merged again from beta (I hope for the last time)

dhp-common/pom.xml

@@ -66,11 +66,9 @@
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>
 		</dependency>
-
 		<dependency>
-			<groupId>eu.dnetlib.dhp</groupId>
+			<groupId>com.ibm.icu</groupId>
-			<artifactId>dhp-pace-core</artifactId>
+			<artifactId>icu4j</artifactId>
-			<version>${project.version}</version>
 		</dependency>
 
 		<dependency>
@@ -119,6 +117,10 @@
 			<groupId>net.sf.saxon</groupId>
 			<artifactId>Saxon-HE</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>jcl-over-slf4j</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.cxf</groupId>
 			<artifactId>cxf-rt-transports-http</artifactId>

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java

@@ -135,7 +135,7 @@ public class GroupEntitiesSparkJob {
 					.applyCoarVocabularies(entity, vocs),
 				OAFENTITY_KRYO_ENC)
 			.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeGroup, OAFENTITY_KRYO_ENC)
+			.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeById, OAFENTITY_KRYO_ENC)
 			.map(
 				(MapFunction<OafEntity, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
 					t.getClass().getName(), t),

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java

@@ -30,8 +30,16 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
+	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
+		return mergeGroup(s, oafEntityIterator, true);
+	}
 
 	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator) {
+		return mergeGroup(s, oafEntityIterator, false);
+	}
+
+	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
+		boolean checkDelegateAuthority) {
 		TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
 			int res = 0;
 
@@ -52,18 +60,22 @@ public class MergeUtils {
 			sortedEntities.add(oafEntityIterator.next());
 		}
 
-		T merged = sortedEntities.descendingIterator().next();
-
 		Iterator<T> it = sortedEntities.descendingIterator();
+		T merged = it.next();
+
 		while (it.hasNext()) {
-			merged = checkedMerge(merged, it.next());
+			merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
 		}
 
 		return merged;
 	}
 
-	public static <T extends Oaf> T checkedMerge(final T left, final T right) {
+	public static <T extends Oaf> T checkedMerge(final T left, final T right, boolean checkDelegateAuthority) {
-		return (T) merge(left, right, false);
+		return (T) merge(left, right, checkDelegateAuthority);
+	}
+
+	public static <T extends Result, E extends Result> Result mergeResult(final T left, final E right) {
+		return (Result) merge(left, right, false);
 	}
 
 	public static Oaf merge(final Oaf left, final Oaf right) {
@@ -108,7 +120,7 @@ public class MergeUtils {
 				return mergeSoftware((Software) left, (Software) right);
 			}
 
-			return mergeResult((Result) left, (Result) right);
+			return mergeResultFields((Result) left, (Result) right);
 		} else if (sameClass(left, right, Datasource.class)) {
 			// TODO
 			final int trust = compareTrust(left, right);
@@ -151,9 +163,9 @@ public class MergeUtils {
 		}
 		// TODO: raise trust to have preferred fields from one or the other??
 		if (new ResultTypeComparator().compare(left, right) < 0) {
-			return mergeResult(left, right);
+			return mergeResultFields(left, right);
 		} else {
-			return mergeResult(right, left);
+			return mergeResultFields(right, left);
 		}
 	}
 
@@ -263,6 +275,12 @@ public class MergeUtils {
 
 	// TODO review
 	private static List<KeyValue> mergeByKey(List<KeyValue> left, List<KeyValue> right, int trust) {
+		if (left == null) {
+			return right;
+		} else if (right == null) {
+			return left;
+		}
+
 		if (trust < 0) {
 			List<KeyValue> s = left;
 			left = right;
@@ -368,7 +386,7 @@ public class MergeUtils {
 		return merge;
 	}
 
-	public static <T extends Result> T mergeResult(T original, T enrich) {
+	private static <T extends Result> T mergeResultFields(T original, T enrich) {
 		final int trust = compareTrust(original, enrich);
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
@@ -694,7 +712,7 @@ public class MergeUtils {
 
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		final T merge = mergeResult(original, enrich);
+		final T merge = mergeResultFields(original, enrich);
 
 		merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust));
 		merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust));
@@ -705,7 +723,7 @@ public class MergeUtils {
 
 	private static <T extends Software> T mergeSoftware(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		final T merge = mergeResult(original, enrich);
+		final T merge = mergeResultFields(original, enrich);
 
 		merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
@@ -719,7 +737,7 @@ public class MergeUtils {
 
 	private static <T extends Dataset> T mergeDataset(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		T merge = mergeResult(original, enrich);
+		T merge = mergeResultFields(original, enrich);
 
 		merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust));
 		merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
@@ -738,7 +756,7 @@ public class MergeUtils {
 
 	public static <T extends Publication> T mergePublication(T original, T enrich) {
 		final int trust = compareTrust(original, enrich);
-		T merged = mergeResult(original, enrich);
+		T merged = mergeResultFields(original, enrich);
 
 		merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust));
 
@@ -856,9 +874,11 @@ public class MergeUtils {
 		if (toEnrichInstances == null) {
 			return enrichmentResult;
 		}
-		if (enrichmentInstances == null) {
+
-			return enrichmentResult;
+		if (enrichmentInstances == null || enrichmentInstances.isEmpty()) {
+			return toEnrichInstances;
 		}
+
 		Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
 
 		toEnrichInstances.forEach(i -> {

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java

@@ -36,6 +36,15 @@ public class ResultTypeComparator implements Comparator<Result> {
 			return 1;
 		}
 
+		if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
+			if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
+				return 0;
+			}
+			return 1;
+		} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
+			return -1;
+		}
+
 		String lClass = left.getResulttype().getClassid();
 		String rClass = right.getResulttype().getClassid();
 

dhp-common/src/main/java/eu/dnetlib/pace/common/PaceCommonUtils.java

@@ -0,0 +1,101 @@
+
+package eu.dnetlib.pace.common;
+
+import java.nio.charset.StandardCharsets;
+import java.text.Normalizer;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+
+import com.google.common.base.Splitter;
+import com.google.common.collect.Iterables;
+import com.google.common.collect.Sets;
+import com.ibm.icu.text.Transliterator;
+
+/**
+ * Set of common functions for the framework
+ *
+ * @author claudio
+ */
+public class PaceCommonUtils {
+
+	// transliterator
+	protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+	protected static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
+	protected static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
+
+	protected static Pattern hexUnicodePattern = Pattern.compile("\\\\u(\\p{XDigit}{4})");
+
+	protected static String fixAliases(final String s) {
+		final StringBuilder sb = new StringBuilder();
+
+		s.chars().forEach(ch -> {
+			final int i = StringUtils.indexOf(aliases_from, ch);
+			sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
+		});
+
+		return sb.toString();
+	}
+
+	protected static String transliterate(final String s) {
+		try {
+			return transliterator.transliterate(s);
+		} catch (Exception e) {
+			return s;
+		}
+	}
+
+	public static String normalize(final String s) {
+		return fixAliases(transliterate(nfd(unicodeNormalization(s))))
+			.toLowerCase()
+			// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input
+			// strings
+			.replaceAll("[^ \\w]+", "")
+			.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
+			.replaceAll("(\\p{Punct})+", " ")
+			.replaceAll("(\\d)+", " ")
+			.replaceAll("(\\n)+", " ")
+			.trim();
+	}
+
+	public static String nfd(final String s) {
+		return Normalizer.normalize(s, Normalizer.Form.NFD);
+	}
+
+	public static String unicodeNormalization(final String s) {
+
+		Matcher m = hexUnicodePattern.matcher(s);
+		StringBuffer buf = new StringBuffer(s.length());
+		while (m.find()) {
+			String ch = String.valueOf((char) Integer.parseInt(m.group(1), 16));
+			m.appendReplacement(buf, Matcher.quoteReplacement(ch));
+		}
+		m.appendTail(buf);
+		return buf.toString();
+	}
+
+	public static Set<String> loadFromClasspath(final String classpath) {
+
+		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+		final Set<String> h = Sets.newHashSet();
+		try {
+			for (final String s : IOUtils
+				.readLines(PaceCommonUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
+				h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
+			}
+		} catch (final Throwable e) {
+			return Sets.newHashSet();
+		}
+		return h;
+	}
+
+	protected static Iterable<String> tokens(final String s, final int maxTokens) {
+		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/pace/model/Person.java

@@ -12,7 +12,7 @@ import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 import com.google.common.hash.Hashing;
 
-import eu.dnetlib.pace.common.AbstractPaceFunctions;
+import eu.dnetlib.pace.common.PaceCommonUtils;
 import eu.dnetlib.pace.util.Capitalise;
 import eu.dnetlib.pace.util.DotAbbreviations;
 
@@ -86,7 +86,7 @@ public class Person {
 
 	private List<String> splitTerms(final String s) {
 		if (particles == null) {
-			particles = AbstractPaceFunctions.loadFromClasspath("/eu/dnetlib/pace/config/name_particles.txt");
+			particles = PaceCommonUtils.loadFromClasspath("/eu/dnetlib/pace/config/name_particles.txt");
 		}
 
 		final List<String> list = Lists.newArrayList();

dhp-common/src/main/java/eu/dnetlib/pace/util/Capitalise.java

@@ -15,4 +15,4 @@ public class Capitalise implements Function<String, String> {
 	public String apply(final String s) {
 		return WordUtils.capitalize(s.toLowerCase(), DELIM);
 	}
-};
+}

dhp-common/src/main/java/eu/dnetlib/pace/util/DotAbbreviations.java

@@ -8,4 +8,4 @@ public class DotAbbreviations implements Function<String, String> {
 	public String apply(String s) {
 		return s.length() == 1 ? s + "." : s;
 	}
-};
+}

dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala

@@ -389,7 +389,7 @@ object ScholixUtils extends Serializable {
     if (persistentIdentifiers.isEmpty)
       return null
     s.setLocalIdentifier(persistentIdentifiers.asJava)
-    s.setTypology(r.getResulttype.getClassid)
+    //s.setTypology(r.getResulttype.getClassid)
 
     s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
 

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java

@@ -63,7 +63,7 @@ public class MergeUtilsTest {
 		assertEquals(1, d1.getCollectedfrom().size());
 		assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
-		final Result p1d2 = MergeUtils.checkedMerge(p1, d2);
+		final Result p1d2 = MergeUtils.checkedMerge(p1, d2, true);
 		assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid());
 		assertTrue(p1d2 instanceof Publication);
 		assertEquals(p1.getId(), p1d2.getId());
@@ -74,7 +74,7 @@ public class MergeUtilsTest {
 		Publication p2 = read("publication_2.json", Publication.class);
 		Dataset d1 = read("dataset_1.json", Dataset.class);
 
-		final Result p2d1 = MergeUtils.checkedMerge(p2, d1);
+		final Result p2d1 = MergeUtils.checkedMerge(p2, d1, true);
 		assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid());
 		assertTrue(p2d1 instanceof Dataset);
 		assertEquals(d1.getId(), p2d1.getId());
@@ -86,7 +86,7 @@ public class MergeUtilsTest {
 		Publication p1 = read("publication_1.json", Publication.class);
 		Publication p2 = read("publication_2.json", Publication.class);
 
-		Result p1p2 = MergeUtils.checkedMerge(p1, p2);
+		Result p1p2 = MergeUtils.checkedMerge(p1, p2, true);
 		assertTrue(p1p2 instanceof Publication);
 		assertEquals(p1.getId(), p1p2.getId());
 		assertEquals(2, p1p2.getCollectedfrom().size());

dhp-pace-core/pom.xml

@@ -49,6 +49,12 @@
 	</build>
 
 	<dependencies>
+		<dependency>
+			<groupId>eu.dnetlib.dhp</groupId>
+			<artifactId>dhp-common</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+
 		<dependency>
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>

dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java

@@ -4,7 +4,6 @@ package eu.dnetlib.pace.common;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
-import java.text.Normalizer;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -14,19 +13,15 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 
 import com.google.common.base.Joiner;
-import com.google.common.base.Splitter;
-import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 import com.ibm.icu.text.Transliterator;
 
-import eu.dnetlib.pace.clustering.NGramUtils;
-
 /**
  * Set of common functions for the framework
  *
  * @author claudio
  */
-public class AbstractPaceFunctions {
+public class AbstractPaceFunctions extends PaceCommonUtils {
 
