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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.dataInserter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.EnumSet;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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import org.joda.time.Partial;
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import org.joda.time.format.DateTimeFormatter;
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import org.springframework.context.event.ContextRefreshedEvent;
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import org.springframework.security.authentication.AuthenticationCredentialsNotFoundException;
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import org.springframework.security.core.GrantedAuthority;
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import org.springframework.transaction.TransactionStatus;
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import com.fasterxml.jackson.core.JsonParseException;
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import com.fasterxml.jackson.databind.JsonMappingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.etaxonomy.cdm.api.application.AbstractDataInserter;
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import eu.etaxonomy.cdm.api.application.CdmRepository;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.GrantedAuthorityImpl;
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import eu.etaxonomy.cdm.model.common.Group;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.name.Registration;
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import eu.etaxonomy.cdm.model.name.RegistrationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.persistence.hibernate.permission.CRUD;
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import eu.etaxonomy.cdm.persistence.hibernate.permission.CdmAuthority;
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import eu.etaxonomy.cdm.persistence.hibernate.permission.CdmPermissionClass;
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import eu.etaxonomy.cdm.persistence.hibernate.permission.Role;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.vaadin.model.registration.KindOfUnitTerms;
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import eu.etaxonomy.cdm.vaadin.security.RolesAndPermissions;
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/**
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*
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* Can create missing registrations for names which have Extensions of the Type <code>IAPTRegdata.json</code>.
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* See https://dev.e-taxonomy.eu/redmine/issues/6621 for further details.
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* This feature can be activated by by supplying one of the following jvm command line arguments:
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* <ul>
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* <li><code>-DregistrationCreate=iapt</code>: create all iapt Registrations if missing</li>
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* <li><code>-DregistrationWipeout=iapt</code>: remove all iapt Registrations</li>
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* <li><code>-DregistrationWipeout=all</code>: remove all Registrations</li>
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* </ul>
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* The <code>-DregistrationWipeout</code> commands are executed before the <code>-DregistrationCreate</code> and will not change the name and type designations.
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*
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* @author a.kohlbecker
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* @since May 9, 2017
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*
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*/
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public class RegistrationRequiredDataInserter extends AbstractDataInserter {
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protected static final String PARAM_NAME_CREATE = "registrationCreate";
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protected static final String PARAM_NAME_WIPEOUT = "registrationWipeout";
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protected static final UUID GROUP_SUBMITTER_UUID = UUID.fromString("c468c6a7-b96c-4206-849d-5a825f806d3e");
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protected static final UUID GROUP_CURATOR_UUID = UUID.fromString("135210d3-3db7-4a81-ab36-240444637d45");
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private static final EnumSet<CRUD> CREATE_READ = EnumSet.of(CRUD.CREATE, CRUD.READ);
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private static final EnumSet<CRUD> CREATE_READ_UPDATE_DELETE = EnumSet.of(CRUD.CREATE, CRUD.READ, CRUD.UPDATE, CRUD.DELETE);
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private static final Logger logger = Logger.getLogger(RegistrationRequiredDataInserter.class);
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private ExtensionType extensionTypeIAPTRegData;
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Map<String, Institution> instituteMap = new HashMap<>();
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public static boolean commandsExecuted = false;
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private CdmRepository repo;
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private boolean hasRun = false;
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public void setCdmRepository(CdmRepository repo){
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this.repo = repo;
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}
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// ==================== Registration creation ======================= //
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/**
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* {@inheritDoc}
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*/
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@Override
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public void onApplicationEvent(ContextRefreshedEvent event) {
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if(hasRun){
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return;
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}
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runAsAuthentication(Role.ROLE_ADMIN);
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insertRequiredData();
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executeSuppliedCommands();
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restoreAuthentication();
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hasRun = true;
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}
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/**
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*
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*/
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private void insertRequiredData() {
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Role roleCuration = RolesAndPermissions.ROLE_CURATION;
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if(repo.getGrantedAuthorityService().find(roleCuration.getUuid()) == null){
