Merge remote-tracking branch 'origin/master' into doiboost
This commit is contained in:
commit
fdc0523e4c
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@ -25,6 +25,7 @@ public class DedupRecordFactory {
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public static <T extends OafEntity> Dataset<T> createDedupRecord(
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final SparkSession spark,
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final DataInfo dataInfo,
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final String mergeRelsInputPath,
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final String entitiesInputPath,
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final Class<T> clazz) {
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@ -67,41 +68,39 @@ public class DedupRecordFactory {
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Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<String, T>, T>)
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(key, values) -> entityMerger(key, values, ts, clazz),
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(key, values) -> entityMerger(key, values, ts, dataInfo),
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Encoders.bean(clazz));
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}
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private static <T extends OafEntity> T entityMerger(
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String id, Iterator<Tuple2<String, T>> entities, long ts, Class<T> clazz) {
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try {
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T entity = clazz.newInstance();
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entity.setId(id);
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entity.setDataInfo(new DataInfo());
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entity.getDataInfo().setTrust("0.9");
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entity.setLastupdatetimestamp(ts);
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String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo) {
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final Collection<String> dates = Lists.newArrayList();
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entities.forEachRemaining(
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t -> {
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T duplicate = t._2();
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entity.mergeFrom(duplicate);
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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Result r1 = (Result) duplicate;
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Result er = (Result) entity;
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er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
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T entity = entities.next()._2();
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if (er.getDateofacceptance() != null) {
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dates.add(r1.getDateofacceptance().getValue());
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}
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final Collection<String> dates = Lists.newArrayList();
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entities.forEachRemaining(
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t -> {
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T duplicate = t._2();
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entity.mergeFrom(duplicate);
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if (ModelSupport.isSubClass(duplicate, Result.class)) {
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Result r1 = (Result) duplicate;
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Result er = (Result) entity;
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er.setAuthor(DedupUtility.mergeAuthor(er.getAuthor(), r1.getAuthor()));
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if (r1.getDateofacceptance() != null) {
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dates.add(r1.getDateofacceptance().getValue());
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}
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});
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}
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});
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if (ModelSupport.isSubClass(entity, Result.class)) {
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((Result) entity).setDateofacceptance(DatePicker.pick(dates));
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}
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return entity;
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} catch (IllegalAccessException | InstantiationException e) {
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throw new RuntimeException(e);
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if (ModelSupport.isSubClass(entity, Result.class)) {
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((Result) entity).setDateofacceptance(DatePicker.pick(dates));
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}
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entity.setId(id);
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entity.setLastupdatetimestamp(ts);
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entity.setDataInfo(dataInfo);
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return entity;
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}
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}
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@ -3,7 +3,9 @@ package eu.dnetlib.dhp.oa.dedup;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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@ -21,6 +23,10 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
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private static final Logger log = LoggerFactory.getLogger(SparkCreateDedupRecord.class);
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public static final String ROOT_TRUST = "0.8";
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public static final String PROVENANCE_ACTION_CLASS = "sysimport:dedup";
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public static final String PROVENANCE_ACTIONS = "dnet:provenanceActions";
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public SparkCreateDedupRecord(ArgumentApplicationParser parser, SparkSession spark) {
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super(parser, spark);
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}
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@ -67,13 +73,30 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
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DedupUtility.createMergeRelPath(workingPath, actionSetId, subEntity);
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final String entityPath = DedupUtility.createEntityPath(graphBasePath, subEntity);
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Class<OafEntity> clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz)
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final Class<OafEntity> clazz =
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ModelSupport.entityTypes.get(EntityType.valueOf(subEntity));
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final DataInfo dataInfo = getDataInfo(dedupConf);
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DedupRecordFactory.createDedupRecord(spark, dataInfo, mergeRelPath, entityPath, clazz)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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}
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private static DataInfo getDataInfo(DedupConfig dedupConf) {
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DataInfo info = new DataInfo();
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info.setDeletedbyinference(false);
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info.setInferred(true);
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info.setInvisible(false);
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info.setTrust(ROOT_TRUST);
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info.setInferenceprovenance(dedupConf.getWf().getConfigurationId());
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Qualifier provenance = new Qualifier();
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provenance.setClassid(PROVENANCE_ACTION_CLASS);
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provenance.setClassname(PROVENANCE_ACTION_CLASS);
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provenance.setSchemeid(PROVENANCE_ACTIONS);
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provenance.setSchemename(PROVENANCE_ACTIONS);
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info.setProvenanceaction(provenance);
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return info;
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}
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}
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@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
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if (docIds.size() > 1) {
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final String s = getMin();
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String prefix = s.split("\\|")[0];
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ccId = prefix + "|dedup_______::" + DedupUtility.md5(s);
