diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index cda44bb341..f3f1b02fe3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -107,7 +107,7 @@ public abstract class AbstractMdRecordToOafMapper { this.forceOriginalId = false; } - public List processMdRecord(final String xml) throws DocumentException { + public List processMdRecord(final String xml) { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); try { @@ -143,7 +143,7 @@ public abstract class AbstractMdRecordToOafMapper { return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); } catch (DocumentException e) { log.error("Error with record:\n" + xml); - throw e; + return Lists.newArrayList(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 6bb18c3756..5f9d980739 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -16,6 +16,9 @@ import org.apache.hadoop.io.compress.GzipCodec; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; import org.slf4j.Logger; @@ -127,8 +130,8 @@ public class GenerateEntitiesApplication { .sequenceFile(sp, Text.class, Text.class) .map(k -> new Tuple2<>(k._1().toString(), k._2().toString())) .map(k -> convertToListOaf(k._1(), k._2(), shouldHashId, vocs)) - .filter(Objects::nonNull) - .flatMap(List::iterator)); + .flatMap(List::iterator) + .filter(Objects::nonNull)); } switch (mode) { @@ -155,11 +158,11 @@ public class GenerateEntitiesApplication { .saveAsTextFile(targetPath, GzipCodec.class); } - private static List convertToListOaf( + public static List convertToListOaf( final String id, final String s, final boolean shouldHashId, - final VocabularyGroup vocs) throws DocumentException { + final VocabularyGroup vocs) { final String type = StringUtils.substringAfter(id, ":"); switch (type.toLowerCase()) { @@ -200,8 +203,7 @@ public class GenerateEntitiesApplication { try { return OBJECT_MAPPER.readValue(s, clazz); } catch (final Exception e) { - log.error("Error parsing object of class: {}", clazz); - log.error(s); + log.error("Error parsing object of class: {}:\n{}", clazz, s); throw new IllegalArgumentException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java new file mode 100644 index 0000000000..a8eb871c89 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/VerifyRecordsApplication.java @@ -0,0 +1,108 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.Arrays; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.rdd.RDD; +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 eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import scala.Tuple2; + +public class VerifyRecordsApplication { + + private static final Logger log = LoggerFactory.getLogger(VerifyRecordsApplication.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + VerifyRecordsApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json"))); + + parser.parseArgument(args); + + final Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String sourcePaths = parser.get("sourcePaths"); + log.info("sourcePaths: {}", sourcePaths); + + final String invalidPath = parser.get("invalidPath"); + log.info("invalidPath: {}", invalidPath); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl); + final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookupService); + + final SparkConf conf = new SparkConf(); + runWithSparkSession(conf, isSparkSessionManaged, spark -> { + HdfsSupport.remove(invalidPath, spark.sparkContext().hadoopConfiguration()); + validateRecords(spark, sourcePaths, invalidPath, vocs); + }); + } + + private static void validateRecords(SparkSession spark, String sourcePaths, String invalidPath, + VocabularyGroup vocs) { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + final List existingSourcePaths = Arrays + .stream(sourcePaths.split(",")) + .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) + .collect(Collectors.toList()); + + log.info("Verify records in files:"); + existingSourcePaths.forEach(log::info); + + for (final String sp : existingSourcePaths) { + RDD invalidRecords = sc + .sequenceFile(sp, Text.class, Text.class) + .map(k -> tryApplyMapping(k._1().toString(), k._2().toString(), true, vocs)) + .filter(Objects::nonNull) + .rdd(); + spark + .createDataset(invalidRecords, Encoders.STRING()) + .write() + .mode(SaveMode.Append) + .option("compression", "gzip") + .text(invalidPath); + } + } + + private static String tryApplyMapping( + final String id, + final String xmlRecord, + final boolean shouldHashId, + final VocabularyGroup vocs) { + + final List oaf = GenerateEntitiesApplication.convertToListOaf(id, xmlRecord, shouldHashId, vocs); + if (Optional.ofNullable(oaf).map(List::isEmpty).orElse(false)) { + return xmlRecord; + } + return null; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index cba64899b5..6f63e93271 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Closeable; import java.io.IOException; import java.util.Arrays; +import java.util.List; import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; import java.util.stream.Collectors; @@ -24,8 +25,11 @@ import org.apache.http.impl.client.HttpClients; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.raw.OafToOafMapper; +import eu.dnetlib.dhp.oa.graph.raw.OdfToOafMapper; import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; -import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.DHPUtils; public class AbstractMigrationApplication implements Closeable { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index c6cc46c0fe..8262c6923c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -446,10 +446,34 @@ - - + + + + + yarn + cluster + VerifyRecords_claim + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_claims,${contentPath}/oaf_claims,${contentPath}/odf_claims + --invalidPath${workingDir}/invalid_records_claim + --isLookupUrl${isLookupUrl} + + + + + yarn @@ -499,6 +523,30 @@ + + + yarn + cluster + VerifyRecords + eu.dnetlib.dhp.oa.graph.raw.VerifyRecordsApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_records,${contentPath}/odf_records,${contentPath}/oaf_records_hdfs,${contentPath}/odf_records_hdfs,${contentPath}/oaf_records_invisible + --invalidPath${workingDir}/invalid_records + --isLookupUrl${isLookupUrl} + + + + + yarn diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json new file mode 100644 index 0000000000..eb00e76097 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/verify_records_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "s", + "paramLongName": "sourcePaths", + "paramDescription": "the HDFS source paths which contains the sequential file (comma separated)", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "invalidPath", + "paramDescription": "the path of the invalid records file", + "paramRequired": false + }, + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the url of the ISLookupService", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index 9e7733123d..806603880f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -21,7 +21,6 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; @@ -722,7 +721,7 @@ class MappersTest { assertEquals(1, p.getInstance().size()); assertNotNull(p.getInstance().get(0).getAlternateIdentifier()); assertEquals(0, p.getInstance().get(0).getAlternateIdentifier().size()); - assertEquals(1, p.getInstance().get(0).getUrl().size()); + assertEquals(2, p.getInstance().get(0).getUrl().size()); } @Test @@ -952,11 +951,9 @@ class MappersTest { void testNotWellFormed() throws IOException { final String xml = IOUtils .toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_notwellformed.xml"))); - final DocumentException generalEx = new DocumentException(); - - DocumentException exception = assertThrows(DocumentException.class, () -> { - new OafToOafMapper(vocs, false, true).processMdRecord(xml); - }); + final List actual = new OafToOafMapper(vocs, false, true).processMdRecord(xml); + assertNotNull(actual); + assertTrue(actual.isEmpty()); } private void assertValidId(final String id) {