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package eu.dnetlib.msro.workers.aggregation.mdstore.mongo;
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import java.time.Duration;
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import java.time.LocalDate;
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import java.time.ZoneId;
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import java.util.Date;
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import java.util.List;
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import java.util.Optional;
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import java.util.TreeSet;
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import java.util.stream.Collectors;
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import javax.annotation.PostConstruct;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import com.mongodb.BasicDBObject;
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import com.mongodb.WriteConcern;
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import com.mongodb.client.MongoCollection;
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import com.mongodb.client.MongoDatabase;
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import com.mongodb.client.model.Filters;
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import com.mongodb.client.model.UpdateOptions;
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import eu.dnetlib.miscutils.streams.DnetStreamSupport;
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import eu.dnetlib.msro.workers.aggregation.mdstore.*;
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import eu.dnetlib.msro.workers.aggregation.mdstore.model.*;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Component;
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import static eu.dnetlib.msro.workers.aggregation.mdstore.MDStoreConstants.*;
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/**
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* Created by claudio on 13/03/2017.
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*/
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@Component
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public class MDStoreTransactionManagerImpl implements MDStoreTransactionManager {
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/**
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* The Constant log.
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*/
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private static final Log log = LogFactory.getLog(MDStoreTransactionManagerImpl.class);
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/**
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* The max number of concurrent transactions per mdstore.
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*/
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private int maxTransactions = 1;
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/**
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* The expired days.
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*/
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private int expiredDays = 3;
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/**
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* The db.
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*/
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@Autowired
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private MongoDatabase db;
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/**
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* The manager table.
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*/
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private MongoCollection<MDStoreManagerInfo> managerTable;
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/**
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* Bootstrap manager.
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*/
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@PostConstruct
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private void bootstrapManager() {
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log.debug("Bootstrap Manager start");
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final MongoCollection<MDStoreDescription> metadataColl = db.getCollection(METADATA_NAME, MDStoreDescription.class);
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managerTable = db.getCollection(METADATA_MANAGER_TABLE, MDStoreManagerInfo.class);
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metadataColl.find().iterator().forEachRemaining(desc -> {
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getManagerTable().insertOne(asManagerInfo(desc.getMdId()));
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log.debug(String.format("Added %s to Metadata Manager data structure", desc.getMdId()));
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});
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log.debug("Create index in MetadaManager");
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getManagerTable().createIndex(new BasicDBObject(MDStoreConstants.MDID, 1));
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}
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private MDStoreManagerInfo asManagerInfo(final String mdId) {
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return MDStoreManagerInfo.create()
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.setMdId(mdId)
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.setCurrentId(createInternalId(mdId));
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void verifyConsistency() throws MDStoreException {
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if (getManagerTable() == null) {
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final int size = DnetStreamSupport.generateStreamFromIterator(
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db.listCollectionNames().iterator())
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.filter(it -> it.contains(METADATA_MANAGER_TABLE))
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.collect(Collectors.toList())
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.size();
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if (size == 0) {
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bootstrapManager();
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} else {
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managerTable = db.getCollection(METADATA_MANAGER_TABLE, MDStoreManagerInfo.class);
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}
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}
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if (getManagerTable() == null) {
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throw new MDStoreException("Something bad happen, unable to create managerTable");
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}
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#createMDStore(String)
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*/
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@Override
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public String createMDStore(final String mdId) throws MDStoreException {
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log.debug("Creating new mdstore");
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verifyConsistency();
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final MDStoreManagerInfo managerInfo = asManagerInfo(mdId);
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getManagerTable().insertOne(managerInfo);
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db.createCollection(managerInfo.getCurrentId());
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return managerInfo.getCurrentId();
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}
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private String createInternalId(final String mdId) {
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String newId = mdId;
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if (mdId.contains("_")) {
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newId = StringUtils.substringBefore(mdId, "_");
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}
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return newId;
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#dropMDStore(String)
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*/
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@Override
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public void dropMDStore(final String mdId) throws MDStoreException {
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verifyConsistency();
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log.debug("Dropping MDStore: " + mdId);
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final MDStoreManagerInfo dropped = getManagerTable().findOneAndDelete(Filters.eq(MDID, mdId));
