forked from D-Net/dnet-hadoop
Merge pull request '8232-mdstore-synch-improve' (#272) from 8232-mdstore-synch-improve into beta
Reviewed-on: D-Net/dnet-hadoop#272
This commit is contained in:
commit
a590c371a9
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@ -0,0 +1,100 @@
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package eu.dnetlib.dhp.common;
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/**
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* This utility represent the Metadata Store information
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* needed during the migration from mongo to HDFS to store
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*/
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public class MDStoreInfo {
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private String mdstore;
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private String currentId;
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private Long latestTimestamp;
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/**
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* Instantiates a new Md store info.
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*/
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public MDStoreInfo() {
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}
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/**
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* Instantiates a new Md store info.
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*
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* @param mdstore the mdstore
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* @param currentId the current id
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* @param latestTimestamp the latest timestamp
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*/
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public MDStoreInfo(String mdstore, String currentId, Long latestTimestamp) {
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this.mdstore = mdstore;
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this.currentId = currentId;
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this.latestTimestamp = latestTimestamp;
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}
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/**
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* Gets mdstore.
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*
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* @return the mdstore
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*/
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public String getMdstore() {
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return mdstore;
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}
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/**
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* Sets mdstore.
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*
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* @param mdstore the mdstore
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* @return the mdstore
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*/
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public MDStoreInfo setMdstore(String mdstore) {
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this.mdstore = mdstore;
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return this;
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}
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/**
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* Gets current id.
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*
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* @return the current id
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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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* Sets current id.
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*
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* @param currentId the current id
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* @return the current id
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*/
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public MDStoreInfo setCurrentId(String currentId) {
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this.currentId = currentId;
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return this;
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}
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/**
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* Gets latest timestamp.
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*
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* @return the latest timestamp
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*/
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public Long getLatestTimestamp() {
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return latestTimestamp;
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}
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/**
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* Sets latest timestamp.
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*
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* @param latestTimestamp the latest timestamp
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* @return the latest timestamp
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*/
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public MDStoreInfo setLatestTimestamp(Long latestTimestamp) {
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this.latestTimestamp = latestTimestamp;
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return this;
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}
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@Override
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public String toString() {
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return "MDStoreInfo{" +
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"mdstore='" + mdstore + '\'' +
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", currentId='" + currentId + '\'' +
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", latestTimestamp=" + latestTimestamp +
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'}';
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}
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}
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@ -1,12 +1,12 @@
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package eu.dnetlib.dhp.common;
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import static com.mongodb.client.model.Sorts.descending;
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import java.io.Closeable;
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import java.io.IOException;
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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.*;
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import java.util.stream.Collectors;
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import java.util.stream.StreamSupport;
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import org.apache.commons.lang3.StringUtils;
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@ -38,6 +38,26 @@ public class MdstoreClient implements Closeable {
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this.db = getDb(client, dbName);
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}
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private Long parseTimestamp(Document f) {
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if (f == null || !f.containsKey("timestamp"))
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return null;