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repo.getGrantedAuthorityService().saveOrUpdate(roleCuration.asNewGrantedAuthority());
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}
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Group groupCurator = repo.getGroupService().load(GROUP_CURATOR_UUID, Arrays.asList("grantedAuthorities"));
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if(groupCurator == null){
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groupCurator = Group.NewInstance();
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groupCurator.setUuid(GROUP_CURATOR_UUID);
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groupCurator.setName("Curator");
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}
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assureGroupHas(groupCurator, new CdmAuthority(CdmPermissionClass.REGISTRATION, CREATE_READ_UPDATE_DELETE).toString());
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repo.getGroupService().saveOrUpdate(groupCurator);
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Group groupSubmitter = repo.getGroupService().load(GROUP_SUBMITTER_UUID, Arrays.asList("grantedAuthorities"));
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if(groupSubmitter == null){
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groupSubmitter = Group.NewInstance();
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groupSubmitter.setUuid(GROUP_SUBMITTER_UUID);
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groupSubmitter.setName("Submitter");
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}
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assureGroupHas(groupSubmitter, new CdmAuthority(CdmPermissionClass.TAXONNAME, CREATE_READ).toString());
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assureGroupHas(groupSubmitter, new CdmAuthority(CdmPermissionClass.TEAMORPERSONBASE, CREATE_READ).toString());
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assureGroupHas(groupSubmitter, new CdmAuthority(CdmPermissionClass.REGISTRATION, CREATE_READ).toString());
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assureGroupHas(groupSubmitter, new CdmAuthority(CdmPermissionClass.SPECIMENOROBSERVATIONBASE, CREATE_READ).toString());
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repo.getGroupService().saveOrUpdate(groupSubmitter);
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if(repo.getTermService().find(KindOfUnitTerms.SPECIMEN().getUuid()) == null){
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repo.getTermService().save(KindOfUnitTerms.SPECIMEN());
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}
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if(repo.getTermService().find(KindOfUnitTerms.PUBLISHED_IMAGE().getUuid()) == null){
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repo.getTermService().save(KindOfUnitTerms.PUBLISHED_IMAGE());
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}
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if(repo.getTermService().find(KindOfUnitTerms.UNPUBLISHED_IMAGE().getUuid()) == null){
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repo.getTermService().save(KindOfUnitTerms.UNPUBLISHED_IMAGE());
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}
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if(repo.getTermService().find(KindOfUnitTerms.CULTURE_METABOLIC_INACTIVE().getUuid()) == null){
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repo.getTermService().save(KindOfUnitTerms.CULTURE_METABOLIC_INACTIVE());
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}
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// --- remove after release 4.12.0 ------------------------------------------------------
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// delete old DerivationEventTypes terms which are no longer used, see #7059
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// UUID_PUBLISHED_IMAGE = UUID.fromString("b8cba359-4202-4741-8ed8-4f17ae94b3e3");
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// UUID UUID_UNPUBLISHED_IMAGE = UUID.fromString("6cd5681f-0918-4ed6-89a8-bda1480dc890");
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// UUID UUID_CULTURE_METABOLIC_INACTIVE = UUID.fromString("eaf1c853-ba8d-4c40-aa0a-56beac96b0d2");
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for(UUID uuid : new UUID[]{
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UUID.fromString("b8cba359-4202-4741-8ed8-4f17ae94b3e3"),
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UUID.fromString("6cd5681f-0918-4ed6-89a8-bda1480dc890"),
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UUID.fromString("eaf1c853-ba8d-4c40-aa0a-56beac96b0d2")}){
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if(repo.getTermService().find(uuid) != null){
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repo.getTermService().delete(uuid);
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}
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}
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// --------------------------------------------------------------------------------------
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repo.getSession().flush();
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}
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private void assureGroupHas(Group group, String authorityString){
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boolean authorityExists = false;
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for(GrantedAuthority ga : group.getGrantedAuthorities()){
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if((authorityExists = ga.getAuthority().equals(authorityString)) == true){
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break;
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}
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}
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if(!authorityExists){
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group.addGrantedAuthority(findGrantedAuthority(authorityString));
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}
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}
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private GrantedAuthorityImpl findGrantedAuthority(String authorityString){
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GrantedAuthorityImpl ga = null;
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try{
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ga = repo.getGrantedAuthorityService().findAuthorityString(authorityString);
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} catch (AuthenticationCredentialsNotFoundException e){
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e.printStackTrace();
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}
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if(ga == null){
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ga = GrantedAuthorityImpl.NewInstance(authorityString);
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repo.getGrantedAuthorityService().save(ga);
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}
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return ga;
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}
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/**
