Merge branch 'beta' into exception_on_invalid_transofmation_rule

CODE_OF_CONDUCT.md

@@ -0,0 +1,43 @@
+# Contributor Code of Conduct
+
+Openness, transparency and our community-driven participatory approach guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+- Using welcoming and inclusive language
+- Being respectful of differing viewpoints and experiences
+- Gracefully accepting constructive criticism
+- Attempting collaboration before conflict
+- Focusing on what is best for the community
+- Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+- Violence, threats of violence, or inciting others to commit self-harm
+- The use of sexualized language or imagery and unwelcome sexual attention or advances
+- Trolling, intentionally spreading misinformation, insulting/derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or electronic address, without explicit permission
+- Abuse of the reporting process to intentionally harass or exclude others
+- Advocating for, or encouraging, any of the above behavior
+- Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/), [version 1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html).

CONTRIBUTING.md

@@ -0,0 +1,10 @@
+# Contributing to D-Net Hadoop
+
+:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:
+
+This project and everyone participating in it is governed by our [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it).
+
+The following is a set of guidelines for contributing to this project and its packages. These are mostly guidelines, not rules, which applies to this project as a while, including all its sub-modules. 
+Use your best judgment, and feel free to propose changes to this document in a pull request.
+
+All contributions are welcome, all contributions will be considered to be contributed under the [project license](LICENSE.md).

README.md

@@ -2,6 +2,11 @@
 
 Dnet-hadoop is the project that defined all the [OOZIE workflows](https://oozie.apache.org/) for the OpenAIRE Graph construction, processing, provisioning.
 
+This project adheres to the Contributor Covenant [code of conduct](CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it).
+
+This project is licensed under the [AGPL v3 or later version](#LICENSE.md).
+
 How to build, package and run oozie workflows
 ====================
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java

@@ -0,0 +1,39 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+public class CategorySummary {
+
+	private String id;
+
+	private String label;
+
+	private boolean hasConcept;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public boolean isHasConcept() {
+		return hasConcept;
+	}
+
+	public CategorySummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public CategorySummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public CategorySummary setHasConcept(final boolean hasConcept) {
+		this.hasConcept = hasConcept;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class CategorySummaryList extends ArrayList<CategorySummary> {
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java

@@ -0,0 +1,52 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.List;
+
+public class ConceptSummary {
+
+	private String id;
+
+	private String label;
+
+	public boolean hasSubConcept;
+
+	private List<ConceptSummary> concepts;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public List<ConceptSummary> getConcepts() {
+		return concepts;
+	}
+
+	public ConceptSummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public ConceptSummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public boolean isHasSubConcept() {
+		return hasSubConcept;
+	}
+
+	public ConceptSummary setHasSubConcept(final boolean hasSubConcept) {
+		this.hasSubConcept = hasSubConcept;
+		return this;
+	}
+
+	public ConceptSummary setConcept(final List<ConceptSummary> concepts) {
+		this.concepts = concepts;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class ConceptSummaryList extends ArrayList<ConceptSummary> {
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java

@@ -0,0 +1,50 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+public class ContextSummary {
+
+	private String id;
+
+	private String label;
+
+	private String type;
+
+	private String status;
+
+	public String getId() {
+		return id;
+	}
+
+	public String getLabel() {
+		return label;
+	}
+
+	public String getType() {
+		return type;
+	}
+
+	public String getStatus() {
+		return status;
+	}
+
+	public ContextSummary setId(final String id) {
+		this.id = id;
+		return this;
+	}
+
+	public ContextSummary setLabel(final String label) {
+		this.label = label;
+		return this;
+	}
+
+	public ContextSummary setType(final String type) {
+		this.type = type;
+		return this;
+	}
+
+	public ContextSummary setStatus(final String status) {
+		this.status = status;
+		return this;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java

@@ -0,0 +1,7 @@
+
+package eu.dnetlib.dhp.common.api.context;
+
+import java.util.ArrayList;
+
+public class ContextSummaryList extends ArrayList<ContextSummary> {
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java

@@ -8,10 +8,13 @@ import java.io.InputStream;
 import java.net.*;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.commons.lang3.time.DateUtils;
 import org.apache.http.HttpHeaders;
+import org.joda.time.Instant;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -94,14 +97,16 @@ public class HttpConnector2 {
 			throw new CollectorException(msg);
 		}
 
-		log.info("Request attempt {} [{}]", retryNumber, requestUrl);
-
 		InputStream input = null;
 
+		long start = System.currentTimeMillis();
 		try {
 			if (getClientParams().getRequestDelay() > 0) {
 				backoffAndSleep(getClientParams().getRequestDelay());
 			}
+
+			log.info("Request attempt {} [{}]", retryNumber, requestUrl);
+
 			final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection();
 			urlConn.setInstanceFollowRedirects(false);
 			urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
@@ -115,9 +120,8 @@ public class HttpConnector2 {
 					urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue());
 				}
 			}
-			if (log.isDebugEnabled()) {
+
 			logHeaderFields(urlConn);
-			}
 
 			int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
 			String rateLimit = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT);
@@ -132,9 +136,7 @@ public class HttpConnector2 {
 			}
 
 			if (is2xx(urlConn.getResponseCode())) {
-				input = urlConn.getInputStream();
-				responseType = urlConn.getContentType();
-				return input;
+				return getInputStream(urlConn, start);
 			}
 			if (is3xx(urlConn.getResponseCode())) {
 				// REDIRECTS
@@ -144,6 +146,7 @@ public class HttpConnector2 {
 					.put(
 						REPORT_PREFIX + urlConn.getResponseCode(),
 						String.format("Moved to: %s", newUrl));
+				logRequestTime(start);
 				urlConn.disconnect();
 				if (retryAfter > 0) {
 					backoffAndSleep(retryAfter);
@@ -159,26 +162,50 @@ public class HttpConnector2 {
 						if (retryAfter > 0) {
 							log
 								.warn(
-									"{} - waiting and repeating request after suggested retry-after {} sec.",
-									requestUrl, retryAfter);
+									"waiting and repeating request after suggested retry-after {} sec for URL {}",
+									retryAfter, requestUrl);
 							backoffAndSleep(retryAfter * 1000);
 						} else {
 							log
 								.warn(
-									"{} - waiting and repeating request after default delay of {} sec.",
-									requestUrl, getClientParams().getRetryDelay());
-							backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000);
+									"waiting and repeating request after default delay of {} sec for URL {}",
+									getClientParams().getRetryDelay(), requestUrl);
+							backoffAndSleep(retryNumber * getClientParams().getRetryDelay());
 						}
 						report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
+
+						logRequestTime(start);
+
 						urlConn.disconnect();
+
 						return attemptDownload(requestUrl, retryNumber + 1, report);
+					case 422: // UNPROCESSABLE ENTITY
+						report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
+						log.warn("waiting and repeating request after 10 sec for URL {}", requestUrl);
+						backoffAndSleep(10000);
+						urlConn.disconnect();
+						logRequestTime(start);
+						try {
+							return getInputStream(urlConn, start);
+						} catch (IOException e) {
+							log
+								.error(
+									"server returned 422 and got IOException accessing the response body from URL {}",
+									requestUrl);
+							log.error("IOException:", e);
+							return attemptDownload(requestUrl, retryNumber + 1, report);
+						}
 					default:
+						log.error("gor error {} from URL: {}", urlConn.getResponseCode(), urlConn.getURL());
+						log.error("response message: {}", urlConn.getResponseMessage());
 						report
 							.put(
 								REPORT_PREFIX + urlConn.getResponseCode(),
 								String
 									.format(
 										"%s Error: %s", requestUrl, urlConn.getResponseMessage()));
+						logRequestTime(start);
+						urlConn.disconnect();
 						throw new CollectorException(urlConn.getResponseCode() + " error " + report);
 				}
 			}
@@ -199,13 +226,27 @@ public class HttpConnector2 {
 		}
 	}
 
+	private InputStream getInputStream(HttpURLConnection urlConn, long start) throws IOException {
+		InputStream input = urlConn.getInputStream();
+		responseType = urlConn.getContentType();
+		logRequestTime(start);
+		return input;
+	}
+
+	private static void logRequestTime(long start) {
+		log
+			.info(
+				"request time elapsed: {}sec",
+				TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - start));
+	}
+
 	private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
-		log.debug("StatusCode: {}", urlConn.getResponseMessage());
+		log.info("Response: {} - {}", urlConn.getResponseCode(), urlConn.getResponseMessage());
 
 		for (Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
 			if (e.getKey() != null) {
 				for (String v : e.getValue()) {
-					log.debug("  key: {} - value: {}", e.getKey(), v);
+					log.info("  key: {} - value: {}", e.getKey(), v);
 				}
 			}
 		}
@@ -225,7 +266,7 @@ public class HttpConnector2 {
 		for (String key : headerMap.keySet()) {
 			if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (!headerMap.get(key).isEmpty())
 				&& NumberUtils.isCreatable(headerMap.get(key).get(0))) {
-				return Integer.parseInt(headerMap.get(key).get(0)) + 10;
+				return Integer.parseInt(headerMap.get(key).get(0));
 			}
 		}
 		return -1;