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Object ts = f.get("timestamp");
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return Long.parseLong(ts.toString());
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}
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public Long getLatestTimestamp(final String collectionId) {
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MongoCollection<Document> collection = db.getCollection(collectionId);
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FindIterable<Document> result = collection.find().sort(descending("timestamp")).limit(1);
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if (result == null) {
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return null;
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}
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Document f = result.first();
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return parseTimestamp(f);
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}
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public MongoCollection<Document> mdStore(final String mdId) {
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BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
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@ -54,6 +74,16 @@ public class MdstoreClient implements Closeable {
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return getColl(db, currentId, true);
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}
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public List<MDStoreInfo> mdStoreWithTimestamp(final String mdFormat, final String mdLayout,
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final String mdInterpretation) {
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Map<String, String> res = validCollections(mdFormat, mdLayout, mdInterpretation);
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return res
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.entrySet()
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.stream()
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.map(e -> new MDStoreInfo(e.getKey(), e.getValue(), getLatestTimestamp(e.getValue())))
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.collect(Collectors.toList());
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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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@ -0,0 +1,36 @@
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package eu.dnetlib.dhp.common;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.List;
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import org.junit.jupiter.api.Test;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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public class MdStoreClientTest {
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@Test
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public void testMongoCollection() throws IOException {
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final MdstoreClient client = new MdstoreClient("mongodb://localhost:27017", "mdstore");
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final ObjectMapper mapper = new ObjectMapper();
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final List<MDStoreInfo> infos = client.mdStoreWithTimestamp("ODF", "store", "cleaned");
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infos.forEach(System.out::println);
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final String s = mapper.writeValueAsString(infos);
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Path fileName = Paths.get("/Users/sandro/mdstore_info.json");
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// Writing into the file
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Files.write(fileName, s.getBytes(StandardCharsets.UTF_8));
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}
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}
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@ -1,31 +1,87 @@
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package eu.dnetlib.dhp.oa.graph.raw;
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import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
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import java.io.Closeable;
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import java.io.IOException;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Objects;
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import java.util.function.Consumer;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocatedFileStatus;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.fs.RemoteIterator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.MDStoreInfo;
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import eu.dnetlib.dhp.common.MdstoreClient;
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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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private static final Logger log = LoggerFactory.getLogger(MigrateMongoMdstoresApplication.class);
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private final MdstoreClient mdstoreClient;
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private static List<MDStoreInfo> snapshotsMDStores(final MdstoreClient client,
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final String format,
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final String layout,
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final String interpretation) {
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return client.mdStoreWithTimestamp(format, layout, interpretation);
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}
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private static MDStoreInfo extractPath(final String path, final String basePath) {
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int res = path.indexOf(basePath);
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if (res > 0) {
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String[] split = path.substring(res).split("/");
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if (split.length > 2) {
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final String ts = split[split.length - 1];
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final String mdStore = split[split.length - 2];
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return new MDStoreInfo(mdStore, null, Long.parseLong(ts));
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}
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}
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return null;
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}
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private static Map<String, MDStoreInfo> hdfsMDStoreInfo(FileSystem fs, final String basePath) throws IOException {
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final Map<String, MDStoreInfo> hdfs_store = new HashMap<>();
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final Path p = new Path(basePath);
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final RemoteIterator<LocatedFileStatus> ls = fs.listFiles(p, true);
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while (ls.hasNext()) {
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String current = ls.next().getPath().toString();
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final MDStoreInfo info = extractPath(current, basePath);
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if (info != null) {
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hdfs_store.put(info.getMdstore(), info);
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}
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}
