forked from D-Net/dnet-hadoop
orcid / orcid_pending cleaning backported from master branch
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dd19c4ac5a
commit
2039bb9f5f
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@ -26,8 +26,9 @@ import eu.dnetlib.dhp.schema.oaf.*;
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public class GraphCleaningFunctions extends CleaningFunctions {
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public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
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public static final int ORCID_LEN = 19;
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public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
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public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
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public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
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public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]";
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public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10;
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@ -281,7 +282,27 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
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final List<Author> authors = Lists.newArrayList();
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r
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.setAuthor(
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r
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.getAuthor()
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.stream()
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.filter(a -> Objects.nonNull(a))
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.filter(a -> StringUtils.isNotBlank(a.getFullname()))
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.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
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.collect(Collectors.toList()));
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boolean nullRank = r
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.getAuthor()
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.stream()
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.anyMatch(a -> Objects.isNull(a.getRank()));
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if (nullRank) {
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int i = 1;
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for (Author author : r.getAuthor()) {
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author.setRank(i++);
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}
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}
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for (Author a : r.getAuthor()) {
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if (Objects.isNull(a.getPid())) {
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a.setPid(Lists.newArrayList());
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@ -295,41 +316,53 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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.filter(p -> Objects.nonNull(p.getQualifier()))
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.map(p -> {
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p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
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// hack to distinguish orcid from orcid_pending
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String pidProvenance = Optional
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.ofNullable(p.getDataInfo())
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.map(
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d -> Optional
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.ofNullable(d.getProvenanceaction())
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.map(Qualifier::getClassid)
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.orElse(""))
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.orElse("");
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if (p
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.getQualifier()
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.getClassid()
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.toLowerCase()
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.contains(ModelConstants.ORCID)) {
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if (pidProvenance
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.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
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p.getQualifier().setClassid(ModelConstants.ORCID);
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} else {
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p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
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}
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final String orcid = p
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.getValue()
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.trim()
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.toLowerCase()
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.replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4");
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if (orcid.length() == ORCID_LEN) {
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p.setValue(orcid);
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} else {
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p.setValue("");
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}
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}
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return p;
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})
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.collect(
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Collectors
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.toMap(
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StructuredProperty::getValue, Function.identity(), (p1, p2) -> p1,
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p -> p.getQualifier().getClassid() + p.getValue(),
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Function.identity(),
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(p1, p2) -> p1,
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LinkedHashMap::new))
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.values()
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.stream()
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.collect(Collectors.toList()));
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}
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if (StringUtils.isBlank(a.getFullname())) {
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if (StringUtils.isNotBlank(a.getName()) && StringUtils.isNotBlank(a.getSurname())) {
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a.setFullname(a.getSurname() + ", " + a.getName());
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}
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}
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if (StringUtils.isNotBlank(a.getFullname()) && isValidAuthorName(a)) {
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authors.add(a);
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}
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}
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boolean nullRank = authors
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.stream()
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.anyMatch(a -> Objects.isNull(a.getRank()));
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if (nullRank) {
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int i = 1;
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for (Author author : authors) {
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author.setRank(i++);
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}
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}
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r.setAuthor(authors);
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}
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if (value instanceof Publication) {
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} else if (value instanceof Dataset) {
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@ -131,6 +131,11 @@ public class OafMapperUtilsTest {
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}
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@Test
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public void testDate() {
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System.out.println(GraphCleaningFunctions.cleanDate("23-FEB-1998"));
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}
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@Test
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public void testMergePubs() throws IOException {
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Publication p1 = read("publication_1.json", Publication.class);
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@ -76,7 +76,9 @@ public abstract class AbstractMdRecordToOafMapper {
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protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
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protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/";
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protected static final Qualifier ORCID_PID_TYPE = qualifier(
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"ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
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ModelConstants.ORCID_PENDING,
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ModelConstants.ORCID_CLASSNAME,
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DNET_PID_TYPES, DNET_PID_TYPES);
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protected static final Qualifier MAG_PID_TYPE = qualifier(
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"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
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@ -102,11 +102,6 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication
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.mapToPair(xml -> new Tuple2<>(new Text(UUID.randomUUID() + ":" + type), new Text(xml)))
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// .coalesce(1)
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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/*
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* .foreach(xml -> { try { writer.append(new Text(UUID.randomUUID() + ":" + type), new Text(xml)); } catch
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* (final Exception e) { throw new RuntimeException(e); } });
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*/
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}
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private static String enrichRecord(final Row r) {
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@ -1,157 +0,0 @@
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<workflow-app name="Test Import of Hdfs Stores" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>graphOutputPath</name>
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<description>the target path to store raw graph</description>
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</property>
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<property>
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<name>contentPath</name>
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<description>path location to store (or reuse) content from the aggregator</description>
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</property>
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<property>
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<name>mdstoreManagerUrl</name>
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<description>the address of the Mdstore Manager</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>the address of the lookUp service</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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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="ImportODF_hdfs"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportODF_hdfs">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ImportODF_hdfs</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.MigrateHdfsMdstoresApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--hdfsPath</arg><arg>${contentPath}/odf_records_hdfs</arg>
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<arg>--mdstoreManagerUrl</arg><arg>${mdstoreManagerUrl}</arg>
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<arg>--mdFormat</arg><arg>ODF</arg>
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<arg>--mdLayout</arg><arg>store</arg>
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<arg>--mdInterpretation</arg><arg>cleaned</arg>
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</spark>
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<ok to="GenerateEntities"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateEntities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>GenerateEntities</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePaths</arg><arg>${contentPath}/odf_records_hdfs</arg>
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<arg>--targetPath</arg><arg>${workingDir}/entities</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--shouldHashId</arg><arg>${shouldHashId}</arg>
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</spark>
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<ok to="GenerateGraph"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateGraph">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>GenerateGraph</name>
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<class>eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
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<arg>--graphRawPath</arg><arg>${workingDir}/graph_raw</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -195,8 +195,8 @@ public class MappersTest {
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.findFirst()
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.get();
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assertEquals("0000-0001-6651-1178", pid.getValue());
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assertEquals("ORCID", pid.getQualifier().getClassid());
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assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname());
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assertEquals(ModelConstants.ORCID_PENDING, pid.getQualifier().getClassid());
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assertEquals(ModelConstants.ORCID_CLASSNAME, pid.getQualifier().getClassname());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
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assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
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assertEquals("Votsi,Nefta", author.get().getFullname());
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