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

@@ -145,105 +145,6 @@ public class AuthorMerger {
 		return null;
 	}
 
-	/**
-	 * This method tries to figure out when two author are the same in the contest
-	 * of ORCID enrichment
-	 *
-	 * @param left  Author in the OAF entity
-	 * @param right Author ORCID
-	 * @return based on a heuristic on the names of the authors if they are the same.
-	 */
-	public static boolean checkORCIDSimilarity(final Author left, final Author right) {
-		final Person pl = parse(left);
-		final Person pr = parse(right);
-
-		// If one of them didn't have a surname we verify if they have the fullName not empty
-		// and verify if the normalized version is equal
-		if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) &&
-			pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) {
-
-			if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
-				&& !pr.getFullname().isEmpty()) {
-				return pl
-					.getFullname()
-					.stream()
-					.anyMatch(
-						fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
-			} else {
-				return false;
-			}
-		}
-		// The Authors have one surname in common
-		if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
-
-			// If one of them has only a surname and is the same we can say that they are the same author
-			if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
-				(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
-				return true;
-			// The authors have the same initials of Name in common
-			if (pl
-				.getName()
-				.stream()
-				.anyMatch(
-					nl -> pr
-						.getName()
-						.stream()
-						.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
-				return true;
-		}
-
-		// Sometimes we noticed that publication have author wrote in inverse order Surname, Name
-		// We verify if we have an exact match between name and surname
-		if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) &&
-			pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl))))
-			return true;
-		else
-			return false;
-	}
-	//
-
-	/**
-	 * Method to enrich ORCID information in one list of authors based on another list
-	 *
-	 * @param baseAuthor  the Author List in the OAF Entity
-	 * @param orcidAuthor The list of ORCID Author intersected
-	 * @return The Author List of the OAF Entity enriched with the orcid Author
-	 */
-	public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
-
-		if (baseAuthor == null || baseAuthor.isEmpty())
-			return orcidAuthor;
-
-		if (orcidAuthor == null || orcidAuthor.isEmpty())
-			return baseAuthor;
-
-		if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
-			return baseAuthor;
-
-		final List<Author> oAuthor = new ArrayList<>();
-		oAuthor.addAll(orcidAuthor);
-
-		baseAuthor.forEach(ba -> {
-			Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
-			if (aMatch.isPresent()) {
-				final Author sameAuthor = aMatch.get();
-				addPid(ba, sameAuthor.getPid());
-				oAuthor.remove(sameAuthor);
-			}
-		});
-		return baseAuthor;
-	}
-
-	private static void addPid(final Author a, final List<StructuredProperty> pids) {
-
-		if (a.getPid() == null) {
-			a.setPid(new ArrayList<>());
-		}
-
-		a.getPid().addAll(pids);
-
-	}
-
 	public static String pidToComparableString(StructuredProperty pid) {
 		final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
 			: "";

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

@@ -1,24 +1,6 @@
 
 package eu.dnetlib.dhp.oa.merge;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.col;
-import static org.apache.spark.sql.functions.when;
-
-import java.util.Map;
-import java.util.Optional;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.ForkJoinPool;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.ReduceFunction;
-import org.apache.spark.sql.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@@ -26,12 +8,29 @@ import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.ReduceFunction;
+import org.apache.spark.sql.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import scala.Tuple2;
 
+import java.util.Map;
+import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ForkJoinPool;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.when;
+
 /**
  * Groups the graph content by entity identifier to ensure ID uniqueness
  */
@@ -135,7 +134,7 @@ public class GroupEntitiesSparkJob {
                                 .applyCoarVocabularies(entity, vocs),
                         OAFENTITY_KRYO_ENC)
                 .groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
-			.reduceGroups((ReduceFunction<OafEntity>) OafMapperUtils::mergeEntities)
+                .reduceGroups((ReduceFunction<OafEntity>) MergeUtils::checkedMerge)
                 .map(
                         (MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
                                 t._2().getClass().getName(), t._2()),

dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java

@@ -0,0 +1,77 @@
+
+package eu.dnetlib.dhp.oozie;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Optional;
+
+import org.apache.commons.lang3.time.DurationFormatUtils;
+import org.apache.commons.text.StringSubstitutor;
+import org.apache.spark.SparkConf;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.google.common.io.Resources;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+
+public class RunSQLSparkJob {
+	private static final Logger log = LoggerFactory.getLogger(RunSQLSparkJob.class);
+
+	private final ArgumentApplicationParser parser;
+
+	public RunSQLSparkJob(ArgumentApplicationParser parser) {
+		this.parser = parser;
+	}
+
+	public static void main(String[] args) throws Exception {
+
+		Map<String, String> params = new HashMap<>();
+		for (int i = 0; i < args.length - 1; i++) {
+			if (args[i].startsWith("--")) {
+				params.put(args[i].substring(2), args[++i]);
+			}
+		}
+
+		/*
+		 * String jsonConfiguration = IOUtils .toString( Objects .requireNonNull( RunSQLSparkJob.class
+		 * .getResourceAsStream( "/eu/dnetlib/dhp/oozie/run_sql_parameters.json"))); final ArgumentApplicationParser
+		 * parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args);
+		 */
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(params.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		URL url = com.google.common.io.Resources.getResource(params.get("sql"));
+		String raw_sql = Resources.toString(url, StandardCharsets.UTF_8);
+
+		String sql = StringSubstitutor.replace(raw_sql, params);
+		log.info("sql: {}", sql);
+
+		SparkConf conf = new SparkConf();
+		conf.set("hive.metastore.uris", params.get("hiveMetastoreUris"));
+
+		runWithSparkHiveSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				for (String statement : sql.split(";\\s*/\\*\\s*EOS\\s*\\*/\\s*")) {
+					log.info("executing: {}", statement);
+					long startTime = System.currentTimeMillis();
+					spark.sql(statement).show();
+					log
+						.info(
+							"executed in {}",
+							DurationFormatUtils.formatDuration(System.currentTimeMillis() - startTime, "HH:mm:ss.S"));
+				}
+			});
+	}
+
+}

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

@@ -312,7 +312,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 		}
 
 		if (value instanceof Datasource) {
-			// nothing to evaluate here
+			final Datasource d = (Datasource) value;
+			return Objects.nonNull(d.getOfficialname()) && StringUtils.isNotBlank(d.getOfficialname().getValue());
 		} else if (value instanceof Project) {
 			final Project p = (Project) value;
 			return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue());

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

@@ -0,0 +1,79 @@
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+//
+// Source code recreated from a .class file by IntelliJ IDEA
+// (powered by FernFlower decompiler)
+//
+
+
+import eu.dnetlib.dhp.schema.common.EntityType;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+public class MergeComparator implements Comparator<Oaf> {
+    public MergeComparator() {
+    }
+
+    public int compare(Oaf left, Oaf right) {
+        // nulls at the end
+        if (left == null && right == null) {
+            return 0;
+        } else if (left == null) {
+            return -1;
+        } else if (right == null) {
+            return 1;
+        }
+
+        // invisible
+        if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) {
+            if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) {
+                return -1;
+            }
+        }
+
+        // collectedfrom
+        HashSet<String> lCf = getCollectedFromIds(left);
+        HashSet<String> rCf = getCollectedFromIds(right);
+        if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
+            return -1;
+        } else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2") && rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
+            return 1;
+        }
+
+
+
+        SubEntityType lClass = SubEntityType.fromClass(left.getClass());
+        SubEntityType rClass = SubEntityType.fromClass(right.getClass());
+        return lClass.ordinal() - rClass.ordinal();
+
+    }
+
+    protected HashSet<String> getCollectedFromIds(Oaf left) {
+        return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> {
+            return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
+        }).orElse(new HashSet());
+    }
+
+    enum SubEntityType {
+        publication, dataset, software, otherresearchproduct, datasource, organization, project;
+
+        /**
+         * Resolves the EntityType, given the relative class name
+         *
+         * @param clazz the given class name
+         * @param <T> actual OafEntity subclass
+         * @return the EntityType associated to the given class
+         */
+        public static <T extends Oaf> SubEntityType fromClass(Class<T> clazz) {
+            return valueOf(clazz.getSimpleName().toLowerCase());
+        }
+    }
+
+}

