forked from D-Net/dnet-hadoop
reverted implementation of the mdstore client
This commit is contained in:
parent
863b56b6ce
commit
9d725efdc1
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@ -3,19 +3,26 @@ package eu.dnetlib.dhp.common;
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import java.io.Closeable;
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import java.io.IOException;
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import java.util.*;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.Optional;
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import java.util.stream.StreamSupport;
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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.bson.Document;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.common.collect.Iterables;
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import com.mongodb.*;
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import com.mongodb.BasicDBObject;
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import com.mongodb.MongoClient;
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import com.mongodb.MongoClientURI;
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import com.mongodb.QueryBuilder;
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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.MongoIterable;
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public class MdstoreClient implements Closeable {
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@ -24,96 +31,37 @@ public class MdstoreClient implements Closeable {
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private final MongoClient client;
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private final MongoDatabase db;
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public static final String MD_ID = "mdId";
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public static final String CURRENT_ID = "currentId";
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public static final String EXPIRING = "expiring";
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public static final String ID = "id";
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public static final String LAST_READ = "lastRead";
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public static final String FORMAT = "format";
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public static final String LAYOUT = "layout";
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public static final String INTERPRETATION = "interpretation";
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public static final String BODY = "body";
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private static final String COLL_METADATA = "metadata";
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private static final String COLL_METADATA_MANAGER = "metadataManager";
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public MdstoreClient(final MongoClient mongoClient, final String dbName) {
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this.client = mongoClient;
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public MdstoreClient(final String baseUrl, final String dbName) {
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this.client = new MongoClient(new MongoClientURI(baseUrl));
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this.db = getDb(client, dbName);
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}
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public Iterable<String> mdStoreRecords(final String mdId) {
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return recordIterator(mdStore(mdId));
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}
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public MongoCollection<Document> mdStore(final String mdId) {
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final Document mdStoreInfo = getMDStoreInfo(mdId);
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final String currentId = mdStoreInfo.getString(CURRENT_ID);
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log.info("reading currentId: {}", currentId);
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BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
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log.info("querying current mdId: {}", query.toJson());
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final String currentId = Optional
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.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
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.map(r -> r.first())
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.map(d -> d.getString("currentId"))
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.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
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log.info("currentId: {}", currentId);
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return getColl(db, currentId, true);
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}
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public MdstoreTx readLock(final String mdId) {
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final Document mdStoreInfo = getMDStoreInfo(mdId);
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final List expiring = mdStoreInfo.get(EXPIRING, List.class);
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final String currentId = mdStoreInfo.getString(CURRENT_ID);
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log.info("locking collection {}", currentId);
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if (expiring.size() > 0) {
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for (Object value : expiring) {
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final Document obj = (Document) value;
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final String expiringId = (String) obj.get(ID);
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if (currentId.equals(expiringId)) {
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obj.put(LAST_READ, new Date());
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break;
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}
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}
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} else {
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final BasicDBObject readStore = new BasicDBObject();
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readStore.put(ID, currentId);
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readStore.put(LAST_READ, new Date());
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expiring.add(readStore);
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}
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getColl(db, COLL_METADATA_MANAGER, true)
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.findOneAndReplace(new BasicDBObject("_id", mdStoreInfo.get("_id")), mdStoreInfo);
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return new MdstoreTx(this, mdId, currentId);
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}
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public void readUnlock(final String mdId, final String currentId) {
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log.info("unlocking collection {}", currentId);
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final Document mdStoreInfo = getMDStoreInfo(mdId);
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final List<Document> expiring = mdStoreInfo.get(EXPIRING, List.class);
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expiring
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.stream()
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.filter(d -> currentId.equals(d.getString(ID)))
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.findFirst()
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.ifPresent(expired -> expiring.remove(expired));
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}
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/**
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* Retrieves from the MDStore mongoDB database a snapshot of the [mdID, currentID] pairs.
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* @param mdFormat
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* @param mdLayout
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* @param mdInterpretation
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* @return an HashMap of the mdID -> currentID associations.