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ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
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return ccId;
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} else {
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return docIds.iterator().next();
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@ -25,7 +25,7 @@ public class ConnectedComponent implements Serializable {
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if (docIds.size() > 1) {
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final String s = getMin();
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String prefix = s.split("\\|")[0];
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ccId = prefix + "|dedup_______::" + DedupUtility.md5(s);
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ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
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return ccId;
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} else {
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return docIds.iterator().next();
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@ -19,6 +19,8 @@ public class GraphHiveImporterJob {
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private static final Logger log = LoggerFactory.getLogger(GraphHiveImporterJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser =
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@ -37,12 +39,12 @@ public class GraphHiveImporterJob {
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String hiveMetastoreUris = parser.get("hiveMetastoreUris");
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log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
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String hiveDbName = parser.get("hiveDbName");
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log.info("hiveDbName: {}", hiveDbName);
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String hiveMetastoreUris = parser.get("hiveMetastoreUris");
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log.info("hiveMetastoreUris: {}", hiveMetastoreUris);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", hiveMetastoreUris);
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@ -58,13 +60,13 @@ public class GraphHiveImporterJob {
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spark.sql(String.format("DROP DATABASE IF EXISTS %s CASCADE", hiveDbName));
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spark.sql(String.format("CREATE DATABASE IF NOT EXISTS %s", hiveDbName));
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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// Read the input file and convert it into RDD of serializable object
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ModelSupport.oafTypes.forEach(
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(name, clazz) ->
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spark.createDataset(
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sc.textFile(inputPath + "/" + name)
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.map(s -> new ObjectMapper().readValue(s, clazz))
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.map(s -> OBJECT_MAPPER.readValue(s, clazz))
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.rdd(),
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Encoders.bean(clazz))
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.write()
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@ -12,19 +12,15 @@
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<name>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>hive_jdbc_url</name>
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<name>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hive_db_name</name>
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<name>hiveDbName</name>
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<value>openaire</value>
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</property>
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</configuration>
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@ -1,10 +1,10 @@
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DROP VIEW IF EXISTS ${hive_db_name}.result;
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DROP VIEW IF EXISTS ${hiveDbName}.result;
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CREATE VIEW IF NOT EXISTS result as
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.publication p
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.publication p
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union all
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.dataset d
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.dataset d
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union all
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.software s
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.software s
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union all
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hive_db_name}.otherresearchproduct o;
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select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, instance from ${hiveDbName}.otherresearchproduct o;
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@ -2,13 +2,21 @@
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<parameters>
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<property>
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<name>sourcePath</name>
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<name>inputPath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>hive_db_name</name>
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<name>hiveDbName</name>
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<description>the target hive database name</description>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<description>hive server jdbc url</description>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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@ -87,9 +95,9 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--hive_db_name</arg><arg>${hive_db_name}</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--inputPath</arg><arg>${inputPath}</arg>
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<arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
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<arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
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</spark>
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<ok to="PostProcessing"/>
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<error to="Kill"/>
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@ -102,12 +110,12 @@
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<configuration>
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<property>
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<name>hive.metastore.uris</name>
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<value>${hive_metastore_uris}</value>
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<value>${hiveMetastoreUris}</value>
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</property>
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</configuration>
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<jdbc-url>${hive_jdbc_url}/${hive_db_name}</jdbc-url>
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<jdbc-url>${hiveJdbcUrl}/${hiveDbName}</jdbc-url>
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<script>lib/scripts/postprocessing.sql</script>
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<param>hive_db_name=${hive_db_name}</param>
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<param>hiveDbName=${hiveDbName}</param>
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</hive2>
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<ok to="End"/>
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<error to="Kill"/>
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@ -216,6 +216,7 @@ public class CreateRelatedEntitiesJob_phase2 {
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(MapFunction<String, E>)
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value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz))
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.filter("dataInfo.invisible == false")
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.map(
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(MapFunction<E, TypedRow>)
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value ->
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6
pom.xml
6
pom.xml
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@ -292,6 +292,12 @@
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-actionmanager-common</artifactId>
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<version>6.0.5</version>
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<exclusions>
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<exclusion>
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<groupId>org.apache.hadoop</groupId>
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<artifactId>hadoop-common</artifactId>
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</exclusion>
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</exclusions>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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