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garbage();
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doDrop(dropped.getCurrentId());
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#getMDStoreCollection(String)
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*/
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@Override
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public String getMDStoreCollection(final String mdId) throws MDStoreException {
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verifyConsistency();
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return getInfoForCurrentMdStore(mdId).getCurrentId();
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#startTransaction(String, boolean)
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*/
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@Override
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public String startTransaction(final String mdId, final boolean refresh) throws MDStoreException {
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verifyConsistency();
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log.info("Start transaction for metadata store " + mdId);
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final MDStoreManagerInfo info = getInfoForCurrentMdStore(mdId);
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final String transactionId = StringUtils.substringBefore(mdId, "_") + "::" + System.currentTimeMillis();
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if (info.getTransactions().size() > getMaxTransactions()) {
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throw new MDStoreException(
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String.format("Cannot create more than %s transactions, found: %s, mdId: %s", getMaxTransactions(), info.getTransactions().size(), mdId));
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}
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info.getTransactions().add(
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MDStoreTransactionInfo.create()
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.setId(transactionId)
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.setRefresh(refresh));
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getManagerTable().findOneAndReplace(Filters.eq(MDID, info.getMdId()), info);
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return transactionId;
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#commit(String, String, MDStore)
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*/
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@Override
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public boolean commit(final String transactionId, final String mdId, final MDStore current) throws MDStoreException {
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verifyConsistency();
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final MDStoreManagerInfo info = getInfoForCurrentMdStore(mdId);
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final List<MDStoreTransactionInfo> transactions = info.getTransactions();
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if (transactions.isEmpty()) {
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throw new MDStoreException("Error, unable to find transaction with Id " + transactionId);
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}
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final MDStoreTransactionInfo tx = findTransaction(transactions, transactionId);
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transactions.remove(tx);
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final String oldId = info.getCurrentId();
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if (tx.getRefresh()) {
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info.setCurrentId(transactionId);
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if (info.getExpiring().isEmpty()) {
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doDrop(oldId);
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}
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log.debug("Replaced collection ");
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} else {
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log.debug("commit incremental ");
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updateIncremental(transactionId, oldId);
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doDrop(transactionId);
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}
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getManagerTable().findOneAndReplace(Filters.eq(MDID, info.getMdId()), info);
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log.info("Committed transaction for metadata store " + mdId);
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return true;
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}
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/**
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* Find transaction.
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*
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* @param transactions the transactions
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* @param transactionId the transaction id
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* @return the DB object
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*/
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private MDStoreTransactionInfo findTransaction(final List<MDStoreTransactionInfo> transactions, final String transactionId) throws MDStoreException {
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final Optional<MDStoreTransactionInfo> tx = transactions.stream()
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.filter(t -> transactionId.equals(t.getId())).findFirst();
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if (!tx.isPresent()) {
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throw new MDStoreException("Error, unable to find transaction with Id " + transactionId);
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} else {
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return tx.get();
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}
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}
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/**
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* {@inheritDoc}
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*
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* @see MDStoreTransactionManager#readMdStore(String)
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*/
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@Override
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public String readMdStore(final String mdId) throws MDStoreException {
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verifyConsistency();
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final MDStoreManagerInfo info = getInfoForCurrentMdStore(mdId);
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final String currentId = info.getCurrentId();
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final List<MDStoreExpiredInfo> expiring = info.getExpiring();
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updateMdstoreUsed(expiring, currentId);
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getManagerTable().findOneAndReplace(Filters.eq(MDID, info.getMdId()), info);
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return currentId;
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}
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/**
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* Update mdstore used.
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*
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* @param expiring the values to be updated
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* @param mdId the mdstore id
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*/
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private void updateMdstoreUsed(final List<MDStoreExpiredInfo> expiring, final String mdId) {
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final Optional<MDStoreExpiredInfo> expiringInfo = expiring.stream()
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.filter(info -> mdId.equals(info.getId()))
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.findFirst();
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if (expiringInfo.isPresent()) {
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expiringInfo.get().setLastRead(new Date());
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} else {
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expiring.add(MDStoreExpiredInfo.create().setId(mdId));
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}
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}
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/**
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* Gets the manager table.
