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dnet-hadoop
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Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

This commit is contained in:
Claudio Atzori 2020-03-10 17:09:44 +01:00
parent a3f184fd3f b6efa9d6ab
commit 60aedb1110
14 changed files with 81 additions and 143 deletions
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8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateDbEntitiesApplication.java
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@ -68,12 +68,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("namenode");
final String hdfsUser = parser.get("hdfsUser");
final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims");
try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, hdfsNameNode, hdfsUser, dbUrl, dbUser, dbPassword)) {
try (final MigrateDbEntitiesApplication smdbe = new MigrateDbEntitiesApplication(hdfsPath, dbUrl, dbUser, dbPassword)) {
if (processClaims) {
log.info("Processing claims...");
smdbe.execute("queryClaims.sql", smdbe::processClaims);
@ -97,9 +95,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
}
}
public MigrateDbEntitiesApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String dbUrl, final String dbUser,
public MigrateDbEntitiesApplication(final String hdfsPath, final String dbUrl, final String dbUser,
final String dbPassword) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser);
super(hdfsPath);
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.lastUpdateTimestamp = new Date().getTime();
}

9
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/step1/MigrateMongoMdstoresApplication.java
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@ -32,18 +32,15 @@ public class MigrateMongoMdstoresApplication extends AbstractMigrationApplicatio
final String mdInterpretation = parser.get("mdInterpretation");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("namenode");
final String hdfsUser = parser.get("hdfsUser");
try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, hdfsNameNode, hdfsUser, mongoBaseUrl, mongoDb)) {
try (MigrateMongoMdstoresApplication app = new MigrateMongoMdstoresApplication(hdfsPath, mongoBaseUrl, mongoDb)) {
app.execute(mdFormat, mdLayout, mdInterpretation);
}
}
public MigrateMongoMdstoresApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser, final String mongoBaseUrl,
final String mongoDb) throws Exception {
super(hdfsPath, hdfsNameNode, hdfsUser);
public MigrateMongoMdstoresApplication(final String hdfsPath, final String mongoBaseUrl, final String mongoDb) throws Exception {
super(hdfsPath);
this.mdstoreClient = new MdstoreClient(mongoBaseUrl, mongoDb);
}

21
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/utils/AbstractMigrationApplication.java
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@ -2,13 +2,11 @@ package eu.dnetlib.dhp.migration.utils;
import java.io.Closeable;
import java.io.IOException;
import java.net.URI;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text;
@ -30,22 +28,21 @@ public class AbstractMigrationApplication implements Closeable {
private static final Log log = LogFactory.getLog(AbstractMigrationApplication.class);
public AbstractMigrationApplication(final String hdfsPath, final String hdfsNameNode, final String hdfsUser) throws Exception {
public AbstractMigrationApplication(final String hdfsPath) throws Exception {
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s, nameNode=%s, user=%s", hdfsPath, hdfsNameNode, hdfsUser));
log.info(String.format("Creating SequenceFile Writer, hdfsPath=%s", hdfsPath));
this.writer = SequenceFile.createWriter(getConf(hdfsNameNode, hdfsUser), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
this.writer = SequenceFile.createWriter(getConf(), SequenceFile.Writer.file(new Path(hdfsPath)), SequenceFile.Writer
.keyClass(Text.class), SequenceFile.Writer.valueClass(Text.class));
}
private Configuration getConf(final String hdfsNameNode, final String hdfsUser) throws IOException {
private Configuration getConf() throws IOException {
final Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
System.setProperty("HADOOP_USER_NAME", hdfsUser);
System.setProperty("hadoop.home.dir", "/");
FileSystem.get(URI.create(hdfsNameNode), conf);
/*
* conf.set("fs.defaultFS", hdfsNameNode); conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
* conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName()); System.setProperty("HADOOP_USER_NAME", hdfsUser);
* System.setProperty("hadoop.home.dir", "/"); FileSystem.get(URI.create(hdfsNameNode), conf);
*/
return conf;
}

12
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_db_entities_parameters.json
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@ -5,18 +5,6 @@
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "u",
"paramLongName": "hdfsUser",
"paramDescription": "the user wich create the hdfs seq file",
"paramRequired": true
},
{
"paramName": "pgurl",
"paramLongName": "postgresUrl",

12
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/migrate_mongo_mstores_parameters.json
View File