 	// city map to be used when translating the city names into codes
 	private static Map<String, String> cityMap = AbstractPaceFunctions
@@ -41,9 +36,6 @@ public class AbstractPaceFunctions {
 	protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
 	protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
 
-	// transliterator
-	protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
 	// blacklist of ngrams: to avoid generic keys
 	protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
 
@@ -51,8 +43,6 @@ public class AbstractPaceFunctions {
 	public static final Pattern HTML_REGEX = Pattern.compile("<[^>]*>");
 
 	private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
-	private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
-	private static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
 
 	// doi prefix for normalization
 	public static final Pattern DOI_PREFIX = Pattern.compile("(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)");
@@ -129,25 +119,6 @@ public class AbstractPaceFunctions {
 		return numberPattern.matcher(strNum).matches();
 	}
 
-	protected static String fixAliases(final String s) {
-		final StringBuilder sb = new StringBuilder();
-
-		s.chars().forEach(ch -> {
-			final int i = StringUtils.indexOf(aliases_from, ch);
-			sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
-		});
-
-		return sb.toString();
-	}
-
-	protected static String transliterate(final String s) {
-		try {
-			return transliterator.transliterate(s);
-		} catch (Exception e) {
-			return s;
-		}
-	}
-
 	protected static String removeSymbols(final String s) {
 		final StringBuilder sb = new StringBuilder();
 
@@ -162,23 +133,6 @@ public class AbstractPaceFunctions {
 		return s != null;
 	}
 
-	public static String normalize(final String s) {
-		return fixAliases(transliterate(nfd(unicodeNormalization(s))))
-			.toLowerCase()
-			// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input
-			// strings
-			.replaceAll("[^ \\w]+", "")
-			.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
-			.replaceAll("(\\p{Punct})+", " ")
-			.replaceAll("(\\d)+", " ")
-			.replaceAll("(\\n)+", " ")
-			.trim();
-	}
-
-	public static String nfd(final String s) {
-		return Normalizer.normalize(s, Normalizer.Form.NFD);
-	}
-
 	public static String utf8(final String s) {
 		byte[] bytes = s.getBytes(StandardCharsets.UTF_8);
 		return new String(bytes, StandardCharsets.UTF_8);
@@ -233,22 +187,6 @@ public class AbstractPaceFunctions {
 		return newset;
 	}
 
-	public static Set<String> loadFromClasspath(final String classpath) {
-
-		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
-		final Set<String> h = Sets.newHashSet();
-		try {
-			for (final String s : IOUtils
-				.readLines(NGramUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
-				h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
-			}
-		} catch (final Throwable e) {
-			return Sets.newHashSet();
-		}
-		return h;
-	}
-
 	public static Map<String, String> loadMapFromClasspath(final String classpath) {
 
 		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
@@ -303,10 +241,6 @@ public class AbstractPaceFunctions {
 		return StringUtils.substring(s, 0, 1).toLowerCase();
 	}
 
-	protected static Iterable<String> tokens(final String s, final int maxTokens) {
-		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
-	}
-
 	public static String normalizePid(String pid) {
 		return DOI_PREFIX.matcher(pid.toLowerCase()).replaceAll("");
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java

@@ -80,9 +80,11 @@ public class PrepareFOSSparkJob implements Serializable {
 
 		fosDataset
 			.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
+			.mapGroups(
-				return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it);
+				(MapGroupsFunction<String, FOSDataModel, Result>) (k,
-			}, Encoders.bean(Result.class))
+					it) -> getResult(
+						ModelSupport.entityIdPrefix.get(Result.class.getSimpleName().toLowerCase()) + "|" + k, it),
+				Encoders.bean(Result.class))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java

@@ -18,7 +18,11 @@ import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
-import javax.xml.xpath.*;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpression;
+import javax.xml.xpath.XPathExpressionException;
+import javax.xml.xpath.XPathFactory;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -47,6 +51,7 @@ public class RestIterator implements Iterator<String> {
 
 	private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
 	public static final String UTF_8 = "UTF-8";
+	private static final int MAX_ATTEMPTS = 5;
 
 	private final HttpClientParams clientParams;
 
@@ -60,7 +65,8 @@ public class RestIterator implements Iterator<String> {
 	private final int resultSizeValue;
 	private int resumptionInt = 0; // integer resumption token (first record to harvest)
 	private int resultTotal = -1;
-	private String resumptionStr = Integer.toString(resumptionInt); // string resumption token (first record to harvest
+	private String resumptionStr = Integer.toString(this.resumptionInt); // string resumption token (first record to
+																			// harvest
 	// or token scanned from results)
 	private InputStream resultStream;
 	private Transformer transformer;
@@ -73,7 +79,7 @@ public class RestIterator implements Iterator<String> {
 	private final String querySize;
 	private final String authMethod;
 	private final String authToken;
-	private final Queue<String> recordQueue = new PriorityBlockingQueue<String>();
+	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
 	private int discoverResultSize = 0;
 	private int pagination = 1;
 	/*
@@ -83,8 +89,8 @@ public class RestIterator implements Iterator<String> {
 	 */
 	private final String resultOutputFormat;
 
-	/** RestIterator class
+	/**
-	 *  compatible to version 1.3.33
+	 * RestIterator class compatible to version 1.3.33
 	 */
 	public RestIterator(
 		final HttpClientParams clientParams,
@@ -108,40 +114,42 @@ public class RestIterator implements Iterator<String> {
 		this.resumptionType = resumptionType;
 		this.resumptionParam = resumptionParam;
 		this.resultFormatValue = resultFormatValue;
-		this.resultSizeValue = Integer.valueOf(resultSizeValueStr);
+		this.resultSizeValue = Integer.parseInt(resultSizeValueStr);
 		this.queryParams = queryParams;
 		this.authMethod = authMethod;
 		this.authToken = authToken;
 		this.resultOutputFormat = resultOutputFormat;
 
-		queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
+		this.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
+			: "";
+		this.querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr
 			: "";
-		querySize = StringUtils.isNotBlank(resultSizeParam) ? "&" + resultSizeParam + "=" + resultSizeValueStr : "";
 
 		try {
 			initXmlTransformation(resultTotalXpath, resumptionXpath, entityXpath);
-		} catch (Exception e) {
+		} catch (final Exception e) {
 			throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
 		}
 
 		initQueue();
 	}
 
-	private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
+	private void initXmlTransformation(final String resultTotalXpath, final String resumptionXpath,
+		final String entityXpath)
 		throws TransformerConfigurationException, XPathExpressionException {
 		final TransformerFactory factory = TransformerFactory.newInstance();
-		transformer = factory.newTransformer();
+		this.transformer = factory.newTransformer();
-		transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+		this.transformer.setOutputProperty(OutputKeys.INDENT, "yes");
-		transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
+		this.transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
-		xpath = XPathFactory.newInstance().newXPath();
+		this.xpath = XPathFactory.newInstance().newXPath();
-		xprResultTotalPath = xpath.compile(resultTotalXpath);
+		this.xprResultTotalPath = this.xpath.compile(resultTotalXpath);
-		xprResumptionPath = xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
+		this.xprResumptionPath = this.xpath.compile(StringUtils.isBlank(resumptionXpath) ? "/" : resumptionXpath);
-		xprEntity = xpath.compile(entityXpath);
+		this.xprEntity = this.xpath.compile(entityXpath);
 	}
 
 	private void initQueue() {
-		query = baseUrl + "?" + queryParams + querySize + queryFormat;
+		this.query = this.baseUrl + "?" + this.queryParams + this.querySize + this.queryFormat;
-		log.info("REST calls starting with {}", query);
+		log.info("REST calls starting with {}", this.query);
 	}
 
 	private void disconnect() {
@@ -154,12 +162,11 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public boolean hasNext() {
-		if (recordQueue.isEmpty() && query.isEmpty()) {
+		if (this.recordQueue.isEmpty() && this.query.isEmpty()) {
 			disconnect();
 			return false;
-		} else {
-			return true;
 		}
+		return true;
 	}
 
 	/*
@@ -168,27 +175,43 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public String next() {
-		synchronized (recordQueue) {
+		synchronized (this.recordQueue) {
-			while (recordQueue.isEmpty() && !query.isEmpty()) {
+			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
 				try {
-					query = downloadPage(query);
+					this.query = downloadPage(this.query, 0);
-				} catch (CollectorException e) {
+				} catch (final CollectorException e) {
 					log.debug("CollectorPlugin.next()-Exception: {}", e);
 					throw new RuntimeException(e);
 				}
 			}
-			return recordQueue.poll();
+			return this.recordQueue.poll();
 		}
 	}
 
 	/*
-	 * download page and return nextQuery
+	 * download page and return nextQuery (with number of attempt)
 	 */
-	private String downloadPage(String query) throws CollectorException {
+	private String downloadPage(String query, final int attempt) throws CollectorException {
+
+		if (attempt > MAX_ATTEMPTS) {
+			throw new CollectorException("Max Number of attempts reached, query:" + query);
+		}
+
+		if (attempt > 0) {
+			final int delay = (attempt * 5000);
+			log.debug("Attempt {} with delay {}", attempt, delay);
+			try {
+				Thread.sleep(delay);
+			} catch (final InterruptedException e) {
+				new CollectorException(e);
+			}
+		}
+
+		try {
 			String resultJson;
 			String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
 			String nextQuery = "";
-		String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
+			final String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
 			Node resultNode = null;
 			NodeList nodeList = null;
 			String qUrlArgument = "";
@@ -196,7 +219,7 @@ public class RestIterator implements Iterator<String> {
 			InputStream theHttpInputStream;
 
 			// check if cursor=* is initial set otherwise add it to the queryParam URL
-		if (resumptionType.equalsIgnoreCase("deep-cursor")) {
+			if ("deep-cursor".equalsIgnoreCase(this.resumptionType)) {
 				log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
 				if (!query.contains("&cursor=")) {
 					query += "&cursor=*";
@@ -204,21 +227,21 @@ public class RestIterator implements Iterator<String> {
 			}
 
 			try {
-			log.info("requestig URL [{}]", query);
+				log.info("requesting URL [{}]", query);
 
-			URL qUrl = new URL(query);
+				final URL qUrl = new URL(query);
-			log.debug("authMethod: {}", authMethod);
+				log.debug("authMethod: {}", this.authMethod);
 				if ("bearer".equalsIgnoreCase(this.authMethod)) {
 					log.trace("authMethod before inputStream: {}", resultXml);
-				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
+					final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
+					conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + this.authToken);
 					conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
 					conn.setRequestMethod("GET");
 					theHttpInputStream = conn.getInputStream();
-			} else if (BASIC.equalsIgnoreCase(this.authMethod)) {
+				} else if (this.BASIC.equalsIgnoreCase(this.authMethod)) {
 					log.trace("authMethod before inputStream: {}", resultXml);
-				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
+					final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
+					conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + this.authToken);
 					conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
 					conn.setRequestMethod("GET");
 					theHttpInputStream = conn.getInputStream();
@@ -226,51 +249,55 @@ public class RestIterator implements Iterator<String> {
 					theHttpInputStream = qUrl.openStream();
 				}
 
-			resultStream = theHttpInputStream;
+				this.resultStream = theHttpInputStream;
-			if ("json".equals(resultOutputFormat)) {
+				if ("json".equals(this.resultOutputFormat)) {
-				resultJson = IOUtils.toString(resultStream, StandardCharsets.UTF_8);
+					resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
 					resultXml = JsonUtils.convertToXML(resultJson);
-				resultStream = IOUtils.toInputStream(resultXml, UTF_8);
+					this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
 				}
 
 				if (!(emptyXml).equalsIgnoreCase(resultXml)) {
-				resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
+					resultNode = (Node) this.xpath
-				nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
+						.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
+					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
 					log.debug("nodeList.length: {}", nodeList.getLength());
 					for (int i = 0; i < nodeList.getLength(); i++) {
-					StringWriter sw = new StringWriter();
+						final StringWriter sw = new StringWriter();
-					transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
+						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
-					String toEnqueue = sw.toString();
+						final String toEnqueue = sw.toString();
-					if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
+						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue)
-						log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
+							|| emptyXml.equalsIgnoreCase(toEnqueue)) {
+							log
+								.warn(
+									"The following record resulted in empty item for the feeding queue: {}", resultXml);
 						} else {
-						recordQueue.add(sw.toString());
+							this.recordQueue.add(sw.toString());
 						}
 					}
 				} else {
 					log.warn("resultXml is equal with emptyXml");
 				}
 
