfile;
}

Example 8 with Visibility

use of org.orcid.jaxb.model.message.Visibility in project ORCID-Source by ORCID.

the class VisibilityFilterImpl method filter.

/**
     * Remove the elements that are not present in the list of set of
     * {@link org.orcid.jaxb.model.message .Visibility}s present in the array
     * passed in.
     * 
     * @param messageToBeFiltered
     *            the {@link org.orcid.jaxb.model.message.OrcidMessage} that
     *            will be traversed looking for
     *            {@link org .orcid.jaxb.model.message.VisibilityType} elements.
     * @param source
     *            The orcid source that is executing the request
     * @param removeAttribute
     *            should all {@link org.orcid.jaxb.model.message.Visibility}
     *            elements be removed from the object graph. This has the effect
     *            that they will not be present in the resulting JAXB
     *            serialisation.
     * @param visibilities
     *            What {@link org.orcid.jaxb.model.message.Visibility} elements
     *            should be allowed.
     * @return the cleansed {@link org.orcid.jaxb.model.message.OrcidMessage}
     */
@Override
public OrcidMessage filter(OrcidMessage messageToBeFiltered, final String sourceId, final boolean allowPrivateWorks, final boolean allowPrivateFunding, final boolean allowPrivateAffiliations, Visibility... visibilities) {
    if (messageToBeFiltered == null || visibilities == null || visibilities.length == 0) {
        return null;
    }
    String messageIdForLog = getMessageIdForLog(messageToBeFiltered);
    LOGGER.debug("About to filter message: " + messageIdForLog);
    final Set<Visibility> visibilitySet = new HashSet<Visibility>(Arrays.asList(visibilities));
    if (visibilitySet.contains(Visibility.SYSTEM)) {
        return messageToBeFiltered;
    } else {
        TreeCleaner treeCleaner = new TreeCleaner();
        treeCleaner.clean(messageToBeFiltered, new TreeCleaningStrategy() {

            public TreeCleaningDecision needsStripping(Object obj) {
                TreeCleaningDecision decision = TreeCleaningDecision.DEFAULT;
                if (obj != null) {
                    Class<?> clazz = obj.getClass();
                    if (!PojoUtil.isEmpty(sourceId)) {
                        if (allowPrivateAffiliations && Affiliation.class.isAssignableFrom(clazz)) {
                            Affiliation affiliation = (Affiliation) obj;
                            Source source = affiliation.getSource();
                            if (source != null) {
                                String sourcePath = source.retrieveSourcePath();
                                if (sourcePath != null) {
                                    if (sourceId.equals(sourcePath)) {
                                        decision = TreeCleaningDecision.IGNORE;
                                    }
                                }
                            }
                        } else if (allowPrivateFunding && Funding.class.isAssignableFrom(clazz)) {
                            Funding funding = (Funding) obj;
                            Source source = funding.getSource();
                            if (source != null) {
                                String sourcePath = source.retrieveSourcePath();
                                if (sourcePath != null) {
                                    if (sourceId.equals(sourcePath)) {
                                        decision = TreeCleaningDecision.IGNORE;
                                    }
                                }
                            }
                        } else if (allowPrivateWorks && OrcidWork.class.isAssignableFrom(clazz)) {
                            OrcidWork work = (OrcidWork) obj;
                            Source source = work.getSource();
                            if (source != null) {
                                if (sourceId.equals(source.retrieveSourcePath())) {
                                    decision = TreeCleaningDecision.IGNORE;
                                }
                            }
                        }
                    }
                    // fields are inside the country element
                    if (Address.class.isAssignableFrom(clazz)) {
                        Address address = (Address) obj;
                        // Remove empty addresses
                        if (address.getCountry() == null) {
                            decision = TreeCleaningDecision.CLEANING_REQUIRED;
                        } else {
                            Country country = address.getCountry();
                            // Allow public addresses
                            if (Visibility.PUBLIC.equals(country.getVisibility())) {
                                decision = TreeCleaningDecision.IGNORE;
                            } else if (visibilitySet.contains(Visibility.LIMITED)) {
                                // Allow limited visibility when possible
                                if (Visibility.LIMITED.equals(country.getVisibility())) {
                                    decision = TreeCleaningDecision.IGNORE;
                                } else {
                                    // As last resource, check the source
                                    Source source = country.getSource();
                                    if (source != null && sourceId != null && sourceId.equals(source.retrieveSourcePath())) {
                                        decision = TreeCleaningDecision.IGNORE;
                                    } else {
                                        decision = TreeCleaningDecision.CLEANING_REQUIRED;
                                    }
                                }
                            }
                        }
                    }
                    if (Email.class.isAssignableFrom(clazz)) {
                        // include all emails if present
                        try {
                            Authentication authentication = getAuthentication();
                            if (authentication != null && messageToBeFiltered.getOrcidProfile() != null) {
                                permissionChecker.checkPermissions(getAuthentication(), ScopePathType.EMAIL_READ_PRIVATE, messageToBeFiltered.getOrcidProfile().retrieveOrcidPath());
                                decision = TreeCleaningDecision.IGNORE;
                            }
                        } catch (AccessControlException e) {
                        // private email can't be read, do nothing here
                        }
                    }
                    // that implements PrivateVisibleToSource
                    if (sourceId != null)
                        if (PrivateVisibleToSource.class.isAssignableFrom(clazz) && visibilitySet.contains(Visibility.LIMITED)) {
                            Source source = ((PrivateVisibleToSource) obj).getSource();
                            if (source != null) {
                                if (sourceId.equals(source.retrieveSourcePath())) {
                                    decision = TreeCleaningDecision.IGNORE;
                                }
                            }
                        }
                    if (TreeCleaningDecision.DEFAULT.equals(decision)) {
                        if (WorkContributors.class.isAssignableFrom(clazz)) {
                            decision = TreeCleaningDecision.IGNORE;
                        } else if (VisibilityType.class.isAssignableFrom(clazz)) {
                            VisibilityType visibilityType = (VisibilityType) obj;
                            if ((visibilityType.getVisibility() == null || !visibilitySet.contains(visibilityType.getVisibility()))) {
                                decision = TreeCleaningDecision.CLEANING_REQUIRED;
                            }
                        }
                    }
                }
                return decision;
            }
        });
        OrcidProfile orcidProfile = messageToBeFiltered.getOrcidProfile();
        if (orcidProfile != null) {
            orcidProfile.setOrcidInternal(null);
        }
        LOGGER.debug("Finished filtering message: " + messageIdForLog);
        return messageToBeFiltered;
    }
}