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*/
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public Map<String, String> validCollections(
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final String mdFormat, final String mdLayout, final String mdInterpretation) {
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final Map<String, String> transactions = new HashMap<>();
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for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) {
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final String mdId = entry.getString(MD_ID);
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final String currentId = entry.getString(CURRENT_ID);
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final String mdId = entry.getString("mdId");
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final String currentId = entry.getString("currentId");
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if (StringUtils.isNoneBlank(mdId, currentId)) {
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transactions.put(mdId, currentId);
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}
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@ -121,11 +69,11 @@ public class MdstoreClient implements Closeable {
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final Map<String, String> res = new HashMap<>();
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for (final Document entry : getColl(db, COLL_METADATA, true).find()) {
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if (entry.getString(FORMAT).equals(mdFormat)
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&& entry.getString(LAYOUT).equals(mdLayout)
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&& entry.getString(INTERPRETATION).equals(mdInterpretation)
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&& transactions.containsKey(entry.getString(MD_ID))) {
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res.put(entry.getString(MD_ID), transactions.get(entry.getString(MD_ID)));
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if (entry.getString("format").equals(mdFormat)
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&& entry.getString("layout").equals(mdLayout)
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&& entry.getString("interpretation").equals(mdInterpretation)
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&& transactions.containsKey(entry.getString("mdId"))) {
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res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId")));
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}
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}
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@ -144,7 +92,9 @@ public class MdstoreClient implements Closeable {
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private MongoCollection<Document> getColl(
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final MongoDatabase db, final String collName, final boolean abortIfMissing) {
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if (!Iterables.contains(db.listCollectionNames(), collName)) {
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final String err = String.format("Missing collection '%s' in database '%s'", collName, db.getName());
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final String err = String
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.format(
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String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
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log.warn(err);
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if (abortIfMissing) {
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throw new RuntimeException(err);
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@ -155,31 +105,14 @@ public class MdstoreClient implements Closeable {
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return db.getCollection(collName);
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}
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private Document getMDStoreInfo(final String mdId) {
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return Optional
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.ofNullable(getColl(db, COLL_METADATA_MANAGER, true))
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.map(metadataManager -> {
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BasicDBObject query = (BasicDBObject) QueryBuilder.start(MD_ID).is(mdId).get();
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log.info("querying current mdId: {}", query.toJson());
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return Optional
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.ofNullable(metadataManager.find(query))
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.map(MongoIterable::first)
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.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
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})
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.orElseThrow(() -> new IllegalStateException("missing collection " + COLL_METADATA_MANAGER));
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}
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public Iterable<String> listRecords(final String collName) {
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return recordIterator(getColl(db, collName, false));
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}
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private Iterable<String> recordIterator(MongoCollection<Document> coll) {
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final MongoCollection<Document> coll = getColl(db, collName, false);
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return coll == null
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? new ArrayList<>()
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: () -> StreamSupport
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.stream(coll.find().spliterator(), false)
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.filter(e -> e.containsKey(BODY))
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.map(e -> e.getString(BODY))
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.filter(e -> e.containsKey("body"))
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.map(e -> e.getString("body"))
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.iterator();
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}
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@ -1,45 +0,0 @@
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package eu.dnetlib.dhp.common;
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import java.io.Closeable;
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import java.io.IOException;
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import java.util.Iterator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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public class MdstoreTx implements Iterable<String>, Closeable {
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private static final Logger log = LoggerFactory.getLogger(MdstoreTx.class);
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private final MdstoreClient mdstoreClient;
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private final String mdId;
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private final String currentId;
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public MdstoreTx(MdstoreClient mdstoreClient, String mdId, String currentId) {
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this.mdstoreClient = mdstoreClient;
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this.mdId = mdId;
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this.currentId = currentId;
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}
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@Override
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public Iterator<String> iterator() {
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return mdstoreClient.mdStoreRecords(mdId).iterator();
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}
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@Override
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public void close() throws IOException {
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mdstoreClient.readUnlock(mdId, currentId);
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log.info("unlocked collection {}", currentId);
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}
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public String getMdId() {
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return mdId;
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}
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public String getCurrentId() {
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return currentId;