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*
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* @return the managerTable
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*/
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private MongoCollection<MDStoreManagerInfo> getManagerTable() {
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return managerTable;
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}
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/**
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* (non-Javadoc)
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*
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* @see eu.dnetlib.msro.workers.aggregation.mdstore.MDStoreTransactionManager#getInfoForCurrentMdStore(java.lang.String)
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*/
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@Override
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public MDStoreManagerInfo getInfoForCurrentMdStore(final String mdId) throws MDStoreException {
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verifyConsistency();
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final MDStoreManagerInfo managerInfo = getManagerTable().find(Filters.eq(MDID, mdId)).first();
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if (managerInfo == null) {
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throw new MDStoreException("Error, unable to find MDStore " + mdId);
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}
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return managerInfo;
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}
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/**
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* (non-Javadoc)
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*
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* @see eu.dnetlib.msro.workers.aggregation.mdstore.MDStoreTransactionManager#dropUsed(java.lang.String, java.lang.String)
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*/
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@Override
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public Boolean dropUsed(final String mdId, final String idToDrop) throws MDStoreException {
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verifyConsistency();
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final MDStoreManagerInfo managerInfo = getInfoForCurrentMdStore(mdId);
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final Optional<MDStoreExpiredInfo> info = managerInfo.getExpiring().stream()
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.filter(i -> idToDrop.equals(i.getId()))
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.findFirst();
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if (info.isPresent()) {
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doDrop(idToDrop);
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managerInfo.getExpiring().remove(info.get());
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getManagerTable().findOneAndReplace(Filters.eq(MDID, managerInfo.getMdId()), managerInfo);
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return true;
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} else {
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throw new MDStoreException("Error, unable to drop collection " + idToDrop);
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}
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}
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private void doDrop(final String mdId) {
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db.getCollection(mdId).drop();
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db.getCollection(DISCARDED_PREFIX + mdId).drop();
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log.debug("deleted collection " + mdId);
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}
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/**
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* (non-Javadoc)
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*
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* @see eu.dnetlib.msro.workers.aggregation.mdstore.MDStoreTransactionManager#garbage()
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*/
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@Override
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public void garbage() throws MDStoreException {
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verifyConsistency();
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log.info("Start garbage collection of MdStore");
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int totalDeleted = 0;
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for (MDStoreManagerInfo currentInfo : getManagerTable().find()) {
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if (log.isDebugEnabled()) {
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log.debug("start to check id: " + currentInfo.getCurrentId());
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}
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garbageExpiring(currentInfo);
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garbageTransactions(currentInfo);
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getManagerTable().findOneAndReplace(Filters.eq(MDID, currentInfo.getMdId()), currentInfo);
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}
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// DELETING Collection that are not in the metadataManager table
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for (String coll : db.listCollectionNames()) {
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if ((coll.length() > 30) && (!coll.contains(DISCARDED_PREFIX)) && (!coll.contains("resolved"))) {
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final MDStoreManagerInfo info = getMetadataObjectForCollections(coll);
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349
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if (shouldDelete(coll, info)) {
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if (log.isDebugEnabled()) {
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log.debug("delete collection: " + coll + " from mongo");
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}
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doDrop(coll);
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if (log.isDebugEnabled()) {
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log.debug("delete collection: discarded-" + coll + " from mongo");
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}
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}
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}
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}
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log.info("Complete garbage collection of MdStore, total store deleted: " + totalDeleted);
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}
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private boolean shouldDelete(final String collection, final MDStoreManagerInfo managerInfo) {
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if (StringUtils.isBlank(managerInfo.getCurrentId())) {
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log.debug("the instance has not currentID");
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return true;
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}
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if (collection.equals(managerInfo.getCurrentId())) {
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return false;
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}
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if (managerInfo.getExpiring().stream().anyMatch(i -> collection.equals(i.getId()))) {
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return false;
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}
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return managerInfo.getTransactions().stream().anyMatch(i -> collection.equals(i.getId()));
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}
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private MDStoreManagerInfo getMetadataObjectForCollections(final String collection) throws MDStoreException {
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380
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if (collection == null) {
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381
|
throw new MDStoreException("missing collection name");
|
|
382
|
}
|
|
383
|
final String tmp = collection.contains(
|
|
384
|
DISCARDED_PREFIX) == true ? StringUtils.substringAfter(collection, DISCARDED_PREFIX) : collection;
|
|
385
|
final String collectionNameCleaned = StringUtils.substringBefore(tmp, "::") + MDSTORE_ID_SUFFIX;
|
|
386
|
|
|
387
|
return getManagerTable().find(Filters.eq(MDID, collectionNameCleaned)).first();
|
|
388
|
}
|
|
389
|
|
|
390
|
/**
|
|
391
|
* Garbage transactions.