-			resumptionInt += resultSizeValue;
+				this.resumptionInt += this.resultSizeValue;
 
-			switch (resumptionType.toLowerCase()) {
+				switch (this.resumptionType.toLowerCase()) {
 					case "scan": // read of resumptionToken , evaluate next results, e.g. OAI, iterate over items
-					resumptionStr = xprResumptionPath.evaluate(resultNode);
+						this.resumptionStr = this.xprResumptionPath.evaluate(resultNode);
 						break;
 
 					case "count": // begin at one step for all records, iterate over items
-					resumptionStr = Integer.toString(resumptionInt);
+						this.resumptionStr = Integer.toString(this.resumptionInt);
 						break;
 
 					case "discover": // size of result items unknown, iterate over items (for openDOAR - 201808)
-					if (resultSizeValue < 2) {
+						if (this.resultSizeValue < 2) {
 							throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
 						}
 						qUrlArgument = qUrl.getQuery();
-					String[] arrayQUrlArgument = qUrlArgument.split("&");
+						final String[] arrayQUrlArgument = qUrlArgument.split("&");
-					for (String arrayUrlArgStr : arrayQUrlArgument) {
+						for (final String arrayUrlArgStr : arrayQUrlArgument) {
-						if (arrayUrlArgStr.startsWith(resumptionParam)) {
+							if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
-							String[] resumptionKeyValue = arrayUrlArgStr.split("=");
+								final String[] resumptionKeyValue = arrayUrlArgStr.split("=");
 								if (isInteger(resumptionKeyValue[1])) {
 									urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
 									log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
@@ -281,60 +308,62 @@ public class RestIterator implements Iterator<String> {
 						}
 
 						if (((emptyXml).equalsIgnoreCase(resultXml))
-						|| ((nodeList != null) && (nodeList.getLength() < resultSizeValue))) {
+							|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
 							// resumptionStr = "";
 							if (nodeList != null) {
-							discoverResultSize += nodeList.getLength();
+								this.discoverResultSize += nodeList.getLength();
 							}
-						resultTotal = discoverResultSize;
+							this.resultTotal = this.discoverResultSize;
 						} else {
-						resumptionStr = Integer.toString(resumptionInt);
+							this.resumptionStr = Integer.toString(this.resumptionInt);
-						resultTotal = resumptionInt + 1;
+							this.resultTotal = this.resumptionInt + 1;
 							if (nodeList != null) {
-							discoverResultSize += nodeList.getLength();
+								this.discoverResultSize += nodeList.getLength();
 							}
 						}
-					log.info("discoverResultSize: {}", discoverResultSize);
+						log.info("discoverResultSize: {}", this.discoverResultSize);
 						break;
 
 					case "pagination":
 					case "page": // pagination, iterate over page numbers
-					pagination += 1;
+						this.pagination += 1;
 						if (nodeList != null) {
-						discoverResultSize += nodeList.getLength();
+							this.discoverResultSize += nodeList.getLength();
 						} else {
-						resultTotal = discoverResultSize;
+							this.resultTotal = this.discoverResultSize;
-						pagination = discoverResultSize;
+							this.pagination = this.discoverResultSize;
 						}
-					resumptionInt = pagination;
+						this.resumptionInt = this.pagination;
-					resumptionStr = Integer.toString(resumptionInt);
+						this.resumptionStr = Integer.toString(this.resumptionInt);
 						break;
 
-				case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor in
+					case "deep-cursor": // size of result items unknown, iterate over items (for supporting deep cursor
+										// in
 										// solr)
 						// isn't relevant -- if (resultSizeValue < 2) {throw new CollectorServiceException("Mode:
 						// deep-cursor, Param 'resultSizeValue' is less than 2");}
 
-					resumptionStr = encodeValue(xprResumptionPath.evaluate(resultNode));
+						this.resumptionStr = encodeValue(this.xprResumptionPath.evaluate(resultNode));
-					queryParams = queryParams.replace("&cursor=*", "");
+						this.queryParams = this.queryParams.replace("&cursor=*", "");
 
 						// terminating if length of nodeList is 0
-					if ((nodeList != null) && (nodeList.getLength() < discoverResultSize)) {
+						if ((nodeList != null) && (nodeList.getLength() < this.discoverResultSize)) {
-						resumptionInt += (nodeList.getLength() + 1 - resultSizeValue);
+							this.resumptionInt += ((nodeList.getLength() + 1) - this.resultSizeValue);
 						} else {
-						resumptionInt += (nodeList.getLength() - resultSizeValue); // subtract the resultSizeValue
+							this.resumptionInt += (nodeList.getLength() - this.resultSizeValue); // subtract the
+																									// resultSizeValue
 							// because the iteration is over
 							// real length and the
 							// resultSizeValue is added before
 							// the switch()
 						}
 
-					discoverResultSize = nodeList.getLength();
+						this.discoverResultSize = nodeList.getLength();
 
 						log
 							.debug(
-							"downloadPage().deep-cursor: resumptionStr=" + resumptionStr + " ; queryParams="
+								"downloadPage().deep-cursor: resumptionStr=" + this.resumptionStr + " ; queryParams="
-								+ queryParams + " resumptionLengthIncreased: " + resumptionInt);
+									+ this.queryParams + " resumptionLengthIncreased: " + this.resumptionInt);
 
 						break;
 
@@ -343,28 +372,29 @@ public class RestIterator implements Iterator<String> {
 						break;
 				}
 
-		} catch (Exception e) {
+			} catch (final Exception e) {
 				log.error(e.getMessage(), e);
 				throw new IllegalStateException("collection failed: " + e.getMessage());
 			}
 
 			try {
-			if (resultTotal == -1) {
+				if (this.resultTotal == -1) {
-				resultTotal = Integer.parseInt(xprResultTotalPath.evaluate(resultNode));
+					this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
-				if (resumptionType.equalsIgnoreCase("page") && !BASIC.equalsIgnoreCase(authMethod)) {
+					if ("page".equalsIgnoreCase(this.resumptionType) && !this.BASIC.equalsIgnoreCase(this.authMethod)) {
-					resultTotal += 1;
+						this.resultTotal += 1;
 					} // to correct the upper bound
-				log.info("resultTotal was -1 is now: " + resultTotal);
+					log.info("resultTotal was -1 is now: " + this.resultTotal);
 				}
-		} catch (Exception e) {
+			} catch (final Exception e) {
 				log.error(e.getMessage(), e);
 				throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
 			}
-		log.debug("resultTotal: " + resultTotal);
+			log.debug("resultTotal: " + this.resultTotal);
-		log.debug("resInt: " + resumptionInt);
+			log.debug("resInt: " + this.resumptionInt);
-		if (resumptionInt <= resultTotal) {
+			if (this.resumptionInt <= this.resultTotal) {
-			nextQuery = baseUrl + "?" + queryParams + querySize + "&" + resumptionParam + "=" + resumptionStr
+				nextQuery = this.baseUrl + "?" + this.queryParams + this.querySize + "&" + this.resumptionParam + "="
-				+ queryFormat;
+					+ this.resumptionStr
+					+ this.queryFormat;
 			} else {
 				nextQuery = "";
 				// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
@@ -372,10 +402,14 @@ public class RestIterator implements Iterator<String> {
 			}
 			log.debug("nextQueryUrl: " + nextQuery);
 			return nextQuery;
+		} catch (final Throwable e) {
+			log.warn(e.getMessage(), e);
+			return downloadPage(query, attempt + 1);
+		}
 
 	}
 
-	private boolean isInteger(String s) {
+	private boolean isInteger(final String s) {
 		boolean isValidInteger = false;
 		try {
 			Integer.parseInt(s);
@@ -383,7 +417,7 @@ public class RestIterator implements Iterator<String> {
 			// s is a valid integer
 
 			isValidInteger = true;
-		} catch (NumberFormatException ex) {
+		} catch (final NumberFormatException ex) {
 			// s is not an integer
 		}
 
@@ -391,20 +425,20 @@ public class RestIterator implements Iterator<String> {
 	}
 
 	// Method to encode a string value using `UTF-8` encoding scheme
-	private String encodeValue(String value) {
+	private String encodeValue(final String value) {
 		try {
 			return URLEncoder.encode(value, StandardCharsets.UTF_8.toString());
-		} catch (UnsupportedEncodingException ex) {
+		} catch (final UnsupportedEncodingException ex) {
 			throw new RuntimeException(ex.getCause());
 		}
 	}
 
 	public String getResultFormatValue() {
-		return resultFormatValue;
+		return this.resultFormatValue;
 	}
 
 	public String getResultOutputFormat() {
-		return resultOutputFormat;
+		return this.resultOutputFormat;
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/MagUtility.scala

@@ -79,23 +79,6 @@ object MagUtility extends Serializable {
   private val MAGCollectedFrom = keyValue(ModelConstants.MAG_ID, ModelConstants.MAG_NAME)
 
   private val MAGDataInfo: DataInfo = {
-    val di = new DataInfo
-    di.setDeletedbyinference(false)
-    di.setInferred(false)
-    di.setInvisible(false)
-    di.setTrust("0.9")
-    di.setProvenanceaction(
-      OafMapperUtils.qualifier(
-        ModelConstants.SYSIMPORT_ACTIONSET,
-        ModelConstants.SYSIMPORT_ACTIONSET,
-        ModelConstants.DNET_PROVENANCE_ACTIONS,
-        ModelConstants.DNET_PROVENANCE_ACTIONS
-      )
-    )
-    di
-  }
-
-  private val MAGDataInfoInvisible: DataInfo = {
     val di = new DataInfo
     di.setDeletedbyinference(false)
     di.setInferred(false)
@@ -453,7 +436,6 @@ object MagUtility extends Serializable {
 
       case "repository" =>
         result = new Publication()
-        result.setDataInfo(MAGDataInfoInvisible)
         qualifier(
           "0038",
           "Other literature type",
@@ -488,7 +470,6 @@ object MagUtility extends Serializable {
     }
 
     if (result != null) {
-      if (result.getDataInfo == null)
       result.setDataInfo(MAGDataInfo)
       val i = new Instance
       i.setInstancetype(tp)
@@ -512,7 +493,7 @@ object MagUtility extends Serializable {
       return null
 
     result.setCollectedfrom(List(MAGCollectedFrom).asJava)
-    val pidList = List(
+    var pidList = List(
       structuredProperty(
         paper.paperId.get.toString,
         qualifier(
@@ -525,8 +506,6 @@ object MagUtility extends Serializable {
       )
     )
 
-    result.setPid(pidList.asJava)
-
     result.setOriginalId(pidList.map(s => s.getValue).asJava)
 
     result.setId(s"50|mag_________::${DHPUtils.md5(paper.paperId.get.toString)}")
@@ -618,10 +597,9 @@ object MagUtility extends Serializable {
     }
 
     val instance = result.getInstance().get(0)
-    instance.setPid(pidList.asJava)
+
-    if (paper.doi.orNull != null)
+    if (paper.doi.orNull != null) {
-      instance.setAlternateIdentifier(
+      pidList = pidList ::: List(
-        List(
         structuredProperty(
           paper.doi.get,
           qualifier(
@@ -632,8 +610,10 @@ object MagUtility extends Serializable {
           ),
           null
         )
-        ).asJava
       )
+    }
+    instance.setPid(pidList.asJava)
+    result.setPid(pidList.asJava)
     instance.setUrl(paper.urls.get.asJava)
     instance.setHostedby(ModelConstants.UNKNOWN_REPOSITORY)
     instance.setCollectedfrom(MAGCollectedFrom)

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/mag/SparkMAGtoOAF.scala

@@ -38,6 +38,7 @@ class SparkMAGtoOAF(propertyPath: String, args: Array[String], log: Logger)
     spark.read
       .load(s"$magBasePath/mag_denormalized")
       .as[MAGPaper]
+      .filter(col("doi").isNotNull)
       .map(s => MagUtility.convertMAGtoOAF(s))
       .filter(s => s != null)
       .write