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return hdfs_store;
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}
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private static String createMDStoreDir(final String basePath, final String mdStoreId) {
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if (basePath.endsWith("/")) {
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return basePath + mdStoreId;
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} else {
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return String.format("%s/%s", basePath, mdStoreId);
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}
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}
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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MigrateMongoMdstoresApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json")));
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Objects
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.requireNonNull(
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MigrateMongoMdstoresApplication.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/migrate_mongo_mstores_parameters.json"))));
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parser.parseArgument(args);
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final String mongoBaseUrl = parser.get("mongoBaseUrl");
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@ -36,30 +92,118 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
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final String mdInterpretation = parser.get("mdInterpretation");
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final String hdfsPath = parser.get("hdfsPath");
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final String nameNode = parser.get("nameNode");
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final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(nameNode));
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final MdstoreClient mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
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final List<MDStoreInfo> mongoMDStores = snapshotsMDStores(mdstoreClient, mdFormat, mdLayout, mdInterpretation);
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final Map<String, MDStoreInfo> hdfsMDStores = hdfsMDStoreInfo(fileSystem, hdfsPath);
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mongoMDStores
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.stream()
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.filter(currentMDStore -> currentMDStore.getLatestTimestamp() != null)
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.forEach(
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consumeMDStore(
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mdFormat, mdLayout, mdInterpretation, hdfsPath, fileSystem, mongoBaseUrl, mongoDb, hdfsMDStores));
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// TODO: DELETE MDStORE FOLDER NOT PRESENT IN MONGO
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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 String mongoBaseUrl, final String mongoDb) throws Exception {
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/**
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* This method is responsible to sync only the stores that have been changed since last time
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* @param mdFormat the MDStore's format
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* @param mdLayout the MDStore'slayout
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* @param mdInterpretation the MDStore's interpretation
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* @param hdfsPath the basePath into hdfs where all MD-stores are stored
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* @param fileSystem The Hadoop File system client
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* @param hdfsMDStores A Map containing as Key the mdstore ID and as value the @{@link MDStoreInfo}
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* @return
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*/
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private static Consumer<MDStoreInfo> consumeMDStore(String mdFormat, String mdLayout, String mdInterpretation,
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String hdfsPath, FileSystem fileSystem, final String mongoBaseUrl, final String mongoDb,
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Map<String, MDStoreInfo> hdfsMDStores) {
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return currentMDStore -> {
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// If the key is missing it means that the mdstore is not present in hdfs
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// that is the hdfs path basePath/MDSTOREID/timestamp is missing
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// So we have to synch it
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if (!hdfsMDStores.containsKey(currentMDStore.getMdstore())) {
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log.info("Adding store " + currentMDStore.getMdstore());
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try {
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synchMDStoreIntoHDFS(
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mdFormat, mdLayout, mdInterpretation, hdfsPath, fileSystem, mongoBaseUrl, mongoDb,
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currentMDStore);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
|
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} else {
|
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final MDStoreInfo current = hdfsMDStores.get(currentMDStore.getMdstore());
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// IF the key is present it means that in hdfs we have a path
|
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// basePath/MDSTOREID/timestamp but the timestamp on hdfs is older that the
|
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// new one in mongo so we have to synch the new mdstore and delete the old one
|
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if (currentMDStore.getLatestTimestamp() > current.getLatestTimestamp()) {
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log.info("Updating MDStore " + currentMDStore.getMdstore());
|
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final String mdstoreDir = createMDStoreDir(hdfsPath, currentMDStore.getMdstore());
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final String rmPath = createMDStoreDir(mdstoreDir, current.getLatestTimestamp().toString());
|
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try {
|
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synchMDStoreIntoHDFS(
|
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mdFormat, mdLayout, mdInterpretation, hdfsPath, fileSystem, mongoBaseUrl, mongoDb,
|
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currentMDStore);
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log.info("deleting " + rmPath);
|
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// DELETE THE OLD MDSTORE
|
||||
fileSystem.delete(new Path(rmPath), true);
|
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} catch (IOException e) {
|
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throw new RuntimeException("Unable to synch and remove path " + rmPath, e);
|
||||
}
|
||||
}
|
||||
}
|
||||
};
|
||||
}
|
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|
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/**
|
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*This method store into hdfs all the MONGO record of a single mdstore into the HDFS File
