mdstore read lock/unlock when bulk copying records from mongodb to hdfs

dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java

@@ -3,26 +3,19 @@ package eu.dnetlib.dhp.common;
 
 import java.io.Closeable;
 import java.io.IOException;
-import java.util.ArrayList;
+import java.util.*;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Optional;
 import java.util.stream.StreamSupport;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.bson.Document;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.google.common.collect.Iterables;
-import com.mongodb.BasicDBObject;
+import com.mongodb.*;
-import com.mongodb.MongoClient;
-import com.mongodb.MongoClientURI;
-import com.mongodb.QueryBuilder;
 import com.mongodb.client.MongoCollection;
 import com.mongodb.client.MongoDatabase;
+import com.mongodb.client.MongoIterable;
 
 public class MdstoreClient implements Closeable {
 
@@ -31,37 +24,96 @@ public class MdstoreClient implements Closeable {
 	private final MongoClient client;
 	private final MongoDatabase db;
 
+	public static final String MD_ID = "mdId";
+	public static final String CURRENT_ID = "currentId";
+	public static final String EXPIRING = "expiring";
+	public static final String ID = "id";
+	public static final String LAST_READ = "lastRead";
+
+	public static final String FORMAT = "format";
+	public static final String LAYOUT = "layout";
+	public static final String INTERPRETATION = "interpretation";
+
+	public static final String BODY = "body";
+
 	private static final String COLL_METADATA = "metadata";
 	private static final String COLL_METADATA_MANAGER = "metadataManager";
 
-	public MdstoreClient(final String baseUrl, final String dbName) {
+	public MdstoreClient(final MongoClient mongoClient, final String dbName) {
-		this.client = new MongoClient(new MongoClientURI(baseUrl));
+		this.client = mongoClient;
 		this.db = getDb(client, dbName);
 	}
 
+	public Iterable<String> mdStoreRecords(final String mdId) {
+		return recordIterator(mdStore(mdId));
+	}
+
 	public MongoCollection<Document> mdStore(final String mdId) {
-		BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
+		final Document mdStoreInfo = getMDStoreInfo(mdId);
-
+		final String currentId = mdStoreInfo.getString(CURRENT_ID);
-		log.info("querying current mdId: {}", query.toJson());
+		log.info("reading currentId: {}", currentId);
-
-		final String currentId = Optional
-			.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
-			.map(r -> r.first())
-			.map(d -> d.getString("currentId"))
-			.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
-
-		log.info("currentId: {}", currentId);
 
 		return getColl(db, currentId, true);
 	}
 
+	public MdstoreTx readLock(final String mdId) {
+
+		final Document mdStoreInfo = getMDStoreInfo(mdId);
+		final List expiring = mdStoreInfo.get(EXPIRING, List.class);
+		final String currentId = mdStoreInfo.getString(CURRENT_ID);
+
+		log.info("locking collection {}", currentId);
+
+		if (expiring.size() > 0) {
+			for (Object value : expiring) {
+				final Document obj = (Document) value;
+				final String expiringId = (String) obj.get(ID);
+				if (currentId.equals(expiringId)) {
+					obj.put(LAST_READ, new Date());
+					break;
+				}
+			}
+		} else {
+			final BasicDBObject readStore = new BasicDBObject();
+			readStore.put(ID, currentId);
+			readStore.put(LAST_READ, new Date());
+			expiring.add(readStore);
+		}
+
+		getColl(db, COLL_METADATA_MANAGER, true)
+			.findOneAndReplace(new BasicDBObject("_id", mdStoreInfo.get("_id")), mdStoreInfo);
+
+		return new MdstoreTx(this, mdId, currentId);
+	}
+
+	public void readUnlock(final String mdId, final String currentId) {
+
+		log.info("unlocking collection {}", currentId);
+
+		final Document mdStoreInfo = getMDStoreInfo(mdId);
+		final List<Document> expiring = mdStoreInfo.get(EXPIRING, List.class);
+
+		expiring
+			.stream()
+			.filter(d -> currentId.equals(d.getString(ID)))
+			.findFirst()
+			.ifPresent(expired -> expiring.remove(expired));
+	}
+
+	/**
+	 * Retrieves from the MDStore mongoDB database a snapshot of the [mdID, currentID] pairs.
+	 * @param mdFormat
+	 * @param mdLayout
+	 * @param mdInterpretation
+	 * @return an HashMap of the mdID -> currentID associations.
+	 */
 	public Map<String, String> validCollections(
 		final String mdFormat, final String mdLayout, final String mdInterpretation) {
 