|
|
392
|
*
|
|
393
|
* @param currentInfo the current object
|
|
394
|
*/
|
|
395
|
private void garbageTransactions(final MDStoreManagerInfo currentInfo) {
|
|
396
|
if (log.isDebugEnabled()) {
|
|
397
|
log.debug("Start garbage transactions ");
|
|
398
|
}
|
|
399
|
|
|
400
|
if (currentInfo.getTransactions().size() <= getMaxTransactions()) {
|
|
401
|
return;
|
|
402
|
}
|
|
403
|
|
|
404
|
final TreeSet<MDStoreTransactionInfo> expiringSet = Sets.newTreeSet(MDStoreUtils.getComparatorOnDate());
|
|
405
|
expiringSet.addAll(currentInfo.getTransactions());
|
|
406
|
|
|
407
|
int toRemove = 0;
|
|
408
|
|
|
409
|
for(MDStoreTransactionInfo i : expiringSet) {
|
|
410
|
if (currentInfo.getTransactions().size() - toRemove >= getMaxTransactions()) {
|
|
411
|
return;
|
|
412
|
}
|
|
413
|
if (!i.getId().equals(currentInfo.getCurrentId())) {
|
|
414
|
if (log.isDebugEnabled()) {
|
|
415
|
log.debug("delete collection: " + i.getId() + " from mongo");
|
|
416
|
}
|
|
417
|
toRemove++;
|
|
418
|
doDrop(i.getId());
|
|
419
|
} else {
|
|
420
|
log.debug("Cannot remove transaction " + i.getId() + " because is the currentId: " + currentInfo.getCurrentId());
|
|
421
|
}
|
|
422
|
}
|
|
423
|
log.info("Deleted " + toRemove + " transactions, mdStore Id:" + currentInfo.getMdId());
|
|
424
|
}
|
|
425
|
|
|
426
|
/**
|
|
427
|
* Garbage expiring.
|
|
428
|
*
|
|
429
|
* @param currentInfo the current object
|
|
430
|
*/
|
|
431
|
private void garbageExpiring(final MDStoreManagerInfo currentInfo) {
|
|
432
|
if (log.isDebugEnabled()) {
|
|
433
|
log.debug("Start to search expiring mdstores for id: " + currentInfo.getMdId());
|
|
434
|
}
|
|
435
|
final List<MDStoreExpiredInfo> expiring = currentInfo.getExpiring();
|
|
436
|
expiring.forEach(i -> {
|
|
437
|
|
|
438
|
final LocalDate readDate = i.getLastRead().toInstant().atZone(ZoneId.systemDefault()).toLocalDate();
|
|
439
|
final long d = Duration.between(LocalDate.now().atTime(0, 0), readDate.atTime(0, 0)).toDays();
|
|
440
|
if (d > getExpiredDays()) {
|
|
441
|
if (!i.getId().equals(currentInfo.getCurrentId())) {
|
|
442
|
doDrop(i.getId());
|
|
443
|
}
|
|
444
|
}
|
|
445
|
});
|
|
446
|
|
|
447
|
log.debug("Deleted expired collections, mdId: " + currentInfo.getMdId());
|
|
448
|
}
|
|
449
|
|
|
450
|
/**
|
|
451
|
* Update incremental.
