[aggregator graph] handle paths including wildcards
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parent
588aca5ce4
commit
7fd89566c2
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@ -9,6 +9,7 @@ import java.util.Objects;
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import java.util.Optional;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.Text;
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@ -36,7 +37,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import scala.Tuple2;
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import scala.Tuple2;
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public class GenerateEntitiesApplication {
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public class GenerateEntitiesApplication extends AbstractMigrationApplication {
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private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class);
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private static final Logger log = LoggerFactory.getLogger(GenerateEntitiesApplication.class);
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@ -112,15 +113,12 @@ public class GenerateEntitiesApplication {
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final boolean shouldHashId,
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final boolean shouldHashId,
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final Mode mode) {
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final Mode mode) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final List<String> existingSourcePaths = listEntityPaths(spark, sourcePaths);
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final List<String> existingSourcePaths = Arrays
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.stream(sourcePaths.split(","))
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
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.collect(Collectors.toList());
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log.info("Generate entities from files:");
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log.info("Generate entities from files:");
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existingSourcePaths.forEach(log::info);
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existingSourcePaths.forEach(log::info);
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Oaf> inputRdd = sc.emptyRDD();
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JavaRDD<Oaf> inputRdd = sc.emptyRDD();
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for (final String sp : existingSourcePaths) {
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for (final String sp : existingSourcePaths) {
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@ -9,6 +9,7 @@ import java.util.Objects;
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import java.util.Optional;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.SparkConf;
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@ -28,7 +29,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import scala.Tuple2;
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import scala.Tuple2;
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public class VerifyRecordsApplication {
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public class VerifyRecordsApplication extends AbstractMigrationApplication {
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private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class);
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private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class);
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@ -69,15 +70,13 @@ public class VerifyRecordsApplication {
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private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath,
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private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath,
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VocabularyGroup vocs) {
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VocabularyGroup vocs) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final List<String> existingSourcePaths = listEntityPaths(spark, sourcePaths);
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final List<String> existingSourcePaths = Arrays
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.stream(sourcePaths.split(","))
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()))
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.collect(Collectors.toList());
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log.info("Verify records in files:");
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log.info("Verify records in files:");
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existingSourcePaths.forEach(log::info);
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existingSourcePaths.forEach(log::info);
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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for (final String sp : existingSourcePaths) {
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for (final String sp : existingSourcePaths) {
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RDD<String> invalidRecords = sc
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RDD<String> invalidRecords = sc
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.sequenceFile(sp, Text.class, Text.class)
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.sequenceFile(sp, Text.class, Text.class)
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@ -3,9 +3,14 @@ package eu.dnetlib.dhp.oa.graph.raw.common;
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import java.io.Closeable;
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import java.io.Closeable;
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import java.io.IOException;
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import java.io.IOException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Set;
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import java.util.Set;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.apache.commons.logging.LogFactory;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.conf.Configuration;
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@ -18,6 +23,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.SparkSession;
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public class AbstractMigrationApplication implements Closeable {
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public class AbstractMigrationApplication implements Closeable {
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@ -94,6 +101,15 @@ public class AbstractMigrationApplication implements Closeable {
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}
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}
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}
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}
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protected static List<String> listEntityPaths(final SparkSession spark, final String paths) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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return Arrays
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.stream(paths.split(","))
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.filter(StringUtils::isNotBlank)
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.filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration()) || p.contains("/*"))
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.collect(Collectors.toList());
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}
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public ObjectMapper getObjectMapper() {
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public ObjectMapper getObjectMapper() {
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return objectMapper;
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return objectMapper;
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}
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}
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