 		final Map<String, String> transactions = new HashMap<>();
 		for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) {
-			final String mdId = entry.getString("mdId");
+			final String mdId = entry.getString(MD_ID);
-			final String currentId = entry.getString("currentId");
+			final String currentId = entry.getString(CURRENT_ID);
 			if (StringUtils.isNoneBlank(mdId, currentId)) {
 				transactions.put(mdId, currentId);
 			}
@@ -69,11 +121,11 @@ public class MdstoreClient implements Closeable {
 
 		final Map<String, String> res = new HashMap<>();
 		for (final Document entry : getColl(db, COLL_METADATA, true).find()) {
-			if (entry.getString("format").equals(mdFormat)
+			if (entry.getString(FORMAT).equals(mdFormat)
-				&& entry.getString("layout").equals(mdLayout)
+				&& entry.getString(LAYOUT).equals(mdLayout)
-				&& entry.getString("interpretation").equals(mdInterpretation)
+				&& entry.getString(INTERPRETATION).equals(mdInterpretation)
-				&& transactions.containsKey(entry.getString("mdId"))) {
+				&& transactions.containsKey(entry.getString(MD_ID))) {
-				res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId")));
+				res.put(entry.getString(MD_ID), transactions.get(entry.getString(MD_ID)));
 			}
 		}
 
@@ -92,9 +144,7 @@ public class MdstoreClient implements Closeable {
 	private MongoCollection<Document> getColl(
 		final MongoDatabase db, final String collName, final boolean abortIfMissing) {
 		if (!Iterables.contains(db.listCollectionNames(), collName)) {
-			final String err = String
+			final String err = String.format("Missing collection '%s' in database '%s'", collName, db.getName());
-				.format(
-					String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
 			log.warn(err);
 			if (abortIfMissing) {
 				throw new RuntimeException(err);
@@ -105,14 +155,31 @@ public class MdstoreClient implements Closeable {
 		return db.getCollection(collName);
 	}
 
+	private Document getMDStoreInfo(final String mdId) {
+		return Optional
+			.ofNullable(getColl(db, COLL_METADATA_MANAGER, true))
+			.map(metadataManager -> {
+				BasicDBObject query = (BasicDBObject) QueryBuilder.start(MD_ID).is(mdId).get();
+				log.info("querying current mdId: {}", query.toJson());
+				return Optional
+					.ofNullable(metadataManager.find(query))
+					.map(MongoIterable::first)
+					.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
+			})
+			.orElseThrow(() -> new IllegalStateException("missing collection " + COLL_METADATA_MANAGER));
+	}
+
 	public Iterable<String> listRecords(final String collName) {
-		final MongoCollection<Document> coll = getColl(db, collName, false);
+		return recordIterator(getColl(db, collName, false));
+	}
+
+	private Iterable<String> recordIterator(MongoCollection<Document> coll) {
 		return coll == null
 			? new ArrayList<>()
 			: () -> StreamSupport
 				.stream(coll.find().spliterator(), false)
-				.filter(e -> e.containsKey("body"))
+				.filter(e -> e.containsKey(BODY))
-				.map(e -> e.getString("body"))
+				.map(e -> e.getString(BODY))
 				.iterator();
 	}
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreTx.java

@@ -0,0 +1,45 @@
+
+package eu.dnetlib.dhp.common;
+
+import java.io.Closeable;
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class MdstoreTx implements Iterable<String>, Closeable {
+
+	private static final Logger log = LoggerFactory.getLogger(MdstoreTx.class);
+
+	private final MdstoreClient mdstoreClient;
+
+	private final String mdId;
+
+	private final String currentId;
+
+	public MdstoreTx(MdstoreClient mdstoreClient, String mdId, String currentId) {
+		this.mdstoreClient = mdstoreClient;
+		this.mdId = mdId;
+		this.currentId = currentId;
+	}
+
+	@Override
+	public Iterator<String> iterator() {
+		return mdstoreClient.mdStoreRecords(mdId).iterator();
+	}
+
+	@Override
+	public void close() throws IOException {
+		mdstoreClient.readUnlock(mdId, currentId);
+		log.info("unlocked collection {}", currentId);
+	}
+
+	public String getMdId() {
+		return mdId;
+	}
+
+	public String getCurrentId() {
+		return currentId;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MDStoreCollectorPlugin.java

@@ -11,6 +11,8 @@ import org.bson.Document;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.mongodb.MongoClient;
+import com.mongodb.MongoClientURI;
 import com.mongodb.client.MongoCollection;
 
 import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
@@ -46,7 +48,8 @@ public class MDStoreCollectorPlugin implements CollectorPlugin {
 			.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MDSTORE_ID)));
 		log.info("mdId: {}", mdId);
 