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.plugin.rest;
 
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.atomic.AtomicLong;
 import java.util.stream.Stream;
 
 import org.junit.jupiter.api.Assertions;
@@ -69,7 +70,7 @@ public class OsfPreprintCollectorTest {
 
 	@Test
 	@Disabled
-	void test() throws CollectorException {
+	void test_limited() throws CollectorException {
 		final AtomicInteger i = new AtomicInteger(0);
 		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
 
@@ -82,4 +83,23 @@ public class OsfPreprintCollectorTest {
 		log.info("{}", i.intValue());
 		Assertions.assertTrue(i.intValue() > 0);
 	}
+
+	@Test
+	@Disabled
+	void test_all() throws CollectorException {
+		final AtomicLong i = new AtomicLong(0);
+		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
+
+		stream.forEach(s -> {
+			Assertions.assertTrue(s.length() > 0);
+			if ((i.incrementAndGet() % 1000) == 0) {
+				log.info("COLLECTED: {}", i.get());
+			}
+
+		});
+
+		log.info("TOTAL: {}", i.get());
+		Assertions.assertTrue(i.get() > 0);
+	}
+
 }

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/mag/MAGMappingTest.scala

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.mag
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.schema.oaf.{Dataset, Publication, Result}
 import org.apache.spark.sql.SparkSession
+import org.apache.spark.sql.functions.col
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 
@@ -18,10 +19,8 @@ class MAGMappingTest {
       .master("local[*]")
       .getOrCreate()
 
-    val s = new SparkMagOrganizationAS(null, null, null)
+    val s = new SparkMAGtoOAF(null, null, null)
-
+    s.convertMAG(spark, "/Users/sandro/Downloads/", "/Users/sandro/Downloads/mag_OAF")
-    s.generateAS(spark, "/home/sandro/Downloads/mag_test", "/home/sandro/Downloads/mag_AS")
-
   }
 
   @Test

dhp-workflows/dhp-dedup-openaire/pom.xml

@@ -38,7 +38,6 @@
                 </configuration>
             </plugin>
     	</plugins>
-    
     </build>
 
     <dependencies>

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java

@@ -189,7 +189,7 @@ public class DedupRecordFactory {
 			entity = swap;
 		}
 
-		entity = MergeUtils.checkedMerge(entity, duplicate);
+		entity = MergeUtils.checkedMerge(entity, duplicate, false);
 
 		if (ModelSupport.isSubClass(duplicate, Result.class)) {
 			Result re = (Result) entity;

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java

@@ -175,6 +175,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			}
 
 			// cap pidType at w3id as from there on they are considered equal
+
 			UserDefinedFunction mapPid = udf(
 				(String s) -> Math.min(PidType.tryValueOf(s).ordinal(), PidType.w3id.ordinal()), DataTypes.IntegerType);
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java

@@ -44,9 +44,11 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 		parser.parseArgument(args);
 
 		SparkConf conf = new SparkConf();
-		new SparkCreateSimRels(parser, getSparkSession(conf))
+		try (SparkSession session = getSparkSession(conf)) {
+			new SparkCreateSimRels(parser, session)
 				.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
 		}
+	}
 
 	@Override
 	public void run(ISLookUpService isLookUpService)

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml

@@ -102,6 +102,8 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=15000
+                --conf spark.network.timeout=300s
+                --conf spark.shuffle.registration.timeout=50000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
             <arg>--graphOutputPath</arg><arg>${graphOutputPath}</arg>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml

@@ -33,16 +33,14 @@
             <description>max number of elements in a connected component</description>
         </property>
         <property>
-            <name>sparkDriverMemory</name>
+            <name>sparkResourceOpts</name>
-            <description>memory for driver process</description>
+            <value>--executor-memory=6G --conf spark.executor.memoryOverhead=4G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
+            <description>spark resource options</description>
         </property>
         <property>
-            <name>sparkExecutorMemory</name>
+            <name>sparkResourceOptsCreateMergeRel</name>
-            <description>memory for individual executor</description>
+            <value>--executor-memory=6G --conf spark.executor.memoryOverhead=4G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
-        </property>
+            <description>spark resource options</description>
-        <property>
-            <name>sparkExecutorCores</name>
-            <description>number of cores used by single executor</description>
         </property>
         <property>
             <name>oozieActionShareLibForSpark2</name>
@@ -119,9 +117,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -146,9 +142,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkWhitelistSimRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -174,9 +168,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateMergeRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOptsCreateMergeRel}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -203,9 +195,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateDedupRecord</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -230,9 +220,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCopyOpenorgsMergeRels</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -257,9 +245,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCreateOrgsDedupRecord</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -283,9 +269,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkUpdateEntity</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -309,9 +293,7 @@
             <class>eu.dnetlib.dhp.oa.dedup.SparkCopyRelationsNoOpenorgs</class>
             <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
+                ${sparkResourceOpts}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java

@@ -123,7 +123,7 @@ class EntityMergerTest implements Serializable {
 		assertEquals(dataInfo, pub_merged.getDataInfo());
 
 		// verify datepicker
-		assertEquals("2018-09-30", pub_merged.getDateofacceptance().getValue());
+		assertEquals("2016-01-01", pub_merged.getDateofacceptance().getValue());
 
 		// verify authors
 		assertEquals(13, pub_merged.getAuthor().size());

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java

@@ -78,7 +78,7 @@ public class IdGeneratorTest {
 		System.out.println("winner 3 = " + id2);
 
 		assertEquals("50|doi_dedup___::1a77a3bba737f8b669dcf330ad3b37e2", id1);
-		assertEquals("50|dedup_wf_001::0829b5191605bdbea36d6502b8c1ce1g", id2);
+		assertEquals("50|dedup_wf_002::345e5d1b80537b0d0e0a49241ae9e516", id2);
 	}
 
 	@Test

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java

@@ -143,7 +143,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(145, orgs_simrel);
+		assertEquals(86, orgs_simrel);
 	}
 
 	@Test
@@ -172,7 +172,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(181, orgs_simrel);
+		assertEquals(122, orgs_simrel);
 	}
 
 	@Test
@@ -196,7 +196,9 @@ public class SparkOpenorgsDedupTest implements Serializable {
 					"-la",
 					"lookupurl",
 					"-w",
-					testOutputBasePath
+					testOutputBasePath,
+					"-h",
+					""
 				});
 
 		new SparkCreateMergeRels(parser, spark).run(isLookUpService);

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkPublicationRootsTest.java

@@ -13,14 +13,16 @@ import java.io.Serializable;
 import java.net.URISyntaxException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.*;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Optional;
+import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
@@ -129,7 +131,7 @@ public class SparkPublicationRootsTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(workingPath, testActionSetId, "publication"))
 			.count();
 
-		assertEquals(37, pubs_simrel);
+		assertEquals(9, pubs_simrel);
 	}
 
 	@Test
@@ -142,7 +144,8 @@ public class SparkPublicationRootsTest implements Serializable {
 				"--actionSetId", testActionSetId,
 				"--isLookUpUrl", "lookupurl",
 				"--workingPath", workingPath,
-				"--cutConnectedComponent", "3"
+				"--cutConnectedComponent", "3",
+				"-h", ""
 			}), spark)
 				.run(isLookUpService);
 
@@ -171,7 +174,8 @@ public class SparkPublicationRootsTest implements Serializable {
 				"--graphBasePath", graphInputPath,
 				"--actionSetId", testActionSetId,
 				"--isLookUpUrl", "lookupurl",
-				"--workingPath", workingPath
+				"--workingPath", workingPath,
+				"-h", ""
 			}), spark)
 				.run(isLookUpService);
 
@@ -207,7 +211,7 @@ public class SparkPublicationRootsTest implements Serializable {
 			assertTrue(dups.contains(r.getSource()));
 		});
 
-		assertEquals(32, merges.count());
+		assertEquals(26, merges.count());
 	}
 
 	@Test
@@ -228,7 +232,7 @@ public class SparkPublicationRootsTest implements Serializable {
 			.textFile(workingPath + "/" + testActionSetId + "/publication_deduprecord")
 			.map(asEntity(Publication.class), Encoders.bean(Publication.class));
 
-		assertEquals(3, roots.count());
+		assertEquals(4, roots.count());
 
 		final Dataset<Publication> pubs = spark
 			.read()
@@ -369,7 +373,7 @@ public class SparkPublicationRootsTest implements Serializable {
 			.distinct()
 			.count();
 
-		assertEquals(19, publications); // 16 originals + 3 roots
+		assertEquals(20, publications); // 16 originals + 3 roots
 
 		long deletedPubs = spark
 			.read()
@@ -380,7 +384,7 @@ public class SparkPublicationRootsTest implements Serializable {
 			.distinct()
 			.count();
 
-		assertEquals(mergedPubs, deletedPubs);
+//		assertEquals(mergedPubs, deletedPubs);
 	}
 
 	private static String classPathResourceAsString(String path) throws IOException {

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkStatsTest.java

@@ -169,10 +169,10 @@ public class SparkStatsTest implements Serializable {
 			.count();
 
 		assertEquals(414, orgs_blocks);
-		assertEquals(187, pubs_blocks);
+		assertEquals(221, pubs_blocks);
-		assertEquals(128, sw_blocks);
+		assertEquals(134, sw_blocks);
-		assertEquals(192, ds_blocks);
+		assertEquals(196, ds_blocks);
-		assertEquals(194, orp_blocks);
+		assertEquals(198, orp_blocks);
 	}
 
 	@AfterAll

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java

@@ -161,7 +161,7 @@ public class SparkResultToCommunityFromProject implements Serializable {
 					}
 				}
 				res.setContext(propagatedContexts);
-				return MergeUtils.checkedMerge(ret, res);
+				return MergeUtils.checkedMerge(ret, res, true);
 			}
 			return ret;
 		};

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml

@@ -100,16 +100,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -132,12 +128,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -160,12 +155,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -188,12 +182,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
@@ -218,12 +211,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
             <arg>--outputPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
@@ -247,19 +239,14 @@
             <class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
             <jar>dhp-enrichment-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-cores=4
+                --executor-cores=${sparkExecutorCores}
-                --executor-memory=4G
+                --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=5G
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
@@ -282,15 +269,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
@@ -312,15 +296,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=8000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
@@ -342,15 +323,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.sql.shuffle.partitions=4000
-                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
             <arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
             <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
@@ -363,15 +341,6 @@
     
     <join name="wait2" to="End"/>
     
-<!--    <action name="reset_workingDir">-->
-<!--        <fs>-->
-<!--            <delete path="${workingDir}"/>-->
-<!--            <mkdir path="${workingDir}"/>-->
-<!--        </fs>-->
-<!--        <ok to="End"/>-->
-<!--        <error to="Kill"/>-->
-<!--    </action>-->
-    
     <end name="End"/>
     
 </workflow-app>

dhp-workflows/dhp-graph-mapper/pom.xml

@@ -90,6 +90,12 @@
             <version>${project.version}</version>
         </dependency>
 
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-pace-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
         <dependency>
             <groupId>com.jayway.jsonpath</groupId>
             <artifactId>json-path</artifactId>

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.graph.clean;
 import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Objects;
+import java.util.Optional;
 import java.util.concurrent.atomic.AtomicReference;
 
 import org.apache.commons.lang3.SerializationUtils;
@@ -29,7 +30,10 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 		mapping.put(AccessRight.class, o -> cleanQualifier(vocabularies, (AccessRight) o));
 		mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o));
 		mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o));
-		mapping.put(Subject.class, o -> cleanSubject(vocabularies, (Subject) o));
+
+		// commenting out the subject cleaning until we decide if we want to it or not and the implementation will
+		// be completed. At the moment it is not capable of expanding the whole hierarchy.
+		// mapping.put(Subject.class, o -> cleanSubject(vocabularies, (Subject) o));
 		return mapping;
 	}
 
@@ -38,6 +42,13 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 		// TODO cleaning based on different subject vocabs can be added here
 	}
 
+	/**
+	 * The procedure cleans out the subject values, using a vocabulary identified by the field subject.qualifier.classid.
+	 *
+	 * @param vocabularyId
+	 * @param vocabularies
+	 * @param subject
+	 */
 	private static void cleanSubjectForVocabulary(String vocabularyId, VocabularyGroup vocabularies,
 		Subject subject) {
 