Example 9 with Visibility

use of org.orcid.jaxb.model.message.Visibility in project ORCID-Source by ORCID.

the class OrcidApiAuthorizationSecurityAspect method visibilityResponseFilter.

@AfterReturning(pointcut = "@annotation(accessControl)", returning = "response")
public void visibilityResponseFilter(Response response, AccessControl accessControl) {
    if (accessControl.requestComesFromInternalApi()) {
        return;
    }
    Object entity = response.getEntity();
    if (entity != null && OrcidMessage.class.isAssignableFrom(entity.getClass())) {
        OrcidMessage orcidMessage = (OrcidMessage) entity;
        //If it is search results, don't filter them, just return them
        if (orcidMessage.getOrcidSearchResults() != null) {
            return;
        }
        // get the client id
        Object authentication = getAuthentication();
        Set<Visibility> visibilities = new HashSet<Visibility>();
        if (allowAnonymousAccess((Authentication) authentication, accessControl)) {
            visibilities.add(Visibility.PUBLIC);
        } else {
            visibilities = permissionChecker.obtainVisibilitiesForAuthentication(getAuthentication(), accessControl.requiredScope(), orcidMessage);
        }
        //If the message contains a bio, and the given name is filtered, restore it as an empty space
        boolean setEmptyGivenNameIfFiltered = false;
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile() != null && orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                setEmptyGivenNameIfFiltered = true;
            }
        }
        ScopePathType requiredScope = accessControl.requiredScope();
        // If the required scope is */read-limited or */update
        if (isUpdateOrReadScope(requiredScope)) {
            // if it should be able to
            if (OrcidOAuth2Authentication.class.isAssignableFrom(authentication.getClass())) {
                OrcidOAuth2Authentication orcidAuth = (OrcidOAuth2Authentication) getAuthentication();
                OAuth2Request authorization = orcidAuth.getOAuth2Request();
                String clientId = authorization.getClientId();
                // #1: Get the user orcid
                String userOrcid = getUserOrcidFromOrcidMessage(orcidMessage);
                // #2: Evaluate the scope to know which field to filter
                boolean allowWorks = false;
                boolean allowFunding = false;
                boolean allowAffiliations = false;
                // Get the update equivalent scope, if it is reading, but,
                // doesnt have the read permissions, check if it have the
                // update permissions
                ScopePathType equivalentUpdateScope = getEquivalentUpdateScope(requiredScope);
                if (requiredScope.equals(ScopePathType.READ_LIMITED)) {
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.ORCID_WORKS_READ_LIMITED.getContent(), ScopePathType.ORCID_WORKS_UPDATE.getContent()))
                        allowWorks = true;
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.FUNDING_READ_LIMITED.getContent(), ScopePathType.FUNDING_UPDATE.getContent()))
                        allowFunding = true;
                    if (hasScopeEnabled(clientId, userOrcid, ScopePathType.AFFILIATIONS_READ_LIMITED.getContent(), ScopePathType.AFFILIATIONS_UPDATE.getContent()))
                        allowAffiliations = true;
                } else if (requiredScope.equals(ScopePathType.ORCID_WORKS_UPDATE) || requiredScope.equals(ScopePathType.ORCID_WORKS_READ_LIMITED)) {
                    // works
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private works
                        allowWorks = true;
                } else if (requiredScope.equals(ScopePathType.FUNDING_UPDATE) || requiredScope.equals(ScopePathType.FUNDING_READ_LIMITED)) {
                    // funding
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private funding
                        allowFunding = true;
                } else if (requiredScope.equals(ScopePathType.AFFILIATIONS_UPDATE) || requiredScope.equals(ScopePathType.AFFILIATIONS_READ_LIMITED)) {
                    // affiliations
                    if (hasScopeEnabled(clientId, userOrcid, requiredScope.getContent(), equivalentUpdateScope == null ? null : equivalentUpdateScope.getContent()))
                        // If so, allow him to see private affiliations
                        allowAffiliations = true;
                }
                visibilityFilter.filter(orcidMessage, clientId, allowWorks, allowFunding, allowAffiliations, visibilities.toArray(new Visibility[visibilities.size()]));
            } else {
