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dnet-hadoop
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code formatting

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pull/157/head
Claudio Atzori 3 years ago
parent d517c71458
commit 512e7b0170
2 changed files with 37 additions and 35 deletions
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38
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafApplication.java
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@ -1,18 +1,10 @@
package eu.dnetlib.dhp.oa.graph.raw;
import com.clearspring.analytics.util.Lists;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
@ -26,9 +18,19 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
import com.clearspring.analytics.util.Lists;
import com.fasterxml.jackson.databind.ObjectMapper;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class CopyHdfsOafApplication extends AbstractMigrationApplication {
@ -96,12 +98,12 @@ public class CopyHdfsOafApplication extends AbstractMigrationApplication {
if (validPaths.length > 0) {
// load the dataset
Dataset<Oaf> oaf = spark
.read()
.load(validPaths)
.as(Encoders.kryo(Oaf.class));
.read()
.load(validPaths)
.as(Encoders.kryo(Oaf.class));
// dispatch each entity type individually in the respective graph subdirectory in append mode
for(Map.Entry<String, Class> e : ModelSupport.oafTypes.entrySet()) {
for (Map.Entry<String, Class> e : ModelSupport.oafTypes.entrySet()) {
oaf
.filter((FilterFunction<Oaf>) o -> o.getClass().getSimpleName().toLowerCase().equals(e.getKey()))
.map((MapFunction<Oaf, String>) OBJECT_MAPPER::writeValueAsString, Encoders.bean(e.getValue()))

34
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java
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@ -8,7 +8,6 @@ import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
@ -17,15 +16,16 @@ 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.schema.mdstore.MDStoreWithInfo;
import eu.dnetlib.dhp.schema.oaf.Oaf;
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;
public class AbstractMigrationApplication implements Closeable {
@ -68,9 +68,9 @@ public class AbstractMigrationApplication implements Closeable {
* @throws IOException in case of HTTP communication issues
*/
protected static Set<String> mdstorePaths(final String mdstoreManagerUrl,
final String format,
final String layout,
final String interpretation) throws IOException {
final String format,
final String layout,
final String interpretation) throws IOException {
final String url = mdstoreManagerUrl + "/mdstores/";
final ObjectMapper objectMapper = new ObjectMapper();
@ -81,15 +81,15 @@ public class AbstractMigrationApplication implements Closeable {
final String json = IOUtils.toString(response.getEntity().getContent());
final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
return Arrays
.stream(mdstores)
.filter(md -> md.getFormat().equalsIgnoreCase(format))
.filter(md -> md.getLayout().equalsIgnoreCase(layout))
.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
.filter(md -> md.getSize() > 0)
.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
.collect(Collectors.toSet());
.stream(mdstores)
.filter(md -> md.getFormat().equalsIgnoreCase(format))
.filter(md -> md.getLayout().equalsIgnoreCase(layout))
.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
.filter(md -> md.getSize() > 0)
.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
.collect(Collectors.toSet());
}
}
}

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