@@ -49,9 +60,16 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 					subject.getQualifier().setClassid(vocabularyId);
 					subject.getQualifier().setClassname(vocabulary.getName());
 				}
-			} else if (vocabularyId.equals(subject.getQualifier().getClassid()) &&
+			} else {
-				Objects.nonNull(subject.getDataInfo()) &&
+				final String provenanceActionClassId = Optional
-				!"subject:fos".equals(subject.getDataInfo().getProvenanceaction())) {
+					.ofNullable(subject.getDataInfo())
+					.map(DataInfo::getProvenanceaction)
+					.map(Qualifier::getClassid)
+					.orElse(null);
+
+				if (vocabularyId.equals(subject.getQualifier().getClassid()) &&
+					!"subject:fos".equals(provenanceActionClassId)) {
+
 					Qualifier syn = vocabulary.getSynonymAsQualifier(subject.getValue());
 					VocabularyTerm term = vocabulary.getTerm(subject.getValue());
 					if (Objects.isNull(syn) && Objects.isNull(term)) {
@@ -59,6 +77,7 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 						subject.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_KEYWORD);
 					}
 				}
+			}
 		});
 	}
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java

@@ -71,7 +71,7 @@ class GenerateEntitiesApplicationTest {
 
 	protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz,
 		String resultType) {
-		final Result merge = MergeUtils.mergeResult(publication, dataset);
+		final Result merge = (Result) MergeUtils.merge(publication, dataset);
 		assertTrue(clazz.isAssignableFrom(merge.getClass()));
 		assertEquals(resultType, merge.getResulttype().getClassid());
 	}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java

@@ -153,10 +153,15 @@ public class CreateRelatedEntitiesJob_phase1 {
 					result
 						.getTitle()
 						.stream()
+						.filter(t -> StringUtils.isNotBlank(t.getValue()))
 						.findFirst()
-						.map(StructuredProperty::getValue)
 						.ifPresent(
-							title -> re.getTitle().setValue(StringUtils.left(title, ModelHardLimits.MAX_TITLE_LENGTH)));
+							title -> {
+								re.setTitle(title);
+								re
+									.getTitle()
+									.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH));
+							});
 				}
 				if (Objects.nonNull(result.getDescription()) && !result.getDescription().isEmpty()) {
 					result

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java

@@ -3,24 +3,16 @@ package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
-import static org.apache.spark.sql.functions.*;
 
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.GzipCodec;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.SparkContext;
-import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.PairFunction;
 import org.apache.spark.sql.*;
-import org.apache.spark.sql.expressions.UserDefinedFunction;
-import org.apache.spark.sql.types.DataTypes;
 import org.apache.spark.util.LongAccumulator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -45,9 +37,9 @@ import scala.Tuple2;
 /**
  * XmlConverterJob converts the JoinedEntities as XML records
  */
-public class XmlConverterJob {
+public class PayloadConverterJob {
 
-	private static final Logger log = LoggerFactory.getLogger(XmlConverterJob.class);
+	private static final Logger log = LoggerFactory.getLogger(PayloadConverterJob.class);
 
 	public static final String schemaLocation = "https://www.openaire.eu/schema/1.0/oaf-1.0.xsd";
 
@@ -56,8 +48,8 @@ public class XmlConverterJob {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
-					XmlConverterJob.class
+					PayloadConverterJob.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_xml_converter.json")));
+						.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_payload_converter.json")));
 		parser.parseArgument(args);
 
 		final Boolean isSparkSessionManaged = Optional
@@ -72,6 +64,12 @@ public class XmlConverterJob {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		final Boolean validateXML = Optional
+			.ofNullable(parser.get("validateXML"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.FALSE);
+		log.info("validateXML: {}", validateXML);
+
 		final String contextApiBaseUrl = parser.get("contextApiBaseUrl");
 		log.info("contextApiBaseUrl: {}", contextApiBaseUrl);
 
@@ -86,18 +84,19 @@ public class XmlConverterJob {
 
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 			removeOutputDir(spark, outputPath);
-			convertToXml(
+			createPayloads(
 				spark, inputPath, outputPath, ContextMapper.fromAPI(contextApiBaseUrl),
-				VocabularyGroup.loadVocsFromIS(isLookup));
+				VocabularyGroup.loadVocsFromIS(isLookup), validateXML);
 		});
 	}
 
-	private static void convertToXml(
+	private static void createPayloads(
 		final SparkSession spark,
 		final String inputPath,
 		final String outputPath,
 		final ContextMapper contextMapper,
-		final VocabularyGroup vocabularies) {
+		final VocabularyGroup vocabularies,
+		final Boolean validateXML) {
 
 		final XmlRecordFactory recordFactory = new XmlRecordFactory(
 			prepareAccumulators(spark.sparkContext()),
@@ -118,7 +117,7 @@ public class XmlConverterJob {
 			.as(Encoders.kryo(JoinedEntity.class))
 			.map(
 				(MapFunction<JoinedEntity, Tuple2<String, SolrRecord>>) je -> new Tuple2<>(
-					recordFactory.build(je),
+					recordFactory.build(je, validateXML),
 					ProvisionModelSupport.transform(je, contextMapper, vocabularies)),
 				Encoders.tuple(Encoders.STRING(), Encoders.bean(SolrRecord.class)))
 			.map(

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java

@@ -2,42 +2,34 @@
 package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.col;
 
 import java.util.HashSet;
 import java.util.Optional;
-import java.util.PriorityQueue;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.FlatMapFunction;
-import org.apache.spark.api.java.function.Function;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoder;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
-import org.apache.spark.sql.expressions.Aggregator;
+import org.apache.spark.sql.expressions.Window;
+import org.apache.spark.sql.expressions.WindowSpec;
+import org.apache.spark.sql.functions;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.base.Joiner;
 import com.google.common.base.Splitter;
-import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
-import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
-import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
 import eu.dnetlib.dhp.schema.oaf.Relation;
-import scala.Tuple2;
 
 /**
  * PrepareRelationsJob prunes the relationships: only consider relationships that are not virtually deleted
@@ -130,132 +122,36 @@ public class PrepareRelationsJob {
 	private static void prepareRelationsRDD(SparkSession spark, String inputRelationsPath, String outputPath,
 		Set<String> relationFilter, int sourceMaxRelations, int targetMaxRelations, int relPartitions) {
 
-		JavaRDD<Relation> rels = readPathRelationRDD(spark, inputRelationsPath)
+		WindowSpec source_w = Window
-			.filter(rel -> !(rel.getSource().startsWith("unresolved") || rel.getTarget().startsWith("unresolved")))
+			.partitionBy("source", "subRelType")
-			.filter(rel -> !rel.getDataInfo().getDeletedbyinference())
+			.orderBy(col("target").desc_nulls_last());
-			.filter(rel -> !relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())));
 
-		JavaRDD<Relation> pruned = pruneRels(
+		WindowSpec target_w = Window
-			pruneRels(
+			.partitionBy("target", "subRelType")
-				rels,
+			.orderBy(col("source").desc_nulls_last());
-				sourceMaxRelations, relPartitions, (Function<Relation, String>) Relation::getSource),
-			targetMaxRelations, relPartitions, (Function<Relation, String>) Relation::getTarget);
-		spark
-			.createDataset(pruned.rdd(), Encoders.bean(Relation.class))
-			.repartition(relPartitions)
-			.write()
-			.mode(SaveMode.Overwrite)
-			.parquet(outputPath);
-	}
 
-	private static JavaRDD<Relation> pruneRels(JavaRDD<Relation> rels, int maxRelations,
-		int relPartitions, Function<Relation, String> idFn) {
-		return rels
-			.mapToPair(r -> new Tuple2<>(SortableRelationKey.create(r, idFn.call(r)), r))
-			.repartitionAndSortWithinPartitions(new RelationPartitioner(relPartitions))
-			.groupBy(Tuple2::_1)
-			.map(Tuple2::_2)
-			.map(t -> Iterables.limit(t, maxRelations))
-			.flatMap(Iterable::iterator)
-			.map(Tuple2::_2);
-	}
-
-	// experimental
-	private static void prepareRelationsDataset(
-		SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
-		int relPartitions) {
 		spark
 			.read()
-			.textFile(inputRelationsPath)
+			.schema(Encoders.bean(Relation.class).schema())
-			.repartition(relPartitions)
+			.json(inputRelationsPath)
-			.map(
+			.where("source NOT LIKE 'unresolved%' AND  target  NOT LIKE 'unresolved%'")
-				(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
+			.where("datainfo.deletedbyinference != true")
-				Encoders.kryo(Relation.class))
+			.where(
-			.filter((FilterFunction<Relation>) rel -> !rel.getDataInfo().getDeletedbyinference())
+				relationFilter.isEmpty() ? ""
-			.filter((FilterFunction<Relation>) rel -> !relationFilter.contains(rel.getRelClass()))
+					: "lower(relClass) NOT IN ("
-			.groupByKey(
+						+ relationFilter.stream().map(s -> "'" + s + "'").collect(Collectors.joining(",")) + ")")
-				(MapFunction<Relation, String>) Relation::getSource,
+			.withColumn("source_w_pos", functions.row_number().over(source_w))
-				Encoders.STRING())
+			.where("source_w_pos < " + sourceMaxRelations)
-			.agg(new RelationAggregator(maxRelations).toColumn())
+			.drop("source_w_pos")
-			.flatMap(
+			.withColumn("target_w_pos", functions.row_number().over(target_w))
-				(FlatMapFunction<Tuple2<String, RelationList>, Relation>) t -> Iterables
+			.where("target_w_pos < " + targetMaxRelations)
-					.limit(t._2().getRelations(), maxRelations)
+			.drop("target_w_pos")
-					.iterator(),
+			.coalesce(relPartitions)
-				Encoders.bean(Relation.class))
-			.repartition(relPartitions)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.parquet(outputPath);
 	}
 
-	public static class RelationAggregator
-		extends Aggregator<Relation, RelationList, RelationList> {
-
-		private final int maxRelations;
-
-		public RelationAggregator(int maxRelations) {
-			this.maxRelations = maxRelations;
-		}
-
-		@Override
-		public RelationList zero() {
-			return new RelationList();
-		}
-
-		@Override
-		public RelationList reduce(RelationList b, Relation a) {
-			b.getRelations().add(a);
-			return getSortableRelationList(b);
-		}
-
-		@Override
-		public RelationList merge(RelationList b1, RelationList b2) {
-			b1.getRelations().addAll(b2.getRelations());
-			return getSortableRelationList(b1);
-		}
-
-		@Override
-		public RelationList finish(RelationList r) {
-			return getSortableRelationList(r);
-		}
-
-		private RelationList getSortableRelationList(RelationList b1) {
-			RelationList sr = new RelationList();
-			sr
-				.setRelations(
-					b1
-						.getRelations()
-						.stream()
-						.limit(maxRelations)
-						.collect(Collectors.toCollection(() -> new PriorityQueue<>(new RelationComparator()))));
-			return sr;
-		}
-
-		@Override
-		public Encoder<RelationList> bufferEncoder() {
-			return Encoders.kryo(RelationList.class);
-		}
-
-		@Override
-		public Encoder<RelationList> outputEncoder() {
-			return Encoders.kryo(RelationList.class);
-		}
-	}
-
-	/**
-	 * Reads a JavaRDD of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
-	 * file,
-	 *
-	 * @param spark
-	 * @param inputPath
-	 * @return the JavaRDD<SortableRelation> containing all the relationships
-	 */
-	private static JavaRDD<Relation> readPathRelationRDD(
-		SparkSession spark, final String inputPath) {
-		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-		return sc.textFile(inputPath).map(s -> OBJECT_MAPPER.readValue(s, Relation.class));
-	}
-
 	private static void removeOutputDir(SparkSession spark, String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java