                visibilityFilter.filter(orcidMessage, null, false, false, false, visibilities.toArray(new Visibility[visibilities.size()]));
            }
        } else {
            visibilityFilter.filter(orcidMessage, null, false, false, false, visibilities.toArray(new Visibility[visibilities.size()]));
        }
        //If the given name was set at the beginning and now is filtered, it means we should restore it as an empty field
        if (setEmptyGivenNameIfFiltered) {
            if (orcidMessage.getOrcidProfile() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio() == null) {
                    orcidMessage.getOrcidProfile().setOrcidBio(new OrcidBio());
                }
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() == null) {
                    orcidMessage.getOrcidProfile().getOrcidBio().setPersonalDetails(new PersonalDetails());
                }
            }
        }
        //Filter given or family names visibility 
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() != null) {
                    if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getGivenNames() != null) {
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getGivenNames().setVisibility(null);
                    } else {
                        //Null given names could break client integrations, so, lets return an empty string
                        GivenNames empty = new GivenNames();
                        empty.setContent(StringUtils.EMPTY);
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().setGivenNames(empty);
                    }
                    if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getFamilyName() != null) {
                        orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getFamilyName().setVisibility(null);
                    }
                }
            }
        }
        //replace section visibilities now we may have filtered items
        if (orcidMessage.getOrcidProfile() != null) {
            if (orcidMessage.getOrcidProfile().getOrcidBio() != null) {
                if (orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails() != null) {
                    OtherNames n = orcidMessage.getOrcidProfile().getOrcidBio().getPersonalDetails().getOtherNames();
                    if (n != null) {
                        n.setVisibility(getMostFromCollection(n.getOtherName()));
                    }
                }
                ExternalIdentifiers ids = orcidMessage.getOrcidProfile().getOrcidBio().getExternalIdentifiers();
                if (ids != null) {
                    ids.setVisibility(getMostFromCollection(ids.getExternalIdentifier()));
                }
                Keywords kws = orcidMessage.getOrcidProfile().getOrcidBio().getKeywords();
                if (kws != null) {
                    kws.setVisibility(getMostFromCollection(kws.getKeyword()));
                }
                ResearcherUrls urls = orcidMessage.getOrcidProfile().getOrcidBio().getResearcherUrls();
                if (urls != null) {
                    urls.setVisibility(getMostFromCollection(urls.getResearcherUrl()));
                }
            }
        }
    }
}

Example 10 with Visibility

use of org.orcid.jaxb.model.message.Visibility in project ORCID-Source by ORCID.

the class Jaxb2JpaAdapterImpl method setBiographyDetails.

private void setBiographyDetails(ProfileEntity profileEntity, Biography biography) {
    if (biography != null) {
        Visibility defaultVisibility = profileEntity.getActivitiesVisibilityDefault() == null ? OrcidVisibilityDefaults.BIOGRAPHY_DEFAULT.getVisibility() : Visibility.fromValue(profileEntity.getActivitiesVisibilityDefault().value());
        if (profileEntity.getBiographyEntity() == null) {
            profileEntity.setBiographyEntity(new BiographyEntity());
            profileEntity.getBiographyEntity().setProfile(profileEntity);
        }
        profileEntity.getBiographyEntity().setBiography(biography.getContent());
        if (profileEntity.getClaimed() == null || !profileEntity.getClaimed()) {
            if (biography.getVisibility() != null) {
                profileEntity.getBiographyEntity().setVisibility(org.orcid.jaxb.model.common_v2.Visibility.fromValue(biography.getVisibility().value()));
            } else {
                profileEntity.getBiographyEntity().setVisibility(org.orcid.jaxb.model.common_v2.Visibility.fromValue(defaultVisibility.value()));
            }
        }
        //Fill the visibility in case it is still null
        if (profileEntity.getBiographyEntity().getVisibility() == null) {
            profileEntity.getBiographyEntity().setVisibility(org.orcid.jaxb.model.common_v2.Visibility.fromValue(defaultVisibility.value()));
        }
    }
}