|
||||
*
|
||||
* @param mdFormat the MDStore's format
|
||||
* @param mdLayout the MDStore'slayout
|
||||
* @param mdInterpretation the MDStore's interpretation
|
||||
* @param hdfsPath the basePath into hdfs where all MD-stores are stored
|
||||
* @param fileSystem The Hadoop File system client
|
||||
* @param currentMDStore The current Mongo MDStore ID
|
||||
* @throws IOException
|
||||
*/
|
||||
private static void synchMDStoreIntoHDFS(String mdFormat, String mdLayout, String mdInterpretation, String hdfsPath,
|
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FileSystem fileSystem, final String mongoBaseUrl, final String mongoDb, MDStoreInfo currentMDStore)
|
||||
throws IOException {
|
||||
// FIRST CREATE the directory basePath/MDSTOREID
|
||||
final String mdstoreDir = createMDStoreDir(hdfsPath, currentMDStore.getMdstore());
|
||||
fileSystem.mkdirs(new Path(mdstoreDir));
|
||||
// Then synch all the records into basePath/MDSTOREID/timestamp
|
||||
final String currentIdDir = createMDStoreDir(mdstoreDir, currentMDStore.getLatestTimestamp().toString());
|
||||
try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(mongoBaseUrl, mongoDb,
|
||||
currentIdDir)) {
|
||||
app.execute(currentMDStore.getCurrentId(), mdFormat, mdLayout, mdInterpretation);
|
||||
} catch (Exception e) {
|
||||
throw new RuntimeException(
|
||||
String
|
||||
.format("Error on sync mdstore with ID %s into path %s", currentMDStore.getMdstore(), currentIdDir),
|
||||
e);
|
||||
}
|
||||
log.info(String.format("Synchronized mdStore id : %s into path %s", currentMDStore.getMdstore(), currentIdDir));
|
||||
}
|
||||
|
||||
public MigrateMongoMdstoresApplication(final String mongoBaseUrl, final String mongoDb, final String hdfsPath)
|
||||
throws Exception {
|
||||
super(hdfsPath);
|
||||
this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
|
||||
}
|
||||
|
||||
public void execute(final String format, final String layout, final String interpretation) {
|
||||
final Map<String, String> colls = mdstoreClient.validCollections(format, layout, interpretation);
|
||||
log.info("Found {} mdstores", colls.size());
|
||||
|
||||
for (final Entry<String, String> entry : colls.entrySet()) {
|
||||
log.info("Processing mdstore {} (collection: {})", entry.getKey(), entry.getValue());
|
||||
final String currentColl = entry.getValue();
|
||||
|
||||
for (final String xml : mdstoreClient.listRecords(currentColl)) {
|
||||
emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
|
||||
}
|
||||
public void execute(final String currentColl, final String format, final String layout,
|
||||
final String interpretation) {
|
||||
for (final String xml : mdstoreClient.listRecords(currentColl)) {
|
||||
emit(xml, String.format("%s-%s-%s", format, layout, interpretation));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -3,33 +3,20 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
|
|||
|
||||
import java.io.Closeable;
|
||||
import java.io.IOException;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.apache.commons.logging.Log;
|
||||
import org.apache.commons.logging.LogFactory;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.Path;
|
||||
import org.apache.hadoop.io.SequenceFile;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
|
||||
import com.fasterxml.jackson.core.JsonProcessingException;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
||||
import eu.dnetlib.dhp.oa.graph.raw.OafToOafMapper;
|
||||
import eu.dnetlib.dhp.oa.graph.raw.OdfToOafMapper;
|
||||
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
|
||||
public class AbstractMigrationApplication implements Closeable {
|
||||
|
|
|
|||
|
|
@ -5,6 +5,12 @@
|
|||
"paramDescription": "the path where storing the sequential file",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "n",
|
||||
"paramLongName": "nameNode",
|
||||
"paramDescription": "the hdfs Name node url",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "mongourl",
|
||||
"paramLongName": "mongoBaseUrl",
|
||||
|
|
|
|||
|
|
@ -301,6 +301,7 @@
|
|||
<arg>--mdFormat</arg><arg>ODF</arg>
|
||||
<arg>--mdLayout</arg><arg>store</arg>
|
||||
<arg>--mdInterpretation</arg><arg>cleaned</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
</java>
|
||||
<ok to="reuse_oaf"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -326,6 +327,7 @@
|
|||
<arg>--mdFormat</arg><arg>OAF</arg>
|
||||
<arg>--mdLayout</arg><arg>store</arg>
|
||||
<arg>--mdInterpretation</arg><arg>cleaned</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
</java>
|
||||
<ok to="ImportOAF_invisible"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -343,6 +345,7 @@
|
|||
<arg>--mdFormat</arg><arg>OAF</arg>
|
||||
<arg>--mdLayout</arg><arg>store</arg>
|
||||
<arg>--mdInterpretation</arg><arg>intersection</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
</java>
|
||||
<ok to="ImportODF_hdfs"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -4,18 +4,6 @@
|
|||
<name>migrationPathStep1</name>
|
||||
<description>the base path to store hdfs file</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>postgresURL</name>
|
||||
<description>the postgres URL to access to the database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>postgresUser</name>
|
||||
<description>the user postgres</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>postgresPassword</name>
|
||||
<description>the password postgres</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>mongoURL</name>
|
||||
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
|
||||
|
|
@ -24,27 +12,6 @@
|
|||
<name>mongoDb</name>
|
||||
<description>mongo database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookupUrl</name>
|
||||
<description>the address of the lookUp service</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>nsPrefixBlacklist</name>
|
||||
<value></value>
|
||||
<description>a blacklist of nsprefixes (comma separeted)</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ResetWorkingPath"/>
|
||||
|
|
@ -58,37 +25,22 @@
|
|||
<delete path='${migrationPathStep1}'/>
|
||||
<mkdir path='${migrationPathStep1}'/>
|
||||
</fs>
|
||||
<ok to="ImportDB"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ImportDB">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
|
||||
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
|
||||
<arg>-pgurl</arg><arg>${postgresURL}</arg>
|
||||
<arg>-pguser</arg><arg>${postgresUser}</arg>
|
||||
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
|
||||
<arg>-islookup</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
|
||||
</java>
|
||||
<ok to="ImportODF"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ImportODF">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
|
||||
<arg>-p</arg><arg>${migrationPathStep1}/odf_records</arg>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
|
||||
<arg>-p</arg><arg>${migrationPathStep1}</arg>
|
||||
<arg>-mongourl</arg><arg>${mongoURL}</arg>
|
||||
<arg>-mongodb</arg><arg>${mongoDb}</arg>
|
||||
<arg>-f</arg><arg>ODF</arg>
|
||||
<arg>-l</arg><arg>store</arg>
|
||||
<arg>-i</arg><arg>cleaned</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
|
||||
</java>
|
||||
<ok to="ImportOAF"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -98,13 +50,14 @@
|
|||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
|
||||
<arg>-p</arg><arg>${migrationPathStep1}/oaf_records</arg>
|
||||
<main-class>eu.dnetlib.dhp.oa.graph.raw.MigrateMongoMdstoresApplication</main-class>
|
||||
<arg>-p</arg><arg>${migrationPathStep1}</arg>
|
||||
<arg>-mongourl</arg><arg>${mongoURL}</arg>
|
||||
<arg>-mongodb</arg><arg>${mongoDb}</arg>
|
||||
<arg>-f</arg><arg>OAF</arg>
|
||||
<arg>-l</arg><arg>store</arg>
|
||||
<arg>-i</arg><arg>cleaned</arg>
|
||||
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
Loading…
Reference in New Issue