@@ -1,44 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision;
-
-import java.util.Comparator;
-import java.util.Map;
-import java.util.Optional;
-
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Maps;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class RelationComparator implements Comparator<Relation> {
-
-	private static final Map<String, Integer> weights = Maps.newHashMap();
-
-	static {
-		weights.put(ModelConstants.OUTCOME, 0);
-		weights.put(ModelConstants.SUPPLEMENT, 1);
-		weights.put(ModelConstants.REVIEW, 2);
-		weights.put(ModelConstants.CITATION, 3);
-		weights.put(ModelConstants.AFFILIATION, 4);
-		weights.put(ModelConstants.RELATIONSHIP, 5);
-		weights.put(ModelConstants.PUBLICATION_DATASET, 6);
-		weights.put(ModelConstants.SIMILARITY, 7);
-
-		weights.put(ModelConstants.PROVISION, 8);
-		weights.put(ModelConstants.PARTICIPATION, 9);
-		weights.put(ModelConstants.DEDUP, 10);
-	}
-
-	private Integer getWeight(Relation o) {
-		return Optional.ofNullable(weights.get(o.getSubRelType())).orElse(Integer.MAX_VALUE);
-	}
-
-	@Override
-	public int compare(Relation o1, Relation o2) {
-		return ComparisonChain
-			.start()
-			.compare(getWeight(o1), getWeight(o2))
-			.result();
-	}
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationList.java

@@ -1,25 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision;
-
-import java.io.Serializable;
-import java.util.PriorityQueue;
-import java.util.Queue;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class RelationList implements Serializable {
-
-	private Queue<Relation> relations;
-
-	public RelationList() {
-		this.relations = new PriorityQueue<>(new RelationComparator());
-	}
-
-	public Queue<Relation> getRelations() {
-		return relations;
-	}
-
-	public void setRelations(Queue<Relation> relations) {
-		this.relations = relations;
-	}
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SortableRelation.java

@@ -1,81 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision;
-
-import java.io.Serializable;
-import java.util.Map;
-import java.util.Optional;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Maps;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class SortableRelation extends Relation implements Comparable<SortableRelation>, Serializable {
-
-	private static final Map<String, Integer> weights = Maps.newHashMap();
-
-	static {
-		weights.put(ModelConstants.OUTCOME, 0);
-		weights.put(ModelConstants.SUPPLEMENT, 1);
-		weights.put(ModelConstants.REVIEW, 2);
-		weights.put(ModelConstants.CITATION, 3);
-		weights.put(ModelConstants.AFFILIATION, 4);
-		weights.put(ModelConstants.RELATIONSHIP, 5);
-		weights.put(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, 6);
-		weights.put(ModelConstants.SIMILARITY, 7);
-
-		weights.put(ModelConstants.PROVISION, 8);
-		weights.put(ModelConstants.PARTICIPATION, 9);
-		weights.put(ModelConstants.DEDUP, 10);
-	}
-
-	private static final long serialVersionUID = 34753984579L;
-
-	private String groupingKey;
-
-	public static SortableRelation create(Relation r, String groupingKey) {
-		SortableRelation sr = new SortableRelation();
-		sr.setGroupingKey(groupingKey);
-		sr.setSource(r.getSource());
-		sr.setTarget(r.getTarget());
-		sr.setRelType(r.getRelType());
-		sr.setSubRelType(r.getSubRelType());
-		sr.setRelClass(r.getRelClass());
-		sr.setDataInfo(r.getDataInfo());
-		sr.setCollectedfrom(r.getCollectedfrom());
-		sr.setLastupdatetimestamp(r.getLastupdatetimestamp());
-		sr.setProperties(r.getProperties());
-		sr.setValidated(r.getValidated());
-		sr.setValidationDate(r.getValidationDate());
-
-		return sr;
-	}
-
-	@JsonIgnore
-	public Relation asRelation() {
-		return this;
-	}
-
-	@Override
-	public int compareTo(SortableRelation o) {
-		return ComparisonChain
-			.start()
-			.compare(getGroupingKey(), o.getGroupingKey())
-			.compare(getWeight(this), getWeight(o))
-			.result();
-	}
-
-	private Integer getWeight(SortableRelation o) {
-		return Optional.ofNullable(weights.get(o.getSubRelType())).orElse(Integer.MAX_VALUE);
-	}
-
-	public String getGroupingKey() {
-		return groupingKey;
-	}
-
-	public void setGroupingKey(String groupingKey) {
-		this.groupingKey = groupingKey;
-	}
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java

@@ -1,8 +1,6 @@
 
 package eu.dnetlib.dhp.oa.provision.model;
 
-import static org.apache.commons.lang3.StringUtils.substringBefore;
-
 import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
@@ -16,16 +14,15 @@ import org.jetbrains.annotations.Nullable;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm;
-import eu.dnetlib.dhp.oa.provision.RelationList;
-import eu.dnetlib.dhp.oa.provision.SortableRelation;
 import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.solr.*;
 import eu.dnetlib.dhp.schema.solr.AccessRight;
 import eu.dnetlib.dhp.schema.solr.Author;
@@ -55,10 +52,7 @@ public class ProvisionModelSupport {
 					.newArrayList(
 						RelatedEntityWrapper.class,
 						JoinedEntity.class,
-						RelatedEntity.class,
+						RelatedEntity.class));
-						SortableRelationKey.class,
-						SortableRelation.class,
-						RelationList.class));
 		return modelClasses.toArray(new Class[] {});
 	}
 
@@ -74,7 +68,11 @@ public class ProvisionModelSupport {
 			.setHeader(
 				SolrRecordHeader
 					.newInstance(
-						e.getId(), e.getOriginalId(), type, deletedbyinference));
+						StringUtils
+							.substringAfter(
+								e.getId(),
+								IdentifierFactory.ID_PREFIX_SEPARATOR),
+						e.getOriginalId(), type, deletedbyinference));
 		r.setCollectedfrom(asProvenance(e.getCollectedfrom()));
 		r.setContext(asContext(e.getContext(), contextMapper));
 		r.setPid(asPid(e.getPid()));
@@ -114,7 +112,8 @@ public class ProvisionModelSupport {
 					.newInstance(
 						relation.getRelType(),
 						relation.getRelClass(),
-						relation.getTarget(), relatedRecordType));
+						StringUtils.substringAfter(relation.getTarget(), IdentifierFactory.ID_PREFIX_SEPARATOR),
+						relatedRecordType));
 
 		rr.setAcronym(re.getAcronym());
 		rr.setCode(re.getCode());
@@ -147,6 +146,7 @@ public class ProvisionModelSupport {
 		ps.setContracttype(mapCodeLabel(p.getContracttype()));
 		ps.setCurrency(mapField(p.getCurrency()));
 		ps.setDuration(mapField(p.getDuration()));
+		ps.setOamandatepublications(mapField(p.getOamandatepublications()));
 		ps.setCallidentifier(mapField(p.getCallidentifier()));
 		ps.setEcarticle29_3(mapField(p.getEcarticle29_3()));
 		ps.setEnddate(mapField(p.getEnddate()));
@@ -387,7 +387,7 @@ public class ProvisionModelSupport {
 							.equals(
 								Optional
 									.ofNullable(t.getQualifier())
-									.map(Qualifier::getClassid)
+									.map(Qualifier::getClassname)
 									.orElse(null)))
 					.map(StructuredProperty::getValue)
 					.collect(Collectors.toList()))
@@ -405,7 +405,7 @@ public class ProvisionModelSupport {
 							.equals(
 								Optional
 									.ofNullable(t.getQualifier())
-									.map(Qualifier::getClassid)
+									.map(Qualifier::getClassname)
 									.orElse(null)))
 					.map(StructuredProperty::getValue)
 					.findFirst())
@@ -472,7 +472,7 @@ public class ProvisionModelSupport {
 	}
 
 	private static String mapQualifier(eu.dnetlib.dhp.schema.oaf.Qualifier q) {
-		return Optional.ofNullable(q).map(Qualifier::getClassid).orElse(null);
+		return Optional.ofNullable(q).map(Qualifier::getClassname).orElse(null);
 	}
 
 	private static Journal mapJournal(eu.dnetlib.dhp.schema.oaf.Journal joaf) {
@@ -581,7 +581,7 @@ public class ProvisionModelSupport {
 			.map(
 				pids -> pids
 					.stream()
-					.map(p -> Pid.newInstance(p.getQualifier().getClassid(), p.getValue()))
+					.map(p -> Pid.newInstance(p.getQualifier().getClassname(), p.getValue()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
@@ -606,8 +606,8 @@ public class ProvisionModelSupport {
 				subjects -> subjects
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
-					.filter(s -> Objects.nonNull(s.getQualifier().getClassid()))
+					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
-					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassid()))
+					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassname()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
@@ -619,8 +619,8 @@ public class ProvisionModelSupport {
 				subjects -> subjects
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
-					.filter(s -> Objects.nonNull(s.getQualifier().getClassid()))
+					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
-					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassid()))
+					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassname()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -93,10 +93,13 @@ public class XmlRecordFactory implements Serializable {
 	}
 
 	public String build(final JoinedEntity je) {
+		return build(je, false);
+	}
+
+	public String build(final JoinedEntity je, final Boolean validate) {
 
 		final Set<String> contexts = Sets.newHashSet();
 
-		// final OafEntity entity = toOafEntity(je.getEntity());
 		final OafEntity entity = je.getEntity();
 		final TemplateFactory templateFactory = new TemplateFactory();
 		try {
@@ -122,7 +125,13 @@ public class XmlRecordFactory implements Serializable {
 				.buildBody(
 					mainType, metadata, relations, listChildren(entity, je, templateFactory), listExtraInfo(entity));
 
-			return templateFactory.buildRecord(entity, schemaLocation, body);
+			String xmlRecord = templateFactory.buildRecord(entity, schemaLocation, body);
+
+			if (Boolean.TRUE.equals(validate)) {
+				// rise an exception when an invalid record was built
+				new SAXReader().read(new StringReader(xmlRecord));
+			}
+			return xmlRecord;
 			// return printXML(templateFactory.buildRecord(entity, schemaLocation, body), indent);
 		} catch (final Throwable e) {
 			throw new RuntimeException(String.format("error building record '%s'", entity.getId()), e);
@@ -1038,13 +1047,21 @@ public class XmlRecordFactory implements Serializable {
 	}
 
 	private List<String> measuresAsXml(List<Measure> measures) {
-		return measures
+		return Stream
+			.concat(
+				measures
 					.stream()
+					.filter(m -> !"downloads".equals(m.getId()) && !"views".equals(m.getId()))
 					.map(m -> {
 						List<Tuple2<String, String>> l = Lists.newArrayList(new Tuple2<>("id", m.getId()));
 						m.getUnit().forEach(kv -> l.add(new Tuple2<>(kv.getKey(), kv.getValue())));
 						return XmlSerializationUtils.asXmlElement("measure", l);
-			})
+					}),
+				measures
+					.stream()
+					.filter(m -> "downloads".equals(m.getId()) || "views".equals(m.getId()))
+					.filter(m -> m.getUnit().stream().anyMatch(u -> Integer.parseInt(u.getValue()) > 0))
+					.map(m -> XmlSerializationUtils.usageMeasureAsXmlElement("measure", m)))
 			.collect(Collectors.toList());
 	}
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java

@@ -5,7 +5,11 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
+import java.util.HashSet;
 import java.util.List;
+import java.util.Optional;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
@@ -166,6 +170,33 @@ public class XmlSerializationUtils {
 		return sb.toString();
 	}
 
+	// <measure downloads="0" views="0">infrastruct_::f66f1bd369679b5b077dcdf006089556||OpenAIRE</measure>
+	public static String usageMeasureAsXmlElement(String name, Measure measure) {
+		HashSet<String> dsIds = Optional
+			.ofNullable(measure.getUnit())
+			.map(
+				m -> m
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.toCollection(HashSet::new)))
+			.orElse(new HashSet<>());
+
+		StringBuilder sb = new StringBuilder();
+		dsIds.forEach(dsId -> {
+			sb
+				.append("<")
+				.append(name);
+			for (KeyValue kv : measure.getUnit()) {
+				sb.append(" ").append(attr(measure.getId(), kv.getValue()));
+			}
+			sb
+				.append(" ")
+				.append(attr("datasource", dsId))
+				.append("/>");
+		});
+		return sb.toString();
+	}
+
 	public static String mapEoscIf(EoscIfGuidelines e) {
 		return asXmlElement(
 			"eoscifguidelines", Lists

