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extended XmlIndexingJob to accept an optional parameter: outputPath. When present, forces the job to write its output on the specified HDFS location

This commit is contained in:
Claudio Atzori 2020-11-18 14:34:55 +01:00
parent 29dcff0f34
commit d9e07a242b
6 changed files with 117 additions and 48 deletions
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77
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
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@ -1,8 +1,31 @@
package eu.dnetlib.dhp.oa.provision; package eu.dnetlib.dhp.oa.provision;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import com.lucidworks.spark.util.SolrSupport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.Text;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import java.io.IOException; import java.io.IOException;
import java.io.StringReader; import java.io.StringReader;
import java.io.StringWriter; import java.io.StringWriter;
@ -10,29 +33,7 @@ import java.text.SimpleDateFormat;
import java.util.Date; import java.util.Date;
import java.util.Optional; import java.util.Optional;
import javax.xml.transform.Transformer; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text;
import org.apache.solr.common.SolrInputDocument;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.rdd.RDD;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.lucidworks.spark.util.SolrSupport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
public class XmlIndexingJob { public class XmlIndexingJob {
@ -48,6 +49,8 @@ public class XmlIndexingJob {
private int batchSize; private int batchSize;
private String outputPath;
private SparkSession spark; private SparkSession spark;
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
@ -72,12 +75,17 @@ public class XmlIndexingJob {
final String format = parser.get("format"); final String format = parser.get("format");
log.info("format: {}", format); log.info("format: {}", format);
final String outputPath = Optional.ofNullable(parser.get("outputPath"))
.orElse(null);
log.info("outputPath: {}", outputPath);
final Integer batchSize = parser.getObjectMap().containsKey("batchSize") final Integer batchSize = parser.getObjectMap().containsKey("batchSize")
? Integer.valueOf(parser.get("batchSize")) ? Integer.valueOf(parser.get("batchSize"))
: DEFAULT_BATCH_SIZE; : DEFAULT_BATCH_SIZE;
log.info("batchSize: {}", batchSize); log.info("batchSize: {}", batchSize);
final SparkConf conf = new SparkConf(); final SparkConf conf = new SparkConf();
conf.registerKryoClasses(new Class[] { SerializableSolrInputDocument.class });
runWithSparkSession( runWithSparkSession(
conf, conf,
@ -86,15 +94,16 @@ public class XmlIndexingJob {
final String isLookupUrl = parser.get("isLookupUrl"); final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl); log.info("isLookupUrl: {}", isLookupUrl);
final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl)); final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
new XmlIndexingJob(spark, inputPath, format, batchSize).run(isLookup); new XmlIndexingJob(spark, inputPath, format, batchSize, outputPath).run(isLookup);
}); });
} }
public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize) { public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize, String outputPath) {
this.spark = spark; this.spark = spark;
this.inputPath = inputPath; this.inputPath = inputPath;
this.format = format; this.format = format;
this.batchSize = batchSize; this.batchSize = batchSize;
this.outputPath = outputPath;
} }
public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException { public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
@ -116,15 +125,23 @@ public class XmlIndexingJob {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
RDD<SolrInputDocument> docs = sc JavaRDD<SolrInputDocument> docs = sc
.sequenceFile(inputPath, Text.class, Text.class) .sequenceFile(inputPath, Text.class, Text.class)
.map(t -> t._2().toString()) .map(t -> t._2().toString())
.map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s)) .map(s -> toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), s))
.map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s)) .map(s -> new StreamingInputDocumentFactory(version, dsId).parseDocument(s));
.rdd();
if (StringUtils.isNotBlank(outputPath)) {
spark.createDataset(
docs.map(s -> new SerializableSolrInputDocument(s)).rdd(),
Encoders.kryo(SerializableSolrInputDocument.class))
.write()
.mode(SaveMode.Overwrite)
.parquet(outputPath);
} else {
final String collection = ProvisionConstants.getCollectionName(format); final String collection = ProvisionConstants.getCollectionName(format);
SolrSupport.indexDocs(zkHost, collection, batchSize, docs); SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
}
} }
protected static String toIndexRecord(Transformer tr, final String record) { protected static String toIndexRecord(Transformer tr, final String record) {

3
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/SerializableSolrInputDocument.java
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@ -6,6 +6,9 @@ import org.apache.solr.common.SolrInputField;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
/**
* Wrapper class needed to make the SolrInputDocument compatible with the Kryo serialization mechanism.
*/
public class SerializableSolrInputDocument extends SolrInputDocument { public class SerializableSolrInputDocument extends SolrInputDocument {
public SerializableSolrInputDocument() { public SerializableSolrInputDocument() {