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

@@ -0,0 +1,707 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import eu.dnetlib.dhp.schema.common.AccessRightComparator;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.tuple.ImmutablePair;
+import org.apache.commons.lang3.tuple.Pair;
+
+import java.text.ParseException;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static com.google.common.base.Objects.firstNonNull;
+import static com.google.common.base.Preconditions.checkArgument;
+
+public class MergeUtils {
+
+    public static <T extends Oaf> T checkedMerge(final T left, final T right) {
+        return (T) merge(left, right, false);
+    }
+
+    public static Oaf merge(final Oaf left, final Oaf right) {
+        return merge(left, right, false);
+    }
+
+    public static Oaf merge(final Oaf left, final Oaf right, boolean checkDelegatedAuthority) {
+        if (sameClass(left, right, OafEntity.class)) {
+            return mergeEntities(left, right, checkDelegatedAuthority);
+        } else if (sameClass(left, right, Relation.class)) {
+            return mergeRelation((Relation) left, (Relation) right);
+        } else {
+            throw new RuntimeException(
+                    String
+                            .format(
+                                    "MERGE_FROM_AND_GET incompatible types: %s, %s",
+                                    left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+        }
+    }
+
+    private static <T extends Oaf> boolean sameClass(Object left, Object right, Class<T> cls) {
+        return cls.isAssignableFrom(left.getClass()) && cls.isAssignableFrom(right.getClass());
+    }
+
+    private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
+
+        if (sameClass(left, right, Result.class)) {
+            if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
+                return mergeResultsOfDifferentTypes((Result)left, (Result) right);
+            }
+
+            if (sameClass(left, right, Publication.class)) {
+                return mergePublication((Publication) left, (Publication) right);
+            }
+            if (sameClass(left, right, Dataset.class)) {
+                return mergeDataset((Dataset) left, (Dataset) right);
+            }
+            if (sameClass(left, right, OtherResearchProduct.class)) {
+                return mergeORP((OtherResearchProduct) left, (OtherResearchProduct) right);
+            }
+            if (sameClass(left, right, Software.class)) {
+                return mergeSoftware((Software) left, (Software) right);
+            }
+
+            return mergeResult((Result) left, (Result) right);
+        } else if (sameClass(left, right, Datasource.class)) {
+            // TODO
+            final int trust = compareTrust(left, right);
+            return mergeOafEntityFields((Datasource) left, (Datasource) right, trust);
+        } else if (sameClass(left, right, Organization.class)) {
+            return mergeOrganization((Organization) left, (Organization) right);
+        } else if (sameClass(left, right, Project.class)) {
+            return mergeProject((Project) left, (Project) right);
+        } else {
+            throw new RuntimeException(
+                    String
+                            .format(
+                                    "MERGE_FROM_AND_GET incompatible types: %s, %s",
+                                    left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+        }
+    }
+
+    /**
+     * This method is used in the global result grouping phase. It checks if one of the two is from a delegated authority
+     * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
+     * such version.
+     * <p>
+     * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
+     * and proceeds with the canonical property merging.
+     *
+     * @param left
+     * @param right
+     * @return
+     */
+    private static <T extends Result> T mergeResultsOfDifferentTypes(T left, T right) {
+
+        final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
+        final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
+
+        if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
+            return left;
+        }
+        if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
+            return right;
+        }
+        //TODO: raise trust to have preferred fields from one or the other??
+        if (new ResultTypeComparator().compare(left, right) < 0) {
+            return mergeResult(left, right);
+        } else {
+            return mergeResult(right, left);
+        }
+    }
+
+    private static DataInfo chooseDataInfo(DataInfo left, DataInfo right, int trust) {
+        if (trust > 0) {
+            return left;
+        } else if (trust == 0) {
+            if (left == null || (left.getInvisible() != null && left.getInvisible().equals(Boolean.TRUE))) {
+                return right;
+            } else {
+                return left;
+            }
+        } else {
+            return right;
+        }
+    }
+
+    private static String chooseString(String left, String right, int trust) {
+        if (trust > 0) {
+            return left;
+        } else if (trust == 0) {
+            return StringUtils.isNotBlank(left) ? left : right;
+        } else {
+            return right;
+        }
+    }
+
+    private static <T> T chooseReference(T left, T right, int trust) {
+        if (trust > 0) {
+            return left;
+        } else if (trust == 0) {
+            return left != null ? left : right;
+        } else {
+            return right;
+        }
+    }
+
+    private static Long max(Long left, Long right) {
+        if (left == null)
+            return right;
+        if (right == null)
+            return left;
+
+        return Math.max(left, right);
+    }
+
+    // trust ??
+    private static Boolean booleanOR(Boolean a, Boolean b) {
+        if (a == null) {
+            return b;
+        } else if (b == null) {
+            return a;
+        }
+
+        return a || b;
+    }
+
+
+    private static <T> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
+        if (left == null) {
+            return right;
+        } else if (right == null) {
+            return left;
+        }
+
+        List<T> h = trust >= 0 ? left : right;
+        List<T> l = trust >= 0 ? right : left;
+
+        return Stream.concat(h.stream(), l.stream())
+                .filter(Objects::nonNull)
+                .distinct()
+                .collect(Collectors.toList());
+    }
+
+    private static List<String> unionDistinctListOfString(final List<String> l, final List<String> r) {
+        if (l == null) {
+            return r;
+        } else if (r == null) {
+            return l;
+        }
+
+        return Stream.concat(l.stream(), r.stream())
+                .filter(StringUtils::isNotBlank)
+                .distinct()
+                .collect(Collectors.toList());
+    }
+
+    //TODO review
+    private static List<KeyValue> mergeKeyValue(List<KeyValue> left, List<KeyValue> right, int trust) {
+        if (trust < 0) {
+            List<KeyValue> s = left;
+            left = right;
+            right = s;
+        }
+
+        HashMap<String, KeyValue> values = new HashMap<>();
+        left.forEach(kv -> values.put(kv.getKey(), kv));
+        right.forEach(kv -> values.putIfAbsent(kv.getKey(), kv));
+
+        return new ArrayList<>(values.values());
+    }
+
+    private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right, int trust) {
+        if (left == null) {
+            return right;
+        } else if (right == null) {
+            return left;
+        }
+
+        List<StructuredProperty> h = trust >= 0 ? left : right;
+        List<StructuredProperty> l = trust >= 0 ? right : left;
+
+        return Stream.concat(h.stream(), l.stream())
+                .filter(Objects::isNull)
+                .distinct()
+                .collect(Collectors.toList());
+    }
+
+    /**
+     * Internal utility that merges the common OafEntity fields
+     *
+     * @param merged
+     * @param enrich
+     * @param <T>
+     * @return
+     */
+    private static <T extends Oaf> T mergeOafFields(T merged, T enrich, int trust) {
+
+        //TODO: union of all values, but what does it mean with KeyValue pairs???
+        merged.setCollectedfrom(mergeKeyValue(merged.getCollectedfrom(), enrich.getCollectedfrom(), trust));
+        merged.setDataInfo(chooseDataInfo(merged.getDataInfo(), enrich.getDataInfo(), trust));
+        merged.setLastupdatetimestamp(max(merged.getLastupdatetimestamp(), enrich.getLastupdatetimestamp()));
+
+        return merged;
+    }
+
+    /**
+     * Internal utility that merges the common OafEntity fields
+     *
+     * @param original
+     * @param enrich
+     * @param <T>
+     * @return
+     */
+    private static <T extends OafEntity> T mergeOafEntityFields(T original, T enrich, int trust) {
+        final T merged = mergeOafFields(original, enrich, trust);
+
+        merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId()));
+        merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust));
+        // dateofcollection mettere today quando si fa merge
+        merged.setDateofcollection(chooseString(merged.getDateofcollection(), enrich.getDateofcollection(), trust));
+        // setDateoftransformation mettere vuota in dedup, nota per Claudio
+        merged.setDateoftransformation(chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
+        // TODO: was missing in OafEntity.merge
+        merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
+        //oaiprovenanze da mettere a null quando si genera merge
+        merged.setOaiprovenance(chooseReference(merged.getOaiprovenance(), enrich.getOaiprovenance(), trust));
+        merged.setMeasures(unionDistinctLists(merged.getMeasures(), enrich.getMeasures(), trust));
+
+        return merged;
+    }
+
+
+    public static <T extends Relation>  T mergeRelation(T original, T enrich) {
+        int trust = compareTrust(original, enrich);
+        T merge = mergeOafFields(original, enrich, trust);
+
+        checkArgument(Objects.equals(merge.getSource(), enrich.getSource()), "source ids must be equal");
+        checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal");
+        checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal");
+        checkArgument(
+                Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
+        checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
+
+        //merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance()));
+
+        //TODO: trust ??
+        merge.setValidated(booleanOR(merge.getValidated(), enrich.getValidated()));
+        try {
+            merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate()));
+        } catch (ParseException e) {
+            throw new IllegalArgumentException(String
+                    .format(
+                            "invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
+                            merge.getTarget(),
+                            merge.getValidationDate()));
+        }
+
+        // TODO keyvalue merge
+        merge.setProperties(mergeKeyValue(merge.getProperties(), enrich.getProperties(), trust));
+
+        return merge;
+    }
+
+    public static <T extends Result> T mergeResult(T original, T enrich) {
+        final int trust = compareTrust(original, enrich);
+        T merge = mergeOafEntityFields(original, enrich, trust);
+
+        if (merge.getProcessingchargeamount() == null || StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
+            merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
+            merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
+        }
+
+        // author = usare la stessa logica che in dedup
+        merge.setAuthor(chooseReference(merge.getAuthor(), enrich.getAuthor(), trust));
+        // il primo che mi arriva secondo l'ordinamento per priorita'
+        merge.setResulttype(chooseReference(merge.getResulttype(), enrich.getResulttype(), trust));
+        // gestito come il resulttype perche' e' un subtype
+        merge.setMetaResourceType(chooseReference(merge.getMetaResourceType(), enrich.getMetaResourceType(), trust));
+        // spostiamo nell'instance e qui prendo il primo che arriva
+        merge.setLanguage(chooseReference(merge.getLanguage(), enrich.getLanguage(), trust));
+        // country lasicamo,o cosi' -> parentesi sul datainfo
+        merge.setCountry(unionDistinctLists(merge.getCountry(), enrich.getCountry(), trust));
+        //ok
+        merge.setSubject(unionDistinctLists(merge.getSubject(), enrich.getSubject(), trust));
+        // union per priority quindi vanno in append
+        merge.setTitle(unionTitle(merge.getTitle(), enrich.getTitle(), trust));
+        //ok
+        merge.setRelevantdate(unionDistinctLists(merge.getRelevantdate(), enrich.getRelevantdate(), trust));
+        // prima trust e poi longest list
+        merge.setDescription(longestLists(merge.getDescription(), enrich.getDescription()));
+        // trust piu' alto e poi piu' vecchia
+        merge.setDateofacceptance(chooseReference(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
+        // ok, ma publisher va messo ripetibile
+        merge.setPublisher(chooseReference(merge.getPublisher(), enrich.getPublisher(), trust));
+        // ok
+        merge.setEmbargoenddate(chooseReference(merge.getEmbargoenddate(), enrich.getEmbargoenddate(), trust));
+        // ok
+        merge.setSource(unionDistinctLists(merge.getSource(), enrich.getSource(), trust));
+        // ok
+        merge.setFulltext(unionDistinctLists(merge.getFulltext(), enrich.getFulltext(), trust));
+        // ok
+        merge.setFormat(unionDistinctLists(merge.getFormat(), enrich.getFormat(), trust));
+        // ok
+        merge.setContributor(unionDistinctLists(merge.getContributor(), enrich.getContributor(), trust));
+
+        // prima prendo l'higher trust, su questo prendo il valore migliore nelle istanze TODO
+        // trust maggiore ma a parita' di trust il piu' specifico (base del vocabolario)
+        // vedi note
+        merge.setResourcetype(firstNonNull(merge.getResourcetype(), enrich.getResourcetype()));
+
+        // ok
+        merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust));
+
+        // most open ok
+        if (enrich.getBestaccessright() != null
+                && new AccessRightComparator<>()
+                .compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) {
+            merge.setBestaccessright(enrich.getBestaccessright());
+        }
+
+        // TODO merge of datainfo given same id
+        merge.setContext(unionDistinctLists(merge.getContext(), enrich.getContext(), trust));
+
+        //ok
+        merge.setExternalReference(unionDistinctLists(merge.getExternalReference(), enrich.getExternalReference(), trust));
+
+        //instance enrichment or union
+        // review instance equals => add pid to comparision
+        if (!isAnEnrichment(merge) && !isAnEnrichment(enrich))
+            merge.setInstance(unionDistinctLists(merge.getInstance(), enrich.getInstance(), trust));
+        else {