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_payload_converter.json

@@ -22,5 +22,11 @@
     "paramLongName": "isLookupUrl",
     "paramDescription": "URL of the context ISLookup Service",
     "paramRequired": true
+  },
+  {
+    "paramName": "val",
+    "paramLongName": "validateXML",
+    "paramDescription": "should the process check the XML validity",
+    "paramRequired": false
   }
 ]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml

@@ -13,6 +13,11 @@
             <name>contextApiBaseUrl</name>
             <description>context API URL</description>
         </property>
+        <property>
+            <name>validateXML</name>
+            <description>should the payload converter validate the XMLs</description>
+            <value>false</value>
+        </property>
         <property>
             <name>relPartitions</name>
             <description>number or partitions for the relations Dataset</description>
@@ -125,7 +130,7 @@
             <case to="prepare_relations">${wf:conf('resumeFrom') eq 'prepare_relations'}</case>
             <case to="fork_join_related_entities">${wf:conf('resumeFrom') eq 'fork_join_related_entities'}</case>
             <case to="fork_join_all_entities">${wf:conf('resumeFrom') eq 'fork_join_all_entities'}</case>
-            <case to="convert_to_xml">${wf:conf('resumeFrom') eq 'convert_to_xml'}</case>
+            <case to="create_payloads">${wf:conf('resumeFrom') eq 'create_payloads'}</case>
             <case to="drop_solr_collection">${wf:conf('resumeFrom') eq 'drop_solr_collection'}</case>
             <case to="to_solr_index">${wf:conf('resumeFrom') eq 'to_solr_index'}</case>
             <default to="prepare_relations"/>
@@ -144,21 +149,23 @@
             <class>eu.dnetlib.dhp.oa.provision.PrepareRelationsJob</class>
             <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-cores=4
-                --executor-memory=${sparkExecutorMemoryForJoining}
+                --executor-memory=6G
                 --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.executor.memoryOverhead=6G
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=15000
+                --conf spark.network.timeout=${sparkNetworkTimeout}
             </spark-opts>
             <arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
             <arg>--sourceMaxRelations</arg><arg>${sourceMaxRelations}</arg>
             <arg>--targetMaxRelations</arg><arg>${targetMaxRelations}</arg>
             <arg>--relationFilter</arg><arg>${relationFilter}</arg>
-            <arg>--relPartitions</arg><arg>5000</arg>
+            <arg>--relPartitions</arg><arg>15000</arg>
         </spark>
         <ok to="fork_join_related_entities"/>
         <error to="Kill"/>
@@ -585,19 +592,20 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_join_phase2" to="convert_to_xml"/>
+    <join name="wait_join_phase2" to="create_payloads"/>
 
-    <action name="convert_to_xml">
+    <action name="create_payloads">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>convert_to_xml</name>
+            <name>create_payloads</name>
-            <class>eu.dnetlib.dhp.oa.provision.XmlConverterJob</class>
+            <class>eu.dnetlib.dhp.oa.provision.PayloadConverterJob</class>
             <jar>dhp-graph-provision-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -607,6 +615,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${workingDir}/join_entities</arg>
             <arg>--outputPath</arg><arg>${workingDir}/xml_json</arg>
+            <arg>--validateXML</arg><arg>${validateXML}</arg>
             <arg>--contextApiBaseUrl</arg><arg>${contextApiBaseUrl}</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/EOSCFuture_Test.java

@@ -50,7 +50,7 @@ public class EOSCFuture_Test {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final OtherResearchProduct p = OBJECT_MAPPER
 			.readValue(

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java

@@ -57,7 +57,7 @@ public class IndexRecordTransformerTest {
 	public void testPublicationRecordTransformation() throws IOException, TransformerException {
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = load("publication.json", Publication.class);
 		final Project pj = load("project.json", Project.class);
@@ -82,7 +82,7 @@ public class IndexRecordTransformerTest {
 	void testPeerReviewed() throws IOException, TransformerException {
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = load("publication.json", Publication.class);
 
@@ -98,7 +98,7 @@ public class IndexRecordTransformerTest {
 	public void testRiunet() throws IOException, TransformerException {
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = load("riunet.json", Publication.class);
 

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java

@@ -37,7 +37,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = OBJECT_MAPPER
 			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
@@ -105,7 +105,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = OBJECT_MAPPER
 			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
@@ -136,7 +136,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = OBJECT_MAPPER
 			.readValue(IOUtils.toString(getClass().getResourceAsStream("publication.json")), Publication.class);
@@ -166,7 +166,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Datasource d = OBJECT_MAPPER
 			.readValue(IOUtils.toString(getClass().getResourceAsStream("datasource.json")), Datasource.class);
@@ -203,7 +203,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final OtherResearchProduct p = OBJECT_MAPPER
 			.readValue(
@@ -226,7 +226,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final OtherResearchProduct p = OBJECT_MAPPER
 			.readValue(
@@ -249,7 +249,7 @@ public class XmlRecordFactoryTest {
 		final ContextMapper contextMapper = new ContextMapper();
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
-			XmlConverterJob.schemaLocation);
+			PayloadConverterJob.schemaLocation);
 
 		final Publication p = OBJECT_MAPPER
 			.readValue(

dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml

@@ -71,6 +71,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -108,6 +109,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -141,6 +143,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -176,6 +179,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -209,6 +213,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -245,6 +250,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -315,6 +321,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -361,6 +368,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -409,6 +417,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -444,6 +453,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkHighDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -482,6 +492,7 @@
 				--executor-memory=${sparkHighExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
 				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -533,6 +544,7 @@
 				--executor-memory=${sparkNormalExecutorMemory}
 				--executor-cores=${sparkExecutorCores}
 				--driver-memory=${sparkNormalDriverMemory}
+				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
 				--conf spark.extraListeners=${spark2ExtraListeners}
 				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
 				--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh

@@ -67,24 +67,21 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
-    return 1
+    exit 2
   fi
 
-  # Make Impala aware of the deletion of the old DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
-  # Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
+  # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
-  # Using max memory of: 50 * 6144 = 300 Gb
+  # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
-  # The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
+  # The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
   # The "ug" args cannot be used as we get a "User does not belong to hive" error.
   # The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
   hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
                 -numListstatusThreads 40 \
                 -copybuffersize 1048576 \
                 -strategy dynamic \
+                -blocksperchunk 8 \
                 -pb \
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
@@ -92,9 +89,9 @@ function copydb() {
   if [ $? -eq 0 ]; then
     echo -e "\nSuccessfully copied the files of '${db}'.\n"
   else
-    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
+    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
-    return 2
+    exit 3
   fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@@ -105,14 +102,11 @@ function copydb() {
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
-  # Make Impala aware of the creation of the new DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
 
   all_create_view_statements=()
+  num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@@ -129,9 +123,11 @@ function copydb() {
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
+      ((num_tables++))
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
+          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -142,74 +138,73 @@ function copydb() {
     fi
   done
 
-  echo -e "\nAll tables have been created, going to create the views..\n"
+  previous_num_of_views_to_retry=${#all_create_view_statements[@]}
+  if [[ $num_tables -gt 0 ]]; then
+    echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
+  else
+    echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
+  fi
 
-  # Time to loop through the views and create them.
-  # At this point all table-schemas should have been created.
-
-  previous_num_of_views_to_retry=${#all_create_view_statements}
   if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
-    echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n"  # DEBUG
+    echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"  # DEBUG
-    # Make Impala aware of the new tables, so it knows them when creating the views.
-    sleep 1
-    impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-    sleep 1
   else
     echo -e "\nDB '${db}' does not contain any views.\n"
   fi
 
   level_counter=0
-  while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
+  while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
     ((level_counter++))
     # The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
     # In this case, we should retry creating this particular view again.
-    should_retry_create_view_statements=()
+    new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
-        should_retry_create_view_statements+=("$create_view_statement")
+        ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
+          all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
           sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
       fi
     done
 
-    new_num_of_views_to_retry=${#should_retry_create_view_statements}
+    all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')")  # Re-index the array, filtering-out any empty elements.
+    # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
+
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      return 3
+      exit 5
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
-      echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
+      echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
-      previous_num_of_views_to_retry=$new_num_of_views_to_retry
     else
       echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
     fi
-    all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
+    previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
-
   echo -e "\nComputing stats for tables..\n"
   entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
+      # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      sleep 1
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
     fi
   done
 
+  # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
   if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
     echo -e "\nAll entities have been copied to Impala cluster.\n"
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    return 4
+    exit 6
   fi
 
   rm -f error.log

dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh

@@ -66,24 +66,21 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
-    return 1
+    exit 2
   fi
 
-  # Make Impala aware of the deletion of the old DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
-  # Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
+  # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
-  # Using max memory of: 50 * 6144 = 300 Gb
+  # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
-  # The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
+  # The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
   # The "ug" args cannot be used as we get a "User does not belong to hive" error.
   # The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
   hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
                 -numListstatusThreads 40 \
                 -copybuffersize 1048576 \
                 -strategy dynamic \
+                -blocksperchunk 8 \
                 -pb \
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
@@ -91,9 +88,9 @@ function copydb() {
   if [ $? -eq 0 ]; then
     echo -e "\nSuccessfully copied the files of '${db}'.\n"
   else
-    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
+    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
-    return 2
+    exit 3
   fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@@ -104,14 +101,11 @@ function copydb() {
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
-  # Make Impala aware of the creation of the new DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
 
   all_create_view_statements=()
+  num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@@ -128,9 +122,11 @@ function copydb() {
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
+      ((num_tables++))
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
+          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -141,74 +137,73 @@ function copydb() {
     fi
   done
 
-  echo -e "\nAll tables have been created, going to create the views..\n"
+  previous_num_of_views_to_retry=${#all_create_view_statements[@]}
+  if [[ $num_tables -gt 0 ]]; then
+    echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
+  else
+    echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
+  fi
 
-  # Time to loop through the views and create them.
-  # At this point all table-schemas should have been created.
-
-  previous_num_of_views_to_retry=${#all_create_view_statements}
   if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
-    echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n"  # DEBUG
+    echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"  # DEBUG
-    # Make Impala aware of the new tables, so it knows them when creating the views.
-    sleep 1
-    impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-    sleep 1
   else
     echo -e "\nDB '${db}' does not contain any views.\n"
   fi
 
   level_counter=0
-  while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
+  while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
     ((level_counter++))
     # The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
     # In this case, we should retry creating this particular view again.
-    should_retry_create_view_statements=()
+    new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
-        should_retry_create_view_statements+=("$create_view_statement")
+        ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
+          all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
           sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
       fi
     done
 
-    new_num_of_views_to_retry=${#should_retry_create_view_statements}
+    all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')")  # Re-index the array, filtering-out any empty elements.
+    # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
+
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      return 3
+      exit 5
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
-      echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
+      echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
-      previous_num_of_views_to_retry=$new_num_of_views_to_retry
     else
       echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
     fi
-    all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
+    previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
-
   echo -e "\nComputing stats for tables..\n"
   entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
+      # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      sleep 1
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
     fi
   done
 
+  # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
   if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
     echo -e "\nAll entities have been copied to Impala cluster.\n"
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    return 4
+    exit 6
   fi
 
   rm -f error.log

dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh

@@ -66,24 +66,21 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
-    return 1
+    exit 2
   fi
 
-  # Make Impala aware of the deletion of the old DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
-  # Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
+  # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
-  # Using max memory of: 50 * 6144 = 300 Gb
+  # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
-  # The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
+  # The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
   # The "ug" args cannot be used as we get a "User does not belong to hive" error.
   # The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
   hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
                 -numListstatusThreads 40 \
                 -copybuffersize 1048576 \
                 -strategy dynamic \
+                -blocksperchunk 8 \
                 -pb \
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
@@ -91,9 +88,9 @@ function copydb() {
   if [ $? -eq 0 ]; then
     echo -e "\nSuccessfully copied the files of '${db}'.\n"
   else
-    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
+    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
-    return 2
+    exit 3
   fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@@ -104,14 +101,11 @@ function copydb() {
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
-  # Make Impala aware of the creation of the new DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
 
   all_create_view_statements=()
+  num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@@ -128,9 +122,11 @@ function copydb() {
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
+      ((num_tables++))
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
+          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -141,74 +137,73 @@ function copydb() {
     fi
   done
 