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*
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*/
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private void executeSuppliedCommands() {
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if(commandsExecuted){
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// do not run twice
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// a second run could take place during initialization of the web context
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return;
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}
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commandsExecuted = true;
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String wipeoutCmd = System.getProperty(PARAM_NAME_WIPEOUT);
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String createCmd = System.getProperty(PARAM_NAME_CREATE);
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// ============ DELETE
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if(wipeoutCmd != null && wipeoutCmd.matches("iapt|all")){
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boolean onlyIapt = wipeoutCmd.equals("iapt");
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List<UUID> deleteCandidates = new ArrayList<UUID>();
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TransactionStatus tx = repo.startTransaction(true);
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List<Registration> allRegs = repo.getRegistrationService().list(null, null, null, null, null);
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for(Registration reg : allRegs){
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if(onlyIapt){
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try {
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@SuppressWarnings("unchecked")
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Set<String> extensions = reg.getName().getExtensions(getExtensionTypeIAPTRegData());
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deleteCandidates.add(reg.getUuid());
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} catch(NullPointerException e){
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// IGNORE
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}
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} else {
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deleteCandidates.add(reg.getUuid());
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}
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}
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repo.commitTransaction(tx);
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repo.getRegistrationService().delete(deleteCandidates);
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}
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// ============ CREATE
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int pageIndex = 0;
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if(createCmd != null && createCmd.equals("iapt")){
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DateTimeFormatter dateFormat1 = org.joda.time.format.DateTimeFormat.forPattern("dd.MM.yy").withPivotYear(1950);
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DateTimeFormatter dateFormat2 = org.joda.time.format.DateTimeFormat.forPattern("yyyy-MM-dd").withPivotYear(1950);
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TransactionStatus tx = repo.startTransaction(false);
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while(true) {
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Pager<TaxonName> pager = repo.getNameService().page(null, 1000, pageIndex, null, null);
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if(pager.getRecords().isEmpty()){
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break;
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}
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List<Registration> newRegs = new ArrayList<>(pager.getRecords().size());
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for(TaxonName name : pager.getRecords()){
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Set<String> extensionValues = name.getExtensions(getExtensionTypeIAPTRegData());
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// there is for sure only one
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if(extensionValues.isEmpty()){
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continue;
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}
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String iaptJson = extensionValues.iterator().next();
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try {
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IAPTRegData iaptData = new ObjectMapper().readValue(iaptJson, IAPTRegData.class);
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if(iaptData.getRegId() == null){
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continue;
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}
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DateTime regDate = null;
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if(iaptData.getDate() != null){
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DateTimeFormatter dateFormat;
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if(iaptData.getDate().matches("\\d{4}-\\d{2}-\\d{2}")){
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dateFormat = dateFormat2;
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} else {
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dateFormat = dateFormat1;
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}
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try {
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regDate = dateFormat.parseDateTime(iaptData.getDate());
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regDate.getYear();
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} catch (Exception e) {
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logger.error("Error parsing date : " + iaptData.getDate(), e);
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continue;
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}
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}
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Registration reg = Registration.NewInstance();
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reg.setStatus(RegistrationStatus.PUBLISHED);
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reg.setIdentifier("http://phycobank.org/" + iaptData.getRegId());
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reg.setSpecificIdentifier(iaptData.getRegId().toString());
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reg.setInstitution(getInstitution(iaptData.getOffice()));
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boolean isPhycobankID = false; // Integer.valueOf(reg.getSpecificIdentifier()) >= 100000;
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Partial youngestDate = null;
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Reference youngestPub = null;
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// find youngest publication
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// NOTE:
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// data imported from IAPT does not have typedesignation citations and sometimes no nomref