+            final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
+                    : enrich.getInstance();
+            final List<Instance> enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance()
+                    : merge.getInstance();
+            if (isAnEnrichment(merge))
+                merge.setDataInfo(enrich.getDataInfo());
+            merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances));
+        }
+
+        merge.setEoscifguidelines(unionDistinctLists(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
+        merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen()));
+        // OK but should be list of values
+        merge.setOpenAccessColor(chooseReference(merge.getOpenAccessColor(), enrich.getOpenAccessColor(), trust));
+        merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal()));
+        merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded()));
+
+        return merge;
+    }
+
+    private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
+        int trust = compareTrust(original, enrich);
+        final T merge = mergeResult(original, enrich);
+
+        merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust));
+        merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust));
+        merge.setTool(unionDistinctLists(merge.getTool(), enrich.getTool(), trust));
+
+        return merge;
+    }
+
+    private static <T extends Software> T mergeSoftware(T original, T enrich) {
+        int trust = compareTrust(original, enrich);
+        final T merge = mergeResult(original, enrich);
+
+        merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
+        merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
+        merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
+        merge.setProgrammingLanguage(chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
+
+        return merge;
+    }
+
+    private static <T extends Dataset> T mergeDataset(T original, T enrich) {
+        int trust = compareTrust(original, enrich);
+        T merge = mergeResult(original, enrich);
+
+        merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust));
+        merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
+        merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
+        merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
+        merge.setLastmetadataupdate(chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+        merge.setMetadataversionnumber(chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
+        merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
+
+        return merge;
+    }
+
+    public static <T extends Publication> T mergePublication(T original, T enrich) {
+        final int trust = compareTrust(original, enrich);
+        T merged = mergeResult(original, enrich);
+
+        merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust));
+
+        return merged;
+    }
+
+    private static <T extends Organization> T mergeOrganization(T left, T enrich) {
+        int trust = compareTrust(left, enrich);
+        T merged = mergeOafEntityFields(left, enrich, trust);
+
+        merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
+        merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
+        merged.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
+        merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
+        merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
+        merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
+        merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
+        merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
+        merged.setEcresearchorganization(chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
+        merged.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+        merged.setEcinternationalorganizationeurinterests(chooseReference(merged.getEcinternationalorganizationeurinterests(), enrich.getEcinternationalorganizationeurinterests(), trust));
+        merged.setEcinternationalorganization(chooseReference(merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
+        merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
+        merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
+        merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
+        merged.setCountry(chooseReference(merged.getCountry(), enrich.getCountry(), trust));
+
+        return merged;
+    }
+
+    public static <T extends Project> T mergeProject(T original, T enrich) {
+        int trust = compareTrust(original, enrich);
+        T merged = mergeOafEntityFields(original, enrich, trust);
+
+        merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
+        merged.setCode(chooseReference(merged.getCode(), enrich.getCode(), trust));
+        merged.setAcronym(chooseReference(merged.getAcronym(), enrich.getAcronym(), trust));
+        merged.setTitle(chooseReference(merged.getTitle(), enrich.getTitle(), trust));
+        merged.setStartdate(chooseReference(merged.getStartdate(), enrich.getStartdate(), trust));
+        merged.setEnddate(chooseReference(merged.getEnddate(), enrich.getEnddate(), trust));
+        merged.setCallidentifier(chooseReference(merged.getCallidentifier(), enrich.getCallidentifier(), trust));
+        merged.setKeywords(chooseReference(merged.getKeywords(), enrich.getKeywords(), trust));
+        merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
+        merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
+        merged.setOamandatepublications(chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
+        merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
+        merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
+        merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
+        merged.setContracttype(chooseReference(merged.getContracttype(), enrich.getContracttype(), trust));
+        merged.setOptional1(chooseReference(merged.getOptional1(), enrich.getOptional1(), trust));
+        merged.setOptional2(chooseReference(merged.getOptional2(), enrich.getOptional2(), trust));
+        merged.setJsonextrainfo(chooseReference(merged.getJsonextrainfo(), enrich.getJsonextrainfo(), trust));
+        merged.setContactfullname(chooseReference(merged.getContactfullname(), enrich.getContactfullname(), trust));
+        merged.setContactfax(chooseReference(merged.getContactfax(), enrich.getContactfax(), trust));
+        merged.setContactphone(chooseReference(merged.getContactphone(), enrich.getContactphone(), trust));
+        merged.setContactemail(chooseReference(merged.getContactemail(), enrich.getContactemail(), trust));
+        merged.setSummary(chooseReference(merged.getSummary(), enrich.getSummary(), trust));
+        merged.setCurrency(chooseReference(merged.getCurrency(), enrich.getCurrency(), trust));
+
+        //missin in Project.merge
+        merged.setTotalcost(chooseReference(merged.getTotalcost(), enrich.getTotalcost(), trust));
+        merged.setFundedamount(chooseReference(merged.getFundedamount(), enrich.getFundedamount(), trust));
+
+        // trust ??
+        if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(merged.getH2020topiccode())) {
+            merged.setH2020topiccode(enrich.getH2020topiccode());
+            merged.setH2020topicdescription(enrich.getH2020topicdescription());
+        }
+
+        merged.setH2020classification(unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
+
+        return merged;
+    }
+
+
+    /**
+     * Longest lists list.
+     *
+     * @param a the a
+     * @param b the b
+     * @return the list
+     */
+    public static List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
+        if (a == null || b == null)
+            return a == null ? b : a;
+
+        return a.size() >= b.size() ? a : b;
+    }
+
+    /**
+     * This main method apply the enrichment of the instances
+     *
+     * @param toEnrichInstances   the instances that could be enriched
+     * @param enrichmentInstances the enrichment instances
+     * @return list of instances possibly enriched
+     */
+    private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,
+                                                  final List<Instance> enrichmentInstances) {
+        final List<Instance> enrichmentResult = new ArrayList<>();
+
+        if (toEnrichInstances == null) {
+            return enrichmentResult;
+        }
+        if (enrichmentInstances == null) {
+            return enrichmentResult;
+        }
+        Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
+
+        toEnrichInstances.forEach(i -> {
+            final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
+            if (e != null && e.size() > 0) {
+                e.forEach(enr -> applyEnrichment(i, enr));
+            } else {
+                final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
+                if (a != null && a.size() > 0) {
+                    a.forEach(enr -> applyEnrichment(i, enr));
+                }
+            }
+            enrichmentResult.add(i);
+        });
+        return enrichmentResult;
+    }
+
+    /**
+     * This method converts the list of instance enrichments
+     * into a Map where the key is the normalized identifier
+     * and the value is the instance itself
+     *
+     * @param ri the list of enrichment instances
+     * @return the result map
+     */
+    private static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
+        return ri
+                .stream()
+                .filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
+                .flatMap(i -> {
+                    final List<Pair<String, Instance>> result = new ArrayList<>();
+                    if (i.getPid() != null)
+                        i
+                                .getPid()
+                                .stream()
+                                .filter(MergeUtils::validPid)
+                                .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+                    if (i.getAlternateIdentifier() != null)
+                        i
+                                .getAlternateIdentifier()
+                                .stream()
+                                .filter(MergeUtils::validPid)
+                                .forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+                    return result.stream();
+                })
+                .collect(
+                        Collectors
+                                .toMap(
+                                        Pair::getLeft,
+                                        Pair::getRight,
+                                        (a, b) -> a));
+    }
+
+    private static boolean isFromDelegatedAuthority(Result r) {
+        return Optional
+                .ofNullable(r.getInstance())
+                .map(
+                        instance -> instance
+                                .stream()
+                                .filter(i -> Objects.nonNull(i.getCollectedfrom()))
+                                .map(i -> i.getCollectedfrom().getKey())
+                                .anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
+                .orElse(false);
+    }
+
+    /**
+     * Valid pid boolean.
+     *
+     * @param p the p
+     * @return the boolean
+     */
+    private static boolean validPid(final StructuredProperty p) {
+        return p.getValue() != null && p.getQualifier() != null && p.getQualifier().getClassid() != null;
+    }
+
+    /**
+     * Normalize pid string.
+     *
+     * @param pid the pid
+     * @return the string
+     */
+    private static String extractKeyFromPid(final StructuredProperty pid) {
+        if (pid == null)
+            return null;
+        final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
+
+        return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
+    }
+
+    /**
+     * This utility method finds the list of enrichment instances
+     * that match one or more PIDs in the input list
+     *
+     * @param pids        the list of PIDs
+     * @param enrichments the List of enrichment instances having the same pid
+     * @return the list
+     */
+    private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids,
+                                                       final Map<String, Instance> enrichments) {
+        if (pids == null || enrichments == null)
+            return null;
+        return pids
+                .stream()
+                .map(MergeUtils::extractKeyFromPid)
+                .map(enrichments::get)
+                .filter(Objects::nonNull)
+                .collect(Collectors.toList());
+    }
+
+    /**
+     * Is an enrichment boolean.
+     *
+     * @param e the e
+     * @return the boolean
+     */
+    private static boolean isAnEnrichment(OafEntity e) {
+        return e.getDataInfo() != null &&
+                e.getDataInfo().getProvenanceaction() != null
+                && ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
+    }
+
+    /**
+     * This method apply enrichment on a single instance
+     * The enrichment consists of replacing values on
+     * single attribute only if in the current instance is missing
+     * The only repeatable field enriched is measures
+     *
+     * @param merge the current instance
+     * @param enrichment      the enrichment instance
+     */
+    private static void applyEnrichment(final Instance merge, final Instance enrichment) {
+        if (merge == null || enrichment == null)
+            return;
+
+        merge.setLicense(firstNonNull(merge.getLicense(), enrichment.getLicense()));
+        merge.setAccessright(firstNonNull(merge.getAccessright(), enrichment.getAccessright()));
+        merge.setInstancetype(firstNonNull(merge.getInstancetype(), enrichment.getInstancetype()));
+        merge.setInstanceTypeMapping(firstNonNull(merge.getInstanceTypeMapping(), enrichment.getInstanceTypeMapping()));
+        merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
+        merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
+        merge.setDistributionlocation(firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
+        merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
+        // pid and alternateId are used for matching
+        merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
+        merge.setProcessingchargeamount(firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+        merge.setProcessingchargecurrency(firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
+        merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
+        merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
+        merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
+    }
+
+    private static int compareTrust(Oaf a, Oaf b) {
+        String left = Optional
+                .ofNullable(a.getDataInfo())
+                .map(DataInfo::getTrust)
+                .orElse("0.0");
+
+        String right = Optional
+                .ofNullable(b.getDataInfo())
+                .map(DataInfo::getTrust)
+                .orElse("0.0");
+
+        return left.compareTo(right);
+    }
+
+}

