EDIT

/**

* Copyright (C) 2017 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.dataInserter;

import java.io.IOException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import org.joda.time.format.DateTimeFormatter;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.beans.factory.annotation.Qualifier;

import org.springframework.context.ApplicationListener;

import org.springframework.context.event.ContextRefreshedEvent;

import org.springframework.transaction.TransactionStatus;

import org.springframework.transaction.annotation.Transactional;

import com.fasterxml.jackson.core.JsonParseException;

import com.fasterxml.jackson.databind.JsonMappingException;

import com.fasterxml.jackson.databind.ObjectMapper;

import com.vaadin.spring.annotation.SpringComponent;

import eu.etaxonomy.cdm.api.application.CdmRepository;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.model.agent.AgentBase;

import eu.etaxonomy.cdm.model.agent.Institution;

import eu.etaxonomy.cdm.model.common.ExtensionType;

import eu.etaxonomy.cdm.model.name.Registration;

import eu.etaxonomy.cdm.model.name.RegistrationStatus;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.name.TypeDesignationBase;

import eu.etaxonomy.cdm.persistence.hibernate.permission.Role;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.cdm.vaadin.model.registration.DerivationEventTypes;

import eu.etaxonomy.cdm.vaadin.security.RolesAndPermissions;

/**

 * @author a.kohlbecker

 * @since May 9, 2017

 *

 */

@SpringComponent

@Transactional(readOnly=true)

public class RegistrationRequiredDataInserter implements ApplicationListener<ContextRefreshedEvent>{

    protected static final String PARAM_NAME_CREATE = "registrationCreate";

    protected static final String PARAM_NAME_WIPEOUT = "registrationWipeout";

    private static final Logger logger = Logger.getLogger(RegistrationRequiredDataInserter.class);

    private ExtensionType extensionTypeIAPTRegData;

    Map<String, Institution> instituteMap = new HashMap<>();

    public static boolean commandsExecuted = false;

    @Autowired

    @Qualifier("cdmRepository")

    private CdmRepository repo;

 // ==================== Registration creation ======================= //

    /**

     * {@inheritDoc}

     */

    @Override

    public void onApplicationEvent(ContextRefreshedEvent event) {

        insertRequiredData();

        executeSuppliedCommands();

    }

    /**

     *

     */

    private void insertRequiredData() {

        Role roleCuration = RolesAndPermissions.ROLE_CURATION;

        if(repo.getGrantedAuthorityService().find(roleCuration.getUuid()) == null){

            repo.getGrantedAuthorityService().saveOrUpdate(roleCuration.asNewGrantedAuthority());

        }

        if(repo.getTermService().find(DerivationEventTypes.PUBLISHED_IMAGE().getUuid()) == null){

            repo.getTermService().save(DerivationEventTypes.PUBLISHED_IMAGE());

        }

        if(repo.getTermService().find(DerivationEventTypes.UNPUBLISHED_IMAGE().getUuid()) == null){

            repo.getTermService().save(DerivationEventTypes.UNPUBLISHED_IMAGE());

        }

        if(repo.getTermService().find(DerivationEventTypes.CULTURE_METABOLIC_INACTIVE().getUuid()) == null){

            repo.getTermService().save(DerivationEventTypes.CULTURE_METABOLIC_INACTIVE());

        }

        repo.getSession().flush();

    }

    /**

     *

     */

    private void executeSuppliedCommands() {

        if(commandsExecuted){

            // do not run twice

            // a second run could take place during initialization of the web context

            return;

        }

        commandsExecuted  = true;

        String wipeoutCmd = System.getProperty(PARAM_NAME_WIPEOUT);

        String createCmd = System.getProperty(PARAM_NAME_CREATE);

        // ============ DELETE

        if(wipeoutCmd != null && wipeoutCmd.matches("iapt|all")){

            boolean onlyIapt = wipeoutCmd.equals("iapt");

            List<UUID> deleteCandidates = new ArrayList<UUID>();

            TransactionStatus tx = repo.startTransaction(true);

            List<Registration> allRegs = repo.getRegistrationService().list(null, null, null, null, null);

            for(Registration reg : allRegs){

                if(onlyIapt){

                    try {

                        @SuppressWarnings("unchecked")