-		final MdstoreClient client = new MdstoreClient(mongoBaseUrl, dbName);
+		final MongoClient mongoClient = new MongoClient(new MongoClientURI(mongoBaseUrl));
+		final MdstoreClient client = new MdstoreClient(mongoClient, dbName);
 		final MongoCollection<Document> mdstore = client.mdStore(mdId);
 		long size = mdstore.count();
 

dhp-workflows/dhp-graph-mapper/pom.xml

@@ -91,6 +91,11 @@
             <groupId>org.mongodb</groupId>
             <artifactId>mongo-java-driver</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.fares.junit.mongodb</groupId>
+            <artifactId>mongodb-junit-test</artifactId>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>dom4j</groupId>
             <artifactId>dom4j</artifactId>

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplication.java

@@ -7,17 +7,20 @@ import java.util.Map;
 import java.util.Map.Entry;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.logging.Log;
+import org.slf4j.Logger;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.LoggerFactory;
+
+import com.mongodb.MongoClient;
+import com.mongodb.MongoClientURI;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.MdstoreClient;
+import eu.dnetlib.dhp.common.MdstoreTx;
 import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
 
-public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication
+public class MigrateMongoMdstoresApplication extends AbstractMigrationApplication implements Closeable {
-	implements Closeable {
 
-	private static final Log log = LogFactory.getLog(MigrateMongoMdstoresApplication.class);
+	private static final Logger log = LoggerFactory.getLogger(MigrateMongoMdstoresApplication.class);
 
 	private final MdstoreClient mdstoreClient;
 
@@ -38,28 +41,35 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
 
 		final String hdfsPath = parser.get("hdfsPath");
 
-		try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoBaseUrl,
+		final MongoClient mongoClient = new MongoClient(new MongoClientURI(mongoBaseUrl));
+
+		try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoClient,
 			mongoDb)) {
 			app.execute(mdFormat, mdLayout, mdInterpretation);
 		}
 	}
 
 	public MigrateMongoMdstoresApplication(
-		final String hdfsPath, final String mongoBaseUrl, final String mongoDb) throws Exception {
+		final String hdfsPath, final MongoClient mongoClient, final String mongoDb) throws Exception {
 		super(hdfsPath);
-		this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
+		this.mdstoreClient = new MdstoreClient(mongoClient, mongoDb);
 	}
 
-	public void execute(final String format, final String layout, final String interpretation) {
+	public void execute(final String format, final String layout, final String interpretation) throws IOException {
 		final Map<String, String> colls = mdstoreClient.validCollections(format, layout, interpretation);
-		log.info("Found " + colls.size() + " mdstores");
+		log.info("Found {} mdstores", colls.size());
 
 		for (final Entry<String, String> entry : colls.entrySet()) {
-			log.info("Processing mdstore " + entry.getKey() + " (collection: " + entry.getValue() + ")");
+			log.info("Processing mdstore {}", entry.getKey());
-			final String currentColl = entry.getValue();
 
-			for (final String xml : mdstoreClient.listRecords(currentColl)) {
+			final String mdID = entry.getKey();
-				emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
+			try (final MdstoreTx tx = mdstoreClient.readLock(mdID)) {
+
+				log.info("locked collection {}", tx.getCurrentId());
+
+				for (final String xml : tx) {
+					emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
+				}
 			}
 		}
 	}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateMongoMdstoresApplicationTest.java

@@ -0,0 +1,75 @@
+
+package eu.dnetlib.dhp.oa.graph.raw;
+
+import com.mongodb.client.MongoDatabase;
+import eu.dnetlib.dhp.common.MdstoreClient;
+import io.fares.junit.mongodb.MongoExtension;
+import io.fares.junit.mongodb.MongoForAllExtension;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.bson.Document;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.RegisterExtension;
+import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+public class MigrateMongoMdstoresApplicationTest {
+
+	private static final Logger log = LoggerFactory.getLogger(MigrateMongoMdstoresApplicationTest.class);
+
+	public static final String COLL_NAME = "9eed8a4d-bb41-47c3-987f-9d06aee0dec0::1453898911558";
+
+	@RegisterExtension
+	public static MongoForAllExtension mongo = MongoForAllExtension.defaultMongo();
+
+	@BeforeAll
+	public static void setUp() throws IOException {
+		MongoDatabase db = mongo.getMongoClient().getDatabase(MongoExtension.UNIT_TEST_DB);
+
+		db.getCollection(COLL_NAME).insertOne(Document.parse(read("mdstore_record.json")));
+		db.getCollection("metadata").insertOne(Document.parse(read("mdstore_metadata.json")));
+		db.getCollection("metadataManager").insertOne(Document.parse(read("mdstore_metadataManager.json")));
+	}
+
+
+	@Test
+	public void test_MdstoreClient() throws IOException {
+		try(MdstoreClient client = new MdstoreClient(mongo.getMongoClient(), MongoExtension.UNIT_TEST_DB)) {
+			for (String xml : client.listRecords(COLL_NAME)) {
+				Assertions.assertTrue(StringUtils.isNotBlank(xml));
+			}
+		}
+	}
+
+	@Test
+	public void test_MigrateMongoMdstoresApplication(@TempDir Path tmpPath) throws Exception {
+
+		final String seqFile = "test_records.seq";
+		Path outputPath = tmpPath.resolve(seqFile);
+
+		try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(
+				outputPath.toString(),
+				mongo.getMongoClient(),
+				MongoExtension.UNIT_TEST_DB)) {
+			app.execute("oai_dc", "store", "native");
+		}
+
+		Assertions.assertTrue(
+				Files.list(tmpPath)
+				.filter(f -> seqFile.contains(f.getFileName().toString()))
+				.findFirst()
+				.isPresent());
+	}
+
+	private static String read(String filename) throws IOException {
+		return IOUtils.toString(MigrateMongoMdstoresApplicationTest.class.getResourceAsStream(filename));
+	}
+
+}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/mdstore_metadata.json

