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[aggregator graph] using dedicated path to sync claims, adjusted paths with wildcards

This commit is contained in:
Claudio Atzori 2023-03-08 21:16:52 +01:00
parent 5b8fd37314
commit e28d395e87
4 changed files with 11 additions and 11 deletions
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2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
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@ -9,7 +9,6 @@ import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
@ -30,6 +29,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java
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@ -9,7 +9,6 @@ import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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.spark.SparkConf; import org.apache.spark.SparkConf;
@ -24,6 +23,7 @@ import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

14
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java
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@ -9,7 +9,6 @@ import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger; import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import eu.dnetlib.dhp.common.HdfsSupport;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
@ -17,14 +16,15 @@ import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.Path; import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
public class AbstractMigrationApplication implements Closeable { public class AbstractMigrationApplication implements Closeable {
@ -104,10 +104,10 @@ public class AbstractMigrationApplication implements Closeable {
protected static List<String> listEntityPaths(final SparkSession spark, final String paths) { protected static List<String> listEntityPaths(final SparkSession spark, final String paths) {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return Arrays return Arrays
.stream(paths.split(",")) .stream(paths.split(","))
.filter(StringUtils::isNotBlank) .filter(StringUtils::isNotBlank)
.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()) || p.contains("/*")) .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()) || p.contains("/*"))
.collect(Collectors.toList()); .collect(Collectors.toList());
} }
public ObjectMapper getObjectMapper() { public ObjectMapper getObjectMapper() {

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
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@ -456,7 +456,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg> <arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims/*/*,${contentPath}/odf_claims/*/*</arg>
<arg>--invalidPath</arg><arg>${workingDir}/invalid_records_claim</arg> <arg>--invalidPath</arg><arg>${workingDir}/invalid_records_claim</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg> <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
</spark> </spark>
@ -480,7 +480,7 @@
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims</arg> <arg>--sourcePaths</arg><arg>${contentPath}/db_claims,${contentPath}/oaf_claims/*/*,${contentPath}/odf_claims/*/*</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg> <arg>--targetPath</arg><arg>${workingDir}/entities_claim</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg> <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--shouldHashId</arg><arg>${shouldHashId}</arg> <arg>--shouldHashId</arg><arg>${shouldHashId}</arg>