-  echo -e "\nAll tables have been created, going to create the views..\n"
+  previous_num_of_views_to_retry=${#all_create_view_statements[@]}
+  if [[ $num_tables -gt 0 ]]; then
+    echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
+  else
+    echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
+  fi
 
-  # Time to loop through the views and create them.
-  # At this point all table-schemas should have been created.
-
-  previous_num_of_views_to_retry=${#all_create_view_statements}
   if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
-    echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n"  # DEBUG
+    echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"  # DEBUG
-    # Make Impala aware of the new tables, so it knows them when creating the views.
-    sleep 1
-    impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-    sleep 1
   else
     echo -e "\nDB '${db}' does not contain any views.\n"
   fi
 
   level_counter=0
-  while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
+  while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
     ((level_counter++))
     # The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
     # In this case, we should retry creating this particular view again.
-    should_retry_create_view_statements=()
+    new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
-        should_retry_create_view_statements+=("$create_view_statement")
+        ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
+          all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
           sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
       fi
     done
 
-    new_num_of_views_to_retry=${#should_retry_create_view_statements}
+    all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')")  # Re-index the array, filtering-out any empty elements.
+    # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
+
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      return 3
+      exit 5
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
-      echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
+      echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
-      previous_num_of_views_to_retry=$new_num_of_views_to_retry
     else
       echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
     fi
-    all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
+    previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
-
   echo -e "\nComputing stats for tables..\n"
   entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
+      # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      sleep 1
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
     fi
   done
 
+  # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
   if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
     echo -e "\nAll entities have been copied to Impala cluster.\n"
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    return 4
+    exit 6
   fi
 
   rm -f error.log

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh

@@ -68,24 +68,21 @@ function copydb() {
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
     rm -f error.log
-    return 1
+    exit 2
   fi
 
-  # Make Impala aware of the deletion of the old DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
-  # Using max-bandwidth of: 50 * 100 Mb/s = 5 Gb/s
+  # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
-  # Using max memory of: 50 * 6144 = 300 Gb
+  # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
-  # The " -Ddistcp.dynamic.recordsPerChunk=50" arg is not available in our version of hadoop
+  # The " -Ddistcp.dynamic.recordsPerChunk=N" arg is not available in our version of hadoop
   # The "ug" args cannot be used as we get a "User does not belong to hive" error.
   # The "p" argument cannot be used, as it blocks the files from being used, giving a "sticky bit"-error, even after applying chmod and chown onm the files.
   hadoop distcp -Dmapreduce.map.memory.mb=6144 -m 70 -bandwidth 150 \
                 -numListstatusThreads 40 \
                 -copybuffersize 1048576 \
                 -strategy dynamic \
+                -blocksperchunk 8 \
                 -pb \
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
@@ -93,9 +90,9 @@ function copydb() {
   if [ $? -eq 0 ]; then
     echo -e "\nSuccessfully copied the files of '${db}'.\n"
   else
-    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT WITH EXIT STATUS: $?\n\n"
+    echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
-    return 2
+    exit 3
   fi
 
   # In case we ever use this script for a writable DB (using inserts/updates), we should perform the following costly operation as well..
@@ -106,14 +103,11 @@ function copydb() {
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
-  # Make Impala aware of the creation of the new DB immediately.
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
 
   all_create_view_statements=()
+  num_tables=0
 
   entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elemetns are single-words.
@@ -130,9 +124,11 @@ function copydb() {
       all_create_view_statements+=("$create_view_statement")
     else
       echo -e "\n'${i}' is a table, so we will check for its parquet files and create the table on Impala cluster.\n"
+      ((num_tables++))
       CURRENT_PRQ_FILE=`hdfs dfs -conf ${IMPALA_CONFIG_FILE} -ls -C "${IMPALA_HDFS_DB_BASE_PATH}/${db}.db/${i}/" | grep -v 'Found' | grep -v '_impala_insert_staging' |  head -1`
       if [ -z "$CURRENT_PRQ_FILE" ]; then # If there is not parquet-file inside.
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
+          exit 4 # Comment out when testing a DB which has such a table, just for performing this exact test-check.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -143,74 +139,73 @@ function copydb() {
     fi
   done
 
-  echo -e "\nAll tables have been created, going to create the views..\n"
+  previous_num_of_views_to_retry=${#all_create_view_statements[@]}
+  if [[ $num_tables -gt 0 ]]; then
+    echo -e "\nAll ${num_tables} tables have been created, for db '${db}', going to create the ${previous_num_of_views_to_retry} views..\n"
+  else
+    echo -e "\nDB '${db}' does not have any tables, moving on to create the ${previous_num_of_views_to_retry} views..\n"
+  fi
 
-  # Time to loop through the views and create them.
-  # At this point all table-schemas should have been created.
-
-  previous_num_of_views_to_retry=${#all_create_view_statements}
   if [[ $previous_num_of_views_to_retry -gt 0 ]]; then
-    echo -e "\nAll_create_view_statements:\n\n${all_create_view_statements[@]}\n"  # DEBUG
+    echo -e "\nAll_create_view_statements (${previous_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"  # DEBUG
-    # Make Impala aware of the new tables, so it knows them when creating the views.
-    sleep 1
-    impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-    sleep 1
   else
     echo -e "\nDB '${db}' does not contain any views.\n"
   fi
 
   level_counter=0
-  while [[ ${#all_create_view_statements[@]} -gt 0 ]]; do
+  while [[ $previous_num_of_views_to_retry -gt 0 ]]; do
     ((level_counter++))
     # The only accepted reason for a view to not be created, is if it depends on another view, which has not been created yet.
     # In this case, we should retry creating this particular view again.
-    should_retry_create_view_statements=()
+    new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep "CREATE VIEW " | sed 's/CREATE VIEW //g' | sed 's/ as select .*//g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
-        should_retry_create_view_statements+=("$create_view_statement")
+        ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
+          all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
           sleep 1 # Wait a bit for Impala to register that the view was created, before possibly referencing it by another view.
       fi
     done
 
-    new_num_of_views_to_retry=${#should_retry_create_view_statements}
+    all_create_view_statements=("$(echo "${all_create_view_statements[@]}" | grep -v '^[\s]*$')")  # Re-index the array, filtering-out any empty elements.
+    # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
+
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
       echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
-      return 3
+      exit 5
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
-      echo -e "\nTo be retried \"create_view_statements\":\n\n${should_retry_create_view_statements[@]}\n"
+      echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
-      previous_num_of_views_to_retry=$new_num_of_views_to_retry
     else
       echo -e "\nFinished creating views, for db: '${db}', in level-${level_counter}.\n"
     fi
-    all_create_view_statements=("${should_retry_create_view_statement[@]}") # This is needed in any case to either move forward with the rest of the views or stop at 0 remaining views.
+    previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  sleep 1
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA"
-  sleep 1
-
   echo -e "\nComputing stats for tables..\n"
   entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
+      # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      sleep 1
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
     fi
   done
 
+  # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
   if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
     echo -e "\nAll entities have been copied to Impala cluster.\n"
   else
     echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
     rm -f error.log
-    return 4
+    exit 6
   fi
 
   rm -f error.log

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql

@@ -1,3 +1,4 @@
+set mapred.job.queue.name=analytics;
 ------------------------------------------------------
 ------------------------------------------------------
 -- Additional relations

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql

@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics;
+
 ------------------------------------------------------
 ------------------------------------------------------
 -- Additional relations

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql

@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics;
+
 -------------------------------------------
 --- Extra tables, mostly used by indicators
 

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql

@@ -249,7 +249,7 @@ create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet a
             left semi join dd on dd.id=pd.datasource
             union all
             select ra.id, 1 as is_gold
-            from ${stats_db_name}.result_accessroute ra on ra.id = pd.id where ra.accessroute = 'gold') tmp on tmp.id=pd.id; /*EOS*/
+            from ${stats_db_name}.result_accessroute ra where ra.accessroute = 'gold') tmp on tmp.id=pd.id; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as parquet as
@@ -294,7 +294,7 @@ left outer join (
     join ${stats_db_name}.indi_pub_gold_oa indi_gold on indi_gold.id=p.id
     left outer join ${stats_db_name}.result_accessroute ra on ra.id=p.id
     where indi_gold.is_gold=0 and
-          ((d.type like '%Journal%' and ri.accessright not in ('Closed Access', 'Restricted', 'Not Available') and ri.license is not null) or ra.accessroute='hybrid')) tmp on pd.i=tmp.id; /*EOS*/
+          ((d.type like '%Journal%' and ri.accessright not in ('Closed Access', 'Restricted', 'Not Available') and ri.license is not null) or ra.accessroute='hybrid')) tmp on p.id=tmp.id; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_org_fairness purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_org_fairness stored as parquet as
@@ -380,7 +380,7 @@ CREATE TEMPORARY VIEW allresults as
 
 drop table if exists ${stats_db_name}.indi_org_fairness_pub purge; /*EOS*/
 
-create table if not exists ${stats_db_name}.indi_org_fairness_pub as
+create table if not exists ${stats_db_name}.indi_org_fairness_pub stored as parquet as
 select ar.organization, rf.no_result_fair/ar.no_allresults org_fairness
 from allresults ar join result_fair rf
 on rf.organization=ar.organization; /*EOS*/
@@ -639,7 +639,7 @@ from ${stats_db_name}.publication p
 
 drop table if exists ${stats_db_name}.indi_result_with_pid purge; /*EOS*/
 
-create table if not exists ${stats_db_name}.indi_result_with_pid as
+create table if not exists ${stats_db_name}.indi_result_with_pid stored as parquet as
 select distinct p.id, coalesce(result_with_pid, 0) as result_with_pid
 from ${stats_db_name}.result p
          left outer join (
@@ -653,7 +653,7 @@ group by rf.id; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_pub_interdisciplinarity purge; /*EOS*/
 
-create table if not exists ${stats_db_name}.indi_pub_interdisciplinarity as
+create table if not exists ${stats_db_name}.indi_pub_interdisciplinarity stored as parquet as
 select distinct p.id as id, coalesce(is_interdisciplinary, 0)
 as is_interdisciplinary
 from pub_fos_totals p
@@ -1006,14 +1006,14 @@ left outer join (
 drop table if exists ${stats_db_name}.result_country purge; /*EOS*/
 
 create table ${stats_db_name}.result_country stored as parquet as
-select distinct *
+select distinct id, country
 from (
     select ro.id, o.country
     from ${stats_db_name}.result_organization ro
     left outer join ${stats_db_name}.organization o on o.id=ro.organization
     union all
     select rp.id, f.country
-    from ${stats_db_name}.result_projects
+    from ${stats_db_name}.result_projects rp
     left outer join ${stats_db_name}.project p on p.id=rp.project
     left outer join ${stats_db_name}.funder f on f.name=p.funder
      ) rc

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql

@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics;
+
 ----------------------------------------------------
 -- Shortcuts for various definitions in stats db ---
 ----------------------------------------------------

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql

@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics;
+
 -- replace the creation of the result view to include the boolean fields from the previous tables (green, gold,
 -- peer reviewed)
 drop table if exists ${stats_db_name}.result_tmp;

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql

@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics;
+
 --------------------------------------------------------------
 --------------------------------------------------------------
 -- Publication table/view and Publication related tables/views

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml

@@ -368,6 +368,7 @@
                 ${sparkClusterOpts}
                 ${sparkResourceOpts}
                 ${sparkApplicationOpts}
+		--queue analytics
             </spark-opts>
             <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql</arg>

dhp-workflows/dhp-usage-raw-data-update/src/main/resources/eu/dnetlib/dhp/oa/graph/usagerawdata/oozie_app/workflow.xml

@@ -30,6 +30,10 @@
                 <name>oozie.launcher.mapred.job.queue.name</name>
                 <value>${oozieLauncherQueueName}</value>
             </property>
+            <property>
+                <name>mapred.child.java.opts</name>
+                <value>-Xmx16g</value>
+            </property>
         </configuration>
     </global>
 

pom.xml

@@ -960,7 +960,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.2-SNAPSHOT]</dhp-schemas.version>
+        <dhp-schemas.version>[6.1.2]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>