@ -5,18 +5,6 @@
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "n",
"paramLongName": "namenode",
"paramDescription": "the Name Node URI",
"paramRequired": true
},
{
"paramName": "u",
"paramLongName": "hdfsUser",
"paramDescription": "the user wich create the hdfs seq file",
"paramRequired": true
},
{
"paramName": "mongourl",
"paramLongName": "mongoBaseUrl",

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/config-default.xml
View File

@ -15,8 +15,4 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/claims/oozie_app/workflow.xml
View File

@ -67,8 +67,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/db_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
@ -84,8 +82,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/odf_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
@ -102,8 +98,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationClaimsPathStep1}/oaf_claims</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/config-default.xml
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@ -15,8 +15,4 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_all_steps/oozie_app/workflow.xml
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@ -67,8 +67,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
@ -83,8 +81,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/odf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
@ -101,8 +97,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/oaf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/config-default.xml
View File

@ -15,8 +15,4 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

6
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step1/oozie_app/workflow.xml
View File

@ -59,8 +59,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateDbEntitiesApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/db_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-pgurl</arg><arg>${postgresURL}</arg>
<arg>-pguser</arg><arg>${postgresUser}</arg>
<arg>-pgpasswd</arg><arg>${postgresPassword}</arg>
@ -75,8 +73,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/odf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>ODF</arg>
@ -93,8 +89,6 @@
<name-node>${nameNode}</name-node>
<main-class>eu.dnetlib.dhp.migration.step1.MigrateMongoMdstoresApplication</main-class>
<arg>-p</arg><arg>${migrationPathStep1}/oaf_records</arg>
<arg>-n</arg><arg>${nameNode}</arg>
<arg>-u</arg><arg>${hdfsUser}</arg>
<arg>-mongourl</arg><arg>${mongoURL}</arg>
<arg>-mongodb</arg><arg>${mongoDb}</arg>
<arg>-f</arg><arg>OAF</arg>

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step2/oozie_app/config-default.xml
View File

@ -15,8 +15,4 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

4
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/wfs/regular_step3/oozie_app/config-default.xml
View File

@ -15,8 +15,4 @@
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hdfsUser</name>
<value>dnet</value>
</property>
</configuration>

46
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/CollectionJobTest.java
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@ -1,17 +1,23 @@
package eu.dnetlib.dhp.collection;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.junit.*;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.model.mdstore.MetadataRecord;
import eu.dnetlib.dhp.model.mdstore.Provenance;
public class CollectionJobTest {
private Path testDir;
@Before
@ -26,48 +32,50 @@ public class CollectionJobTest {
@Test
public void tesCollection() throws Exception {
Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix");
final Provenance provenance = new Provenance("pippo", "puppa", "ns_prefix");
GenerateNativeStoreSparkJob.main(new String[] {
"-mt", "local",
"-w", "wid",
"-e", "XML",
"-d", ""+System.currentTimeMillis(),
"-d", "" + System.currentTimeMillis(),
"-p", new ObjectMapper().writeValueAsString(provenance),
"-x", "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']",
"-i", this.getClass().getResource("/eu/dnetlib/dhp/collection/native.seq").toString(),
"-o", testDir.toString()+"/store",
"-o", testDir.toString() + "/store",
"-t", "true",
"-ru", "",
"-rp", "",
"-rh", "",
"-ro", "",
"-rr", ""});
"-rr", "" });
System.out.println(new ObjectMapper().writeValueAsString(provenance));
}
@Test
public void testGenerationMetadataRecord() throws Exception {
final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml"));
MetadataRecord record = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
final MetadataRecord record = GenerateNativeStoreSparkJob
.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar",
"ns_prefix"), System.currentTimeMillis(), null, null);
assert record != null;
System.out.println(record.getId());
System.out.println(record.getOriginalId());
}
@Test
public void TestEquals () throws IOException {
public void TestEquals() throws IOException {
final String xml = IOUtils.toString(this.getClass().getResourceAsStream("./record.xml"));
MetadataRecord record = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
MetadataRecord record1 = GenerateNativeStoreSparkJob.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar", "ns_prefix"), System.currentTimeMillis(), null,null);
final MetadataRecord record = GenerateNativeStoreSparkJob
.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar",
"ns_prefix"), System.currentTimeMillis(), null, null);
final MetadataRecord record1 = GenerateNativeStoreSparkJob
.parseRecord(xml, "./*[local-name()='record']/*[local-name()='header']/*[local-name()='identifier']", "XML", new Provenance("foo", "bar",
"ns_prefix"), System.currentTimeMillis(), null, null);
assert record != null;
record.setBody("ciao");
assert record1 != null;