                        Set<String> extensions = reg.getName().getExtensions(getExtensionTypeIAPTRegData());

                        deleteCandidates.add(reg.getUuid());

                    } catch(NullPointerException e){

                        // IGNORE

                    }

                } else {

                    deleteCandidates.add(reg.getUuid());

                }

            }

            repo.commitTransaction(tx);

            repo.getRegistrationService().delete(deleteCandidates);

        }

        // ============ CREATE

        int pageIndex = 0;

        if(createCmd != null && createCmd.equals("iapt")){

            DateTimeFormatter dateFormat = org.joda.time.format.DateTimeFormat.forPattern("dd.MM.yy").withPivotYear(1950);

            TransactionStatus tx = repo.startTransaction(false);

            while(true) {

                Pager<TaxonName> pager = repo.getNameService().page(null, 1000, pageIndex, null, null);

                if(pager.getRecords().isEmpty()){

                    break;

                }

                List<Registration> newRegs = new ArrayList<>(pager.getRecords().size());

                for(TaxonName name : pager.getRecords()){

                    Set<String> extensionValues = name.getExtensions(getExtensionTypeIAPTRegData());

                    // there is for sure only one

                    if(extensionValues.isEmpty()){

                        continue;

                    }

                    String iaptJson = extensionValues.iterator().next();

                    try {

                        IAPTRegData iaptData = new ObjectMapper().readValue(iaptJson, IAPTRegData.class);

                        if(iaptData.getRegId() == null){

                            continue;

                        }

                        DateTime regDate = null;

                        if(iaptData.getDate() != null){

                            try {

                                regDate = dateFormat.parseDateTime(iaptData.getDate());

                                regDate.getYear();

                            } catch (Exception e) {

                                logger.error("Error parsing date: " + iaptData.getDate(), e);

                                continue;

                            }

                        }

                        Registration reg = Registration.NewInstance();

                        reg.setStatus(RegistrationStatus.PUBLISHED);

                        reg.setIdentifier("http://phycobank/" + iaptData.getRegId());

                        reg.setSpecificIdentifier(iaptData.getRegId().toString());

                        reg.setInstitution(getInstitution(iaptData.getOffice()));

                        reg.setName(name);

                        if(name.getTypeDesignations() != null && !name.getTypeDesignations().isEmpty()){

                            // do not add the collection directly to avoid "Found shared references to a collection" problem

                            HashSet<TypeDesignationBase> typeDesignations = new HashSet<>(name.getTypeDesignations().size());

                            typeDesignations.addAll(name.getTypeDesignations());

                            reg.setTypeDesignations(typeDesignations);

                        }

                        reg.setRegistrationDate(regDate);

                        logger.debug("IAPT Registraion for " + name.getTitleCache());

                        newRegs.add(reg);

                    } catch (JsonParseException e) {

                        logger.error("Error parsing IAPTRegData from extension", e);

                    } catch (JsonMappingException e) {

                        logger.error("Error mapping json from extension to IAPTRegData", e);

                    } catch (IOException e) {

                        logger.error(e);

                    }

                }

                repo.getRegistrationService().save(newRegs);

                repo.getRegistrationService().getSession().flush();

                logger.debug("Registrations saved");

                pageIndex++;

            }

            repo.commitTransaction(tx);

        }

    }

    /**

     * @param office

     * @return

     */

    private Institution getInstitution(String office) {

        Institution institution;

        if(instituteMap.containsKey(office)){

            institution = instituteMap.get(office);

        } else {

            Pager<AgentBase> pager = repo.getAgentService().findByTitle(Institution.class, office, MatchMode.EXACT, null, null, null, null, null);

            if(!pager.getRecords().isEmpty()){

                institution =  (Institution) pager.getRecords().get(0);

            } else {

                Institution institute = (Institution) repo.getAgentService().save(Institution.NewNamedInstance(office));

                institution = institute;

            }

            instituteMap.put(office, institution);

        }

        return institution;

    }

    private ExtensionType getExtensionTypeIAPTRegData() {

        if(extensionTypeIAPTRegData == null){

            extensionTypeIAPTRegData = (ExtensionType) repo.getTermService().load(UUID.fromString("9be1bfe3-6ba0-4560-af15-86971ab96e09"));

        }

        return extensionTypeIAPTRegData;

    }

}