6
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json
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@ -22,5 +22,11 @@
"paramLongName": "batchSize", "paramLongName": "batchSize",
"paramDescription": "size of the batch of documents sent to solr", "paramDescription": "size of the batch of documents sent to solr",
"paramRequired": false "paramRequired": false
},
{
"paramName": "o",
"paramLongName": "outputPath",
"paramDescription": "path on hdfs activating an alternative output for the SolrInputDocuments",
"paramRequired": false
} }
] ]

1
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
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@ -638,6 +638,7 @@
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg> <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--format</arg><arg>${format}</arg> <arg>--format</arg><arg>${format}</arg>
<arg>--batchSize</arg><arg>${batchSize}</arg> <arg>--batchSize</arg><arg>${batchSize}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark> </spark>
<ok to="commit_solr_collection"/> <ok to="commit_solr_collection"/>
<error to="Kill"/> <error to="Kill"/>

11
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java
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@ -54,13 +54,14 @@ public abstract class SolrTest {
miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME);
// override settings in the solrconfig include // override settings in the solrconfig include
// System.setProperty("solr.tests.maxBufferedDocs", "100000"); System.setProperty("solr.tests.maxBufferedDocs", "100000");
// System.setProperty("solr.tests.maxIndexingThreads", "-1"); System.setProperty("solr.tests.maxIndexingThreads", "-1");
// System.setProperty("solr.tests.ramBufferSizeMB", "100"); System.setProperty("solr.tests.ramBufferSizeMB", "100");
// use non-test classes so RandomizedRunner isn't necessary // use non-test classes so RandomizedRunner isn't necessary
// System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler");
// System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory");
System.setProperty("solr.lock.type", "single");
log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString()); log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
log log

59
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
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@ -1,26 +1,33 @@
package eu.dnetlib.dhp.oa.provision; package eu.dnetlib.dhp.oa.provision;
import java.io.IOException; import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
import java.net.URI; import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.solr.client.solrj.SolrQuery; import org.apache.solr.client.solrj.SolrQuery;
import org.apache.solr.client.solrj.response.QueryResponse; import org.apache.solr.client.solrj.response.QueryResponse;
import org.apache.solr.common.SolrInputField;
import org.apache.solr.common.params.CommonParams; import org.apache.solr.common.params.CommonParams;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaPairRDD;
import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
import org.junit.jupiter.api.extension.ExtendWith; import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.Mockito; import org.mockito.Mockito;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; import java.io.IOException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import java.io.StringReader;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.net.URI;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class XmlIndexingJobTest extends SolrTest { public class XmlIndexingJobTest extends SolrTest {
@ -58,6 +65,7 @@ public class XmlIndexingJobTest extends SolrTest {
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
conf.registerKryoClasses(new Class[] { SerializableSolrInputDocument.class });
conf.setMaster("local[1]"); conf.setMaster("local[1]");
conf.set("spark.driver.host", "localhost"); conf.set("spark.driver.host", "localhost");
@ -78,7 +86,7 @@ public class XmlIndexingJobTest extends SolrTest {
} }
@Test @Test
public void testXmlIndexingJob() throws Exception { public void testXmlIndexingJob_onSolr() throws Exception {
String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
@ -87,13 +95,46 @@ public class XmlIndexingJobTest extends SolrTest {
.sequenceFile(inputPath, Text.class, Text.class) .sequenceFile(inputPath, Text.class, Text.class)
.count(); .count();
new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient); new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, null).run(isLookupClient);
Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*")); QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*"));
Assertions.assertEquals(nRecord, rsp.getResults().getNumFound()); Assertions.assertEquals(nRecord, rsp.getResults().getNumFound(),
"the number of indexed records should be equal to the number of input records");
}
@Test
public void testXmlIndexingJob_saveOnHDFS() throws Exception {
final String ID_XPATH = "//header/*[local-name()='objIdentifier']";
String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
final JavaPairRDD<Text, Text> xmlRecords = JavaSparkContext
.fromSparkContext(spark.sparkContext())
.sequenceFile(inputPath, Text.class, Text.class);
long nRecord = xmlRecords.count();
long xmlIdUnique = xmlRecords
.map(t -> t._2().toString())
.map(s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH))
.distinct().count();
Assertions.assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records");
final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString();
new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, outputPath).run(isLookupClient);
final Dataset<SerializableSolrInputDocument> solrDocs = spark.read()
.load(outputPath)
.as(Encoders.kryo(SerializableSolrInputDocument.class));
long docIdUnique = solrDocs.map((MapFunction<SerializableSolrInputDocument, String>) doc -> {
final SolrInputField id = doc.getField("__indexrecordidentifier");
return id.getFirstValue().toString();
}, Encoders.STRING())
.distinct()
.count();
Assertions.assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output records");
} }
} }