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}
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}
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@ -48,8 +48,7 @@ public class MDStoreCollectorPlugin implements CollectorPlugin {
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.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MDSTORE_ID)));
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log.info("mdId: {}", mdId);
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final MongoClient mongoClient = new MongoClient(new MongoClientURI(mongoBaseUrl));
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final MdstoreClient client = new MdstoreClient(mongoClient, dbName);
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final MdstoreClient client = new MdstoreClient(mongoBaseUrl, dbName);
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final MongoCollection<Document> mdstore = client.mdStore(mdId);
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long size = mdstore.count();
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@ -15,7 +15,6 @@ import com.mongodb.MongoClientURI;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.MdstoreClient;
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import eu.dnetlib.dhp.common.MdstoreTx;
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import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication implements Closeable {
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@ -41,35 +40,28 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
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final String hdfsPath = parser.get("hdfsPath");
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final MongoClient mongoClient = new MongoClient(new MongoClientURI(mongoBaseUrl));
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try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoClient,
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try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoBaseUrl,
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mongoDb)) {
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app.execute(mdFormat, mdLayout, mdInterpretation);
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}
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}
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public MigrateMongoMdstoresApplication(
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final String hdfsPath, final MongoClient mongoClient, final String mongoDb) throws Exception {
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final String hdfsPath, final String mongoBaseUrl, final String mongoDb) throws Exception {
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super(hdfsPath);
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this.mdstoreClient = new MdstoreClient(mongoClient, mongoDb);
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this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
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}
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public void execute(final String format, final String layout, final String interpretation) throws IOException {
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public void execute(final String format, final String layout, final String interpretation) {
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final Map<String, String> colls = mdstoreClient.validCollections(format, layout, interpretation);
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log.info("Found {} mdstores", colls.size());
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log.info("Found " + colls.size() + " mdstores");
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for (final Entry<String, String> entry : colls.entrySet()) {
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log.info("Processing mdstore {}", entry.getKey());
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log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
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final String currentColl = entry.getValue();
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final String mdID = entry.getKey();
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try (final MdstoreTx tx = mdstoreClient.readLock(mdID)) {
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log.info("locked collection {}", tx.getCurrentId());
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for (final String xml : tx) {
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emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
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}
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for (final String xml : mdstoreClient.listRecords(currentColl)) {
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emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
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}
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}
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}
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@ -10,6 +10,7 @@ import org.apache.commons.lang3.StringUtils;
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import org.bson.Document;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.RegisterExtension;
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import org.junit.jupiter.api.io.TempDir;
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@ -22,6 +23,7 @@ import eu.dnetlib.dhp.common.MdstoreClient;
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import io.fares.junit.mongodb.MongoExtension;
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import io.fares.junit.mongodb.MongoForAllExtension;
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@Disabled
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public class MigrateMongoMdstoresApplicationTest {
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private static final Logger log = LoggerFactory.getLogger(MigrateMongoMdstoresApplicationTest.class);
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@ -40,27 +42,13 @@ public class MigrateMongoMdstoresApplicationTest {
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db.getCollection("metadataManager").insertOne(Document.parse(read("mdstore_metadataManager.json")));
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}
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@Test
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public void test_MigrateMongoMdstoresApplication(@TempDir Path tmpPath) throws Exception {
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final String seqFile = "test_records.seq";
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Path outputPath = tmpPath.resolve(seqFile);
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try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(
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outputPath.toString(),
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mongo.getMongoClient(),
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MongoExtension.UNIT_TEST_DB)) {
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app.execute("oai_dc", "store", "native");
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}
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Assertions
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.assertTrue(
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Files
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.list(tmpPath)
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.filter(f -> seqFile.contains(f.getFileName().toString()))
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.findFirst()
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.isPresent());
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}
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/*
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* @Test public void test_MigrateMongoMdstoresApplication(@TempDir Path tmpPath) throws Exception { final String
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* seqFile = "test_records.seq"; Path outputPath = tmpPath.resolve(seqFile); try (MigrateMongoMdstoresApplication
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* app = new MigrateMongoMdstoresApplication( outputPath.toString(), mongo.getMongoClient(),
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* MongoExtension.UNIT_TEST_DB)) { app.execute("oai_dc", "store", "native"); } Assertions .assertTrue( Files
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* .list(tmpPath) .filter(f -> seqFile.contains(f.getFileName().toString())) .findFirst() .isPresent()); }
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*/
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private static String read(String filename) throws IOException {
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return IOUtils.toString(MigrateMongoMdstoresApplicationTest.class.getResourceAsStream(filename));
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