|
|
452
|
*
|
|
453
|
* @param transactionId the transaction id
|
|
454
|
* @param currentId the current id
|
|
455
|
*/
|
|
456
|
private void updateIncremental(final String transactionId, final String currentId) {
|
|
457
|
final MongoCollection<MDStoreRecord> transaction = db.getCollection(transactionId, MDStoreRecord.class);
|
|
458
|
final MongoCollection<MDStoreRecord> mdstore = db.getCollection(currentId, MDStoreRecord.class);
|
|
459
|
|
|
460
|
for (MDStoreRecord record : transaction.find().noCursorTimeout(true)) {
|
|
461
|
|
|
462
|
final MDStoreRecord r = record.clone();
|
|
463
|
if (StringUtils.isNotBlank(r.getId())) {
|
|
464
|
//setting to journaled write concern to be sure that when the write returns everything has been flushed to disk (https://docs.mongodb.org/manual/faq/developers/#when-does-mongodb-write-updates-to-disk)
|
|
465
|
//the explicit fsync command can't be run anymore: 'Command failed with error 13: 'fsync may only be run against the admin database.'
|
|
466
|
final MongoCollection<MDStoreRecord> mdstoreWrite = mdstore.withWriteConcern(WriteConcern.JOURNALED);
|
|
467
|
mdstoreWrite.replaceOne(Filters.eq(ID, r.getId()), r, new UpdateOptions().upsert(true));
|
|
468
|
}
|
|
469
|
}
|
|
470
|
}
|
|
471
|
|
|
472
|
/**
|
|
473
|
* (non-Javadoc)
|
|
474
|
*
|
|
475
|
* @see eu.dnetlib.msro.workers.aggregation.mdstore.MDStoreTransactionManager#dropTransaction(java.lang.String, java.lang.String)
|
|
476
|
*/
|
|
477
|
@Override
|
|
478
|
public Boolean dropTransaction(final String mdId, final String idToDrop) throws MDStoreException {
|
|
479
|
verifyConsistency();
|
|
480
|
final MDStoreManagerInfo managerInfo = getInfoForCurrentMdStore(mdId);
|
|
481
|
managerInfo.getTransactions().removeIf(info -> {
|
|
482
|
if (idToDrop.equals(info.getId())) {
|
|
483
|
doDrop(idToDrop);
|
|
484
|
return true;
|
|
485
|
} else {
|
|
486
|
return false;
|
|
487
|
}
|
|
488
|
});
|
|
489
|
getManagerTable().findOneAndReplace(Filters.eq(MDID, managerInfo.getMdId()), managerInfo);
|
|
490
|
return true;
|
|
491
|
}
|
|
492
|
|
|
493
|
public void garbageTransactionsOnStart() throws MDStoreException {
|
|
494
|
verifyConsistency();
|
|
495
|
for (MDStoreManagerInfo info : getManagerTable().find()) {
|
|
496
|
info.getTransactions().forEach(tx -> doDrop(tx.getId()));
|
|
497
|
info.setTransactions(Lists.newArrayList());
|
|
498
|
getManagerTable().findOneAndReplace(Filters.eq(MDID, info.getMdId()), info);
|
|
499
|
}
|
|
500
|
}
|
|
501
|
|
|
502
|
/**
|
|
503
|
* Gets the max transactions.
|
|
504
|
*
|
|
505
|
* @return the maxTransactions
|
|
506
|
*/
|
|
507
|
public int getMaxTransactions() {
|
|
508
|
return maxTransactions;
|
|
509
|
}
|
|
510
|
|
|
511
|
/**
|
|
512
|
* Sets the max transactions.
|
|
513
|
*
|
|
514
|
* @param maxTransactions the maxTransactions to set
|
|
515
|
*/
|
|
516
|
public void setMaxTransactions(final int maxTransactions) {
|
|
517
|
this.maxTransactions = maxTransactions;
|
|
518
|
}
|
|
519
|
|
|
520
|
/**
|
|
521
|
* Gets the expired days.
|
|
522
|
*
|
|
523
|
* @return the expiredDays
|
|
524
|
*/
|
|
525
|
public int getExpiredDays() {
|
|
526
|
return expiredDays;
|
|
527
|
}
|
|
528
|
|
|
529
|
/**
|
|
530
|
* Sets the expired days.
|
|
531
|
*
|
|
532
|
* @param expiredDays the expiredDays to set
|
|
533
|
*/
|
|
534
|
public void setExpiredDays(final int expiredDays) {
|
|
535
|
this.expiredDays = expiredDays;
|
|
536
|
}
|
|
537
|
}
|