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

@@ -14,7 +14,6 @@ import java.util.stream.Collectors;
 import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class OafMapperUtils {
@@ -22,65 +21,6 @@ public class OafMapperUtils {
 	private OafMapperUtils() {
 	}
 
-	public static Oaf merge(final Oaf left, final Oaf right) {
-		if (ModelSupport.isSubClass(left, OafEntity.class)) {
-			return mergeEntities((OafEntity) left, (OafEntity) right);
-		} else if (ModelSupport.isSubClass(left, Relation.class)) {
-			((Relation) left).mergeFrom((Relation) right);
-		} else {
-			throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
-		}
-		return left;
-	}
-
-	public static OafEntity mergeEntities(OafEntity left, OafEntity right) {
-		if (ModelSupport.isSubClass(left, Result.class)) {
-			return mergeResults((Result) left, (Result) right);
-		} else if (ModelSupport.isSubClass(left, Datasource.class)) {
-			left.mergeFrom(right);
-		} else if (ModelSupport.isSubClass(left, Organization.class)) {
-			left.mergeFrom(right);
-		} else if (ModelSupport.isSubClass(left, Project.class)) {
-			left.mergeFrom(right);
-		} else {
-			throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
-		}
-		return left;
-	}
-
-	public static Result mergeResults(Result left, Result right) {
-
-		final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
-		final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
-
-		if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
-			return left;
-		}
-		if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
-			return right;
-		}
-
-		if (new ResultTypeComparator().compare(left, right) < 0) {
-			left.mergeFrom(right);
-			return left;
-		} else {
-			right.mergeFrom(left);
-			return right;
-		}
-	}
-
-	private static boolean isFromDelegatedAuthority(Result r) {
-		return Optional
-			.ofNullable(r.getInstance())
-			.map(
-				instance -> instance
-					.stream()
-					.filter(i -> Objects.nonNull(i.getCollectedfrom()))
-					.map(i -> i.getCollectedfrom().getKey())
-					.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
-			.orElse(false);
-	}
-
 	public static KeyValue keyValue(final String k, final String v) {
 		final KeyValue kv = new KeyValue();
 		kv.setKey(k);

dhp-common/src/main/resources/eu/dnetlib/dhp/oozie/run_sql_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "hmu",
+    "paramLongName": "hiveMetastoreUris",
+    "paramDescription": "the hive metastore uris",
+    "paramRequired": true
+  },
+  {
+    "paramName": "sql",
+    "paramLongName": "sql",
+    "paramDescription": "sql script to execute",
+    "paramRequired": true
+  }
+]

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

@@ -0,0 +1,111 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class MergeUtilsTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+
+	@Test
+	void testMergePubs() throws IOException {
+		Publication p1 = read("publication_1.json", Publication.class);
+		Publication p2 = read("publication_2.json", Publication.class);
+		Dataset d1 = read("dataset_1.json", Dataset.class);
+		Dataset d2 = read("dataset_2.json", Dataset.class);
+
+		assertEquals(1, p1.getCollectedfrom().size());
+		assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
+		assertEquals(1, d2.getCollectedfrom().size());
+		assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
+
+		assertEquals(1, p2.getCollectedfrom().size());
+		assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
+		assertEquals(1, d1.getCollectedfrom().size());
+		assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
+
+		final Result p1d2 = MergeUtils.checkedMerge(p1, d2);
+		assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,  p1d2.getResulttype().getClassid());
+		assertTrue(p1d2 instanceof Publication);
+		assertEquals(p1.getId(), p1d2.getId());
+	}
+
+	@Test
+	void testMergePubs_1() throws IOException {
+		Publication p2 = read("publication_2.json", Publication.class);
+		Dataset d1 = read("dataset_1.json", Dataset.class);
+
+		final Result p2d1 = MergeUtils.checkedMerge(p2, d1);
+		assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid());
+		assertTrue(p2d1 instanceof Dataset);
+		assertEquals(d1.getId(), p2d1.getId());
+		assertEquals(2, p2d1.getCollectedfrom().size());
+	}
+
+	@Test
+	void testMergePubs_2() throws IOException {
+		Publication p1 = read("publication_1.json", Publication.class);
+		Publication p2 = read("publication_2.json", Publication.class);
+
+		Result p1p2 = MergeUtils.checkedMerge(p1, p2);
+		assertTrue(p1p2 instanceof Publication);
+		assertEquals(p1.getId(), p1p2.getId());
+		assertEquals(2, p1p2.getCollectedfrom().size());
+	}
+
+	@Test
+	void testDelegatedAuthority_1() throws IOException {
+		Dataset d1 = read("dataset_2.json", Dataset.class);
+		Dataset d2 = read("dataset_delegated.json", Dataset.class);
+
+		assertEquals(1, d2.getCollectedfrom().size());
+		assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
+
+		Result res = (Result) MergeUtils.merge(d1, d2, true);
+
+		assertEquals(d2, res);
+	}
+
+	@Test
+	void testDelegatedAuthority_2() throws IOException {
+		Dataset p1 = read("publication_1.json", Dataset.class);
+		Dataset d2 = read("dataset_delegated.json", Dataset.class);
+
+		assertEquals(1, d2.getCollectedfrom().size());
+		assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
+
+		Result res = (Result) MergeUtils.merge(p1, d2, true);
+
+		assertEquals(d2, res);
+	}
+
+	protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
+		return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
+	}
+
+	protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {
+		final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
+		return OBJECT_MAPPER.readValue(json, clazz);
+	}
+
+}

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

@@ -149,7 +149,7 @@ class OafMapperUtilsTest {
 	void testDate() {
 		final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
 		assertNotNull(date);
-		System.out.println(date);
+		assertEquals("1998-02-23", date);
 	}
 
 	@Test
@@ -166,8 +166,8 @@ class OafMapperUtilsTest {
 
 		assertEquals(
 			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
-			OafMapperUtils
-				.mergeResults(p1, d2)
+			MergeUtils
+				.mergeResult(p1, d2)
 				.getResulttype()
 				.getClassid());
 
@@ -178,8 +178,8 @@ class OafMapperUtilsTest {
 
 		assertEquals(
 			ModelConstants.DATASET_RESULTTYPE_CLASSID,
-			OafMapperUtils
-				.mergeResults(p2, d1)
+			MergeUtils
+				.mergeResult(p2, d1)
 				.getResulttype()
 				.getClassid());
 	}
@@ -192,7 +192,7 @@ class OafMapperUtilsTest {
 		assertEquals(1, d2.getCollectedfrom().size());
 		assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
 
-		Result res = OafMapperUtils.mergeResults(d1, d2);
+		Result res = MergeUtils.mergeResult(d1, d2);
 
 		assertEquals(d2, res);
 

dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/InstanceTypeMatch.java

@@ -23,15 +23,18 @@ public class InstanceTypeMatch extends AbstractListComparator {
 
 		// jolly types
 		translationMap.put("Conference object", "*");
+		translationMap.put("Research", "*");
 		translationMap.put("Other literature type", "*");
 		translationMap.put("Unknown", "*");
 		translationMap.put("UNKNOWN", "*");
 
 		// article types
 		translationMap.put("Article", "Article");
+		translationMap.put("Journal", "Article");
 		translationMap.put("Data Paper", "Article");
 		translationMap.put("Software Paper", "Article");
 		translationMap.put("Preprint", "Article");
+		translationMap.put("Part of book or chapter of book", "Article");
 
 		// thesis types
 		translationMap.put("Thesis", "Thesis");

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java

@@ -1,14 +1,13 @@
 
 package eu.dnetlib.dhp.actionmanager.promote;
 
-import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
+import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 
 import java.util.function.BiFunction;
 
-import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
 
 /** OAF model merging support. */
 public class MergeAndGet {
@@ -46,20 +45,7 @@ public class MergeAndGet {
 	}
 
 	private static <G extends Oaf, A extends Oaf> G mergeFromAndGet(G x, A y) {
-		if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
-			((Relation) x).mergeFrom((Relation) y);
-			return x;
-		} else if (isSubClass(x, OafEntity.class)
-			&& isSubClass(y, OafEntity.class)
-			&& isSubClass(x, y)) {
-			((OafEntity) x).mergeFrom((OafEntity) y);
-			return x;
-		}
-		throw new RuntimeException(
-			String
-				.format(
-					"MERGE_FROM_AND_GET incompatible types: %s, %s",
-					x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
+		return (G) MergeUtils.merge(x, y);
 	}
 
 	@SuppressWarnings("unchecked")

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteAction.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.actionmanager.promote;
+
+/** Encodes the Actionset promotion strategies */
+public class PromoteAction {
+
+	/** The supported actionset promotion strategies
+	 *
+	 * ENRICH: promotes only records in the actionset matching another record in the
+	 *  graph and enriches them applying the given MergeAndGet strategy
+	 * UPSERT: promotes all the records in an actionset, matching records are updated
+	 *  using the given MergeAndGet strategy, the non-matching record as inserted as they are.
+	 */
+	public enum Strategy {
+		ENRICH, UPSERT
+	}
+
+	/**
+	 * Returns the string representation of the join type implementing the given PromoteAction.
+	 *
+	 * @param strategy the strategy to be used to promote the Actionset contents
+	 * @return the join type used to implement the promotion strategy
+	 */
+	public static String joinTypeForStrategy(PromoteAction.Strategy strategy) {
+		switch (strategy) {
+			case ENRICH:
+				return "left_outer";
+			case UPSERT:
+				return "full_outer";
+			default:
+				throw new IllegalStateException("unsupported PromoteAction: " + strategy.toString());
+		}
+	}
+}

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java

@@ -67,8 +67,9 @@ public class PromoteActionPayloadForGraphTableJob {
 		String outputGraphTablePath = parser.get("outputGraphTablePath");
 		logger.info("outputGraphTablePath: {}", outputGraphTablePath);
 
-		MergeAndGet.Strategy strategy = MergeAndGet.Strategy.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
-		logger.info("strategy: {}", strategy);
+		MergeAndGet.Strategy mergeAndGetStrategy = MergeAndGet.Strategy
+			.valueOf(parser.get("mergeAndGetStrategy").toUpperCase());
+		logger.info("mergeAndGetStrategy: {}", mergeAndGetStrategy);
 
 		Boolean shouldGroupById = Optional
 			.ofNullable(parser.get("shouldGroupById"))
@@ -76,6 +77,12 @@ public class PromoteActionPayloadForGraphTableJob {
 			.orElse(true);
 		logger.info("shouldGroupById: {}", shouldGroupById);
 
+		PromoteAction.Strategy promoteActionStrategy = Optional
+			.ofNullable(parser.get("promoteActionStrategy"))
+			.map(PromoteAction.Strategy::valueOf)
+			.orElse(PromoteAction.Strategy.UPSERT);
+		logger.info("promoteActionStrategy: {}", promoteActionStrategy);
+
 		@SuppressWarnings("unchecked")
 		Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
 		@SuppressWarnings("unchecked")
@@ -97,7 +104,8 @@ public class PromoteActionPayloadForGraphTableJob {
 					inputGraphTablePath,
 					inputActionPayloadPath,
 					outputGraphTablePath,
-					strategy,
+					mergeAndGetStrategy,
+					promoteActionStrategy,
 					rowClazz,
 					actionPayloadClazz,
 					shouldGroupById);
@@ -124,14 +132,16 @@ public class PromoteActionPayloadForGraphTableJob {
 		String inputGraphTablePath,
 		String inputActionPayloadPath,
 		String outputGraphTablePath,
-		MergeAndGet.Strategy strategy,
+		MergeAndGet.Strategy mergeAndGetStrategy,
+		PromoteAction.Strategy promoteActionStrategy,
 		Class<G> rowClazz,
 		Class<A> actionPayloadClazz, Boolean shouldGroupById) {
 		Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
 		Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
 
 		Dataset<G> result = promoteActionPayloadForGraphTable(
-			rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz, shouldGroupById)
+			rowDS, actionPayloadDS, mergeAndGetStrategy, promoteActionStrategy, rowClazz, actionPayloadClazz,
+			shouldGroupById)
 				.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
 
 		saveGraphTable(result, outputGraphTablePath);
@@ -183,7 +193,8 @@ public class PromoteActionPayloadForGraphTableJob {
 	private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(
 		Dataset<G> rowDS,
 		Dataset<A> actionPayloadDS,
-		MergeAndGet.Strategy strategy,
+		MergeAndGet.Strategy mergeAndGetStrategy,
+		PromoteAction.Strategy promoteActionStrategy,
 		Class<G> rowClazz,
 		Class<A> actionPayloadClazz,
 		Boolean shouldGroupById) {
@@ -195,8 +206,9 @@ public class PromoteActionPayloadForGraphTableJob {
 
 		SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
 		SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
-		SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
-		SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
+		SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet
+			.functionFor(mergeAndGetStrategy);
+		SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(mergeAndGetStrategy);
 		SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
 		SerializableSupplier<Function<G, Boolean>> isNotZeroFn = PromoteActionPayloadForGraphTableJob::isNotZeroFnUsingIdOrSourceAndTarget;
 
@@ -207,6 +219,7 @@ public class PromoteActionPayloadForGraphTableJob {
 				rowIdFn,
 				actionPayloadIdFn,
 				mergeRowWithActionPayloadAndGetFn,
+				promoteActionStrategy,
 				rowClazz,
 				actionPayloadClazz);
 

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java

@@ -34,6 +34,7 @@ public class PromoteActionPayloadFunctions {
 	 * @param rowIdFn Function used to get the id of graph table row
 	 * @param actionPayloadIdFn Function used to get id of action payload instance
 	 * @param mergeAndGetFn Function used to merge graph table row and action payload instance
+	 * @param promoteActionStrategy the Actionset promotion strategy
 	 * @param rowClazz Class of graph table
 	 * @param actionPayloadClazz Class of action payload
 	 * @param <G> Type of graph table row
@@ -46,6 +47,7 @@ public class PromoteActionPayloadFunctions {
 		SerializableSupplier<Function<G, String>> rowIdFn,
 		SerializableSupplier<Function<A, String>> actionPayloadIdFn,
 		SerializableSupplier<BiFunction<G, A, G>> mergeAndGetFn,
+		PromoteAction.Strategy promoteActionStrategy,
 		Class<G> rowClazz,
 		Class<A> actionPayloadClazz) {
 		if (!isSubClass(rowClazz, actionPayloadClazz)) {
@@ -61,7 +63,7 @@ public class PromoteActionPayloadFunctions {
 			.joinWith(
 				actionPayloadWithIdDS,
 				rowWithIdDS.col("_1").equalTo(actionPayloadWithIdDS.col("_1")),
-				"full_outer")
+				PromoteAction.joinTypeForStrategy(promoteActionStrategy))
 			.map(
 				(MapFunction<Tuple2<Tuple2<String, G>, Tuple2<String, A>>, G>) value -> {
 					Optional<G> rowOpt = Optional.ofNullable(value._1()).map(Tuple2::_2);

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json

@@ -41,6 +41,12 @@
     "paramDescription": "strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET",
     "paramRequired": true
   },
+  {
+    "paramName": "pas",
+    "paramLongName": "promoteActionStrategy",
+    "paramDescription": "strategy for promoting the actionset contents into the graph tables, ENRICH or UPSERT (default)",
+    "paramRequired": false
+  },
   {
     "paramName": "sgid",
     "paramLongName": "shouldGroupById",

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml

@@ -115,6 +115,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--outputGraphTablePath</arg><arg>${workingDir}/dataset</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="DecisionPromoteResultActionPayloadForDatasetTable"/>
@@ -167,6 +168,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/dataset</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml

@@ -106,6 +106,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/datasource</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml

@@ -106,6 +106,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/organization</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml

@@ -114,6 +114,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--outputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="DecisionPromoteResultActionPayloadForOtherResearchProductTable"/>
@@ -166,6 +167,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/otherresearchproduct</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml

@@ -106,6 +106,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/project</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml

@@ -115,6 +115,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--outputGraphTablePath</arg><arg>${workingDir}/publication</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="DecisionPromoteResultActionPayloadForPublicationTable"/>
@@ -167,6 +168,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/publication</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml

@@ -107,6 +107,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/relation</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml

@@ -114,6 +114,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--outputGraphTablePath</arg><arg>${workingDir}/software</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="DecisionPromoteResultActionPayloadForSoftwareTable"/>
@@ -166,6 +167,7 @@
             <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Result</arg>
             <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/software</arg>
             <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
             <arg>--shouldGroupById</arg><arg>${shouldGroupById}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java

@@ -54,7 +54,7 @@ public class PromoteActionPayloadFunctionsTest {
 				RuntimeException.class,
 				() -> PromoteActionPayloadFunctions
 					.joinGraphTableWithActionPayloadAndMerge(
-						null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
+						null, null, null, null, null, null, OafImplSubSub.class, OafImpl.class));
 		}
 
 		@Test
@@ -104,6 +104,7 @@ public class PromoteActionPayloadFunctionsTest {
 					rowIdFn,
 					actionPayloadIdFn,
 					mergeAndGetFn,
+					PromoteAction.Strategy.UPSERT,
 					OafImplSubSub.class,
 					OafImplSubSub.class)
 				.collectAsList();
@@ -183,6 +184,7 @@ public class PromoteActionPayloadFunctionsTest {
 					rowIdFn,
 					actionPayloadIdFn,
 					mergeAndGetFn,
+					PromoteAction.Strategy.UPSERT,
 					OafImplSubSub.class,
 					OafImplSub.class)
 				.collectAsList();

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java

@@ -64,6 +64,9 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String pubmedInputPath = parser.get("pubmedInputPath");
 		log.info("pubmedInputPath: {}", pubmedInputPath);
 
+		final String openapcInputPath = parser.get("openapcInputPath");
+		log.info("openapcInputPath: {}", openapcInputPath);
+
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -85,8 +88,14 @@ public class PrepareAffiliationRelations implements Serializable {
 				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
 					spark, pubmedInputPath, collectedFromPubmed);
 
+				List<KeyValue> collectedFromOpenAPC = OafMapperUtils
+					.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
+				JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
+					spark, openapcInputPath, collectedFromOpenAPC);
+
 				crossrefRelations
 					.union(pubmedRelations)
+					.union(openAPCRelations)
 					.saveAsHadoopFile(
 						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java

@@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 
 		return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
 			Project project = new Project();
-			project.setId(bipProjectScores.getProjectId());
+			//project.setId(bipProjectScores.getProjectId());
 			project.setMeasures(bipProjectScores.toMeasures());
 			return project;
 		}, Encoders.bean(Project.class))

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipmodel/score/deserializers/BipProjectModel.java

@@ -34,6 +34,11 @@ public class BipProjectModel {
 
 	String totalCitationCount;
 
+	public String getProjectId() {
+		return projectId;
+	}
+
+
 	// each project bip measure has exactly one value, hence one key-value pair
 	private Measure createMeasure(String measureId, String measureValue) {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java

@@ -1,12 +1,20 @@
 
 package eu.dnetlib.dhp.actionmanager.project;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.util.Arrays;
-import java.util.Objects;
-import java.util.Optional;
-
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.H2020Classification;
+import eu.dnetlib.dhp.schema.oaf.H2020Programme;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Project;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
+import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -18,24 +26,14 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
-import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
-import eu.dnetlib.dhp.actionmanager.project.utils.model.JsonTopic;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.H2020Classification;
-import eu.dnetlib.dhp.schema.oaf.H2020Programme;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Project;
-import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
+import java.util.Arrays;
+import java.util.Objects;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
 /**
  * Class that makes the ActionSet. To prepare the AS two joins are needed
  *
@@ -160,9 +158,11 @@ public class SparkAtomicActionJob {
 				(MapFunction<Project, String>) OafEntity::getId,
 				Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
-				Project first = it.next();
-				it.forEachRemaining(first::mergeFrom);
-				return first;
+				Project merge = it.next();
+				while (it.hasNext()) {
+					merge = MergeUtils.mergeProject(merge, it.next());
+				}
+				return merge;
 			}, Encoders.bean(Project.class))
 			.toJavaRDD()
 			.map(p -> new AtomicAction(Project.class, p))

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateActionSetSparkJob.java

@@ -0,0 +1,195 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+
+import org.apache.commons.cli.ParseException;
+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.api.java.JavaRDD;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Country;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
+import scala.Tuple2;
+
+public class CreateActionSetSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static final String IREL_PROJECT = "40|100018998___::1e5e62235d094afd01cd56e65112fc63";
+	private static final String TRANSFORMATIVE_AGREEMENT = "openapc::transformativeagreement";
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							CreateActionSetSparkJob.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> createActionSet(spark, inputPath, outputPath));
+
+	}
+
+	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
+		JavaRDD<AtomicAction> relations = spark
+				.read()
+				.textFile(inputPath)
+				.map(
+						(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
+								.readValue(value, TransformativeAgreementModel.class),
+						Encoders.bean(TransformativeAgreementModel.class))
+				.flatMap(
+						(FlatMapFunction<TransformativeAgreementModel, Relation>) value -> createRelation(
+								value)
+								.iterator(),
+						Encoders.bean(Relation.class))
+				.filter((FilterFunction<Relation>) Objects::nonNull)
+				.toJavaRDD()
+				.map(p -> new AtomicAction(p.getClass(), p));
+//TODO relations in stand-by waiting to know if we need to create them or not In case we need just make a union before saving the sequence file
+				spark
+					.read()
+					.textFile(inputPath)
+					.map(
+						(MapFunction<String, TransformativeAgreementModel>) value -> OBJECT_MAPPER
+							.readValue(value, TransformativeAgreementModel.class),
+						Encoders.bean(TransformativeAgreementModel.class))
+					.map(
+						(MapFunction<TransformativeAgreementModel, Result>) value -> createResult(
+							value),
+						Encoders.bean(Result.class))
+					.filter((FilterFunction<Result>) r -> r != null)
+					.toJavaRDD()
+					.map(p -> new AtomicAction(p.getClass(), p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+
+	}
+
+	private static Result createResult(TransformativeAgreementModel value) {
+		Result r = new Result();
+		r
+			.setId(
+				"50|doi_________::"
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi())));
+		r.setTransformativeAgreement(value.getAgreement());
+		Country country = new Country();
+		country.setClassid(value.getCountry());
+		country.setClassname(value.getCountry());
+		country
+			.setDataInfo(
+				OafMapperUtils
+					.dataInfo(
+						false, ModelConstants.SYSIMPORT_ACTIONSET, false, false,
+						OafMapperUtils
+							.qualifier(
+								"openapc::transformativeagreement",
+								"Harvested from Trnasformative Agreement file from OpenAPC",
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.9"));
+		country.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
+		country.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
+		r.setCountry(Arrays.asList(country));
+		return r;
+	}
+
+	private static List<Relation> createRelation(TransformativeAgreementModel value) {
+
+		List<Relation> relationList = new ArrayList<>();
+
+		if (value.getAgreement().startsWith("IReL")) {
+			String paper;
+
+			paper = "50|doi_________::"
+				+ IdentifierFactory
+					.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), value.getDoi()));
+
+			relationList
+				.add(
+					getRelation(
+						paper,
+						IREL_PROJECT, ModelConstants.IS_PRODUCED_BY));
+
+			relationList.add(getRelation(IREL_PROJECT, paper, ModelConstants.PRODUCES));
+		}
+		return relationList;
+	}
+
+	public static Relation getRelation(
+		String source,
+		String target,
+		String relClass) {
+
+		return OafMapperUtils
+			.getRelation(
+				source,
+				target,
+				ModelConstants.RESULT_PROJECT,
+				ModelConstants.OUTCOME,
+				relClass,
+				Arrays
+					.asList(
+						OafMapperUtils.keyValue(ModelConstants.OPEN_APC_ID, ModelConstants.OPEN_APC_NAME)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								TRANSFORMATIVE_AGREEMENT, "Transformative Agreement",
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.9"),
+				null);
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/model/TransformativeAgreementModel.java

@@ -0,0 +1,51 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement.model;
+
+import java.io.Serializable;
+
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+/**
+ * @author miriam.baglioni
+ * @Date 18/12/23
+ */
+@JsonIgnoreProperties(ignoreUnknown = true)
+
+public class TransformativeAgreementModel implements Serializable {
+	private String institution;
+	private String doi;
+	private String agreement;
+	private String country;
+
+	public String getCountry() {
+		return country;
+	}
+
+	public void setCountry(String country) {
+		this.country = country;
+	}
+
+	public String getInstitution() {
+		return institution;
+	}
+
+	public void setInstitution(String institution) {
+		this.institution = institution;
+	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
+
+	public String getAgreement() {
+		return agreement;
+	}
+
+	public void setAgreement(String agreement) {
+		this.agreement = agreement;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java

@@ -19,6 +19,7 @@ import org.slf4j.LoggerFactory;
 import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
 import eu.dnetlib.dhp.aggregation.common.ReportingJob;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
@@ -120,6 +121,8 @@ public class CollectorWorker extends ReportingJob {
 				return new FileCollectorPlugin(fileSystem);
 			case fileGzip:
 				return new FileGZipCollectorPlugin(fileSystem);
+			case baseDump:
+				return new BaseCollectorPlugin(this.fileSystem);
 			case other:
 				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(api.getParams().get("other_plugin_type"))

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDWorker.java

@@ -0,0 +1,244 @@
+
+package eu.dnetlib.dhp.collection.orcid;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.concurrent.BlockingQueue;
+
+import javax.swing.*;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.Text;
+import org.apache.http.HttpHeaders;
+import org.jetbrains.annotations.NotNull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class ORCIDWorker extends Thread {
+
+	final static Logger log = LoggerFactory.getLogger(ORCIDWorker.class);
+
+	public static String JOB_COMPLETE = "JOB_COMPLETE";
+
+	private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
+
+	private final BlockingQueue<String> queue;
+
+	private boolean hasComplete = false;
+
+	private final SequenceFile.Writer employments;
+
+	private final SequenceFile.Writer summary;
+	private final SequenceFile.Writer works;
+
+	private final String token;
+
+	private final String id;
+
+	public static ORCIDWorkerBuilder builder() {
+		return new ORCIDWorkerBuilder();
+	}
+
+	public ORCIDWorker(String id, BlockingQueue<String> myqueue, SequenceFile.Writer employments,
+		SequenceFile.Writer summary, SequenceFile.Writer works, String token) {
+		this.id = id;
+		this.queue = myqueue;
+		this.employments = employments;
+		this.summary = summary;
+		this.works = works;
+		this.token = token;
+	}
+
+	public static String retrieveURL(final String id, final String apiUrl, String token) {
+		try {
+			final HttpURLConnection urlConn = getHttpURLConnection(apiUrl, token);
+			if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) {
+				InputStream input = urlConn.getInputStream();
+				return IOUtils.toString(input);
+			} else {
+				log
+					.error(
+						"Thread {} UNABLE TO DOWNLOAD FROM THIS URL {} , status code {}", id, apiUrl,
+						urlConn.getResponseCode());
+			}
+		} catch (Exception e) {
+			log.error("Thread {}  Error on retrieving URL {} {}", id, apiUrl, e);
+		}
+		return null;
+	}
+
+	@NotNull
+	private static HttpURLConnection getHttpURLConnection(String apiUrl, String token) throws IOException {
+		final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiUrl).openConnection();
+		final HttpClientParams clientParams = new HttpClientParams();
+		urlConn.setInstanceFollowRedirects(false);
+		urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
+		urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
+		urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
+		urlConn.addRequestProperty(HttpHeaders.AUTHORIZATION, String.