@@ -0,0 +1,8 @@
+{
+  "_id" : ObjectId("53cf633a8274eb9536b614de"),
+  "mdId" : "9eed8a4d-bb41-47c3-987f-9d06aee0dec0_TURTdG9yZURTUmVzb3VyY2VzL01EU3RvcmVEU1Jlc291cmNlVHlwZQ==",
+  "format" : "oai_dc",
+  "layout" : "store",
+  "interpretation" : "native",
+  "size" : 1
+}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/mdstore_metadataManager.json

@@ -0,0 +1 @@
+{ "_id" : ObjectId("53cf63678274eb9536b61940"), "mdId" : "9eed8a4d-bb41-47c3-987f-9d06aee0dec0_TURTdG9yZURTUmVzb3VyY2VzL01EU3RvcmVEU1Jlc291cmNlVHlwZQ==", "currentId" : "9eed8a4d-bb41-47c3-987f-9d06aee0dec0::1453898911558", "expiring" : [ { "id" : "9eed8a4d-bb41-47c3-987f-9d06aee0dec0::1453898911558", "lastRead" : ISODate("2021-04-30T03:34:29.699Z") } ], "transactions" : [ ] }

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/mdstore_record.json

@@ -0,0 +1,6 @@
+{
+  "id" : "od________76::c6e4a36099aba4b0c390a365251428c9",
+  "originalId" : null,
+  "body" : "<?xml version=\"1.0\" encoding=\"UTF-8\"?><oai:record xmlns:dri=\"http://www.driver-repository.eu/namespace/dri\" xmlns=\"http://namespace.openaire.eu/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:oai=\"http://www.openarchives.org/OAI/2.0/\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dr=\"http://www.driver-repository.eu/namespace/dr\" xmlns:oaf=\"http://namespace.openaire.eu/oaf\" xmlns:prov=\"http://www.openarchives.org/OAI/2.0/provenance\"><oai:header status=\"deleted\"><dri:objIdentifier>od________76::c6e4a36099aba4b0c390a365251428c9</dri:objIdentifier><dri:recordIdentifier>oai:DiVA.org:du-10007</dri:recordIdentifier><dri:dateOfCollection>2016-01-27T12:48:31.609Z</dri:dateOfCollection><dri:repositoryId>dc42663d-5257-4c6f-bf09-53cf47e36fed_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU=</dri:repositoryId><oaf:datasourceprefix>od________76</oaf:datasourceprefix><identifier xmlns=\"http://www.openarchives.org/OAI/2.0/\">oai:DiVA.org:du-10007</identifier><datestamp xmlns=\"http://www.openarchives.org/OAI/2.0/\">2012-04-20T14:05:25Z</datestamp><setSpec xmlns=\"http://www.openarchives.org/OAI/2.0/\">HumanitiesTheology</setSpec><setSpec xmlns=\"http://www.openarchives.org/OAI/2.0/\">du</setSpec><setSpec xmlns=\"http://www.openarchives.org/OAI/2.0/\">studentThesis</setSpec></oai:header></oai:record>",
+  "timestamp" : NumberLong("1453898911613")
+}

pom.xml

@@ -412,6 +412,11 @@
 				<artifactId>mongo-java-driver</artifactId>
 				<version>${mongodb.driver.version}</version>
 			</dependency>
+			<dependency>
+				<groupId>io.fares.junit.mongodb</groupId>
+				<artifactId>mongodb-junit-test</artifactId>
+				<version>1.1.0</version>
+			</dependency>
 			<dependency>
 				<groupId>org.postgresql</groupId>
 				<artifactId>postgresql</artifactId>