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if(isPhycobankID){
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youngestPub = (Reference) name.getNomenclaturalReference();
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youngestDate = partial(youngestPub.getDatePublished());
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if(name.getTypeDesignations() != null && !name.getTypeDesignations().isEmpty()){
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for(TypeDesignationBase td : name.getTypeDesignations()){
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if(td.getCitation() == null){
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continue;
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}
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Partial pubdate = partial(td.getCitation().getDatePublished());
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if(youngestDate.compareTo(pubdate) < 0){
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youngestDate = pubdate;
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youngestPub = td.getCitation();
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}
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}
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}
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}
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if((isPhycobankID && youngestPub == name.getNomenclaturalReference()) || !isPhycobankID) {
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reg.setName(name);
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} else {
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logger.debug("skipping name published in older referece");
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}
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if(name.getTypeDesignations() != null && !name.getTypeDesignations().isEmpty()){
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// do not add the collection directly to avoid "Found shared references to a collection" problem
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HashSet<TypeDesignationBase> typeDesignations = new HashSet<>(name.getTypeDesignations().size());
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for(TypeDesignationBase td : name.getTypeDesignations()){
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if(td.getCitation() == null && isPhycobankID){
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logger.error("Missing TypeDesignation Citation in Phycobank data");
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continue;
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}
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if((isPhycobankID && youngestPub == td.getCitation()) || !isPhycobankID){
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typeDesignations.add(td);
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} else {
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logger.debug("skipping typedesignation published in older reference");
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}
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}
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reg.setTypeDesignations(typeDesignations);
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}
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reg.setRegistrationDate(regDate);
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logger.debug("IAPT Registration for " + name.getTitleCache());
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newRegs.add(reg);
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} catch (JsonParseException e) {
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logger.error("Error parsing IAPTRegData from extension", e);
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} catch (JsonMappingException e) {
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logger.error("Error mapping json from extension to IAPTRegData", e);
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} catch (IOException e) {
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logger.error(e);
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}
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}
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repo.getRegistrationService().save(newRegs);
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repo.getRegistrationService().getSession().flush();
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logger.debug("Registrations saved");
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pageIndex++;
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}
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repo.commitTransaction(tx);
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}
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}
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/**
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* @param datePublished
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* @return
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*/
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private Partial partial(TimePeriod datePublished) {
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if(datePublished != null){
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if(datePublished.getEnd() != null){
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return datePublished.getEnd();
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} else {
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return datePublished.getStart();
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}
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}
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return null;
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}
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398
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/**
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* @param office
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* @return
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*/
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402
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private Institution getInstitution(String office) {
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Institution institution;
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if(instituteMap.containsKey(office)){
|
405
|
institution = instituteMap.get(office);
|
406
|
} else {
|
407
|
|
408
|
Pager<AgentBase> pager = repo.getAgentService().findByTitle(Institution.class, office, MatchMode.EXACT, null, null, null, null, null);
|
409
|
if(!pager.getRecords().isEmpty()){
|
410
|
institution = (Institution) pager.getRecords().get(0);
|
411
|
} else {
|
412
|
Institution institute = (Institution) repo.getAgentService().save(Institution.NewNamedInstance(office));
|
413
|
institution = institute;
|
414
|
}
|
415
|
instituteMap.put(office, institution);
|
416
|
}
|
417
|
return institution;
|
418
|
}
|
419
|
|
420
|
|
421
|
private ExtensionType getExtensionTypeIAPTRegData() {
|
422
|
if(extensionTypeIAPTRegData == null){
|
423
|
extensionTypeIAPTRegData = (ExtensionType) repo.getTermService().load(UUID.fromString("9be1bfe3-6ba0-4560-af15-86971ab96e09"));
|
424
|
}
|
425
|
return extensionTypeIAPTRegData;
|
426
|
}
|
427
|
|
428
|
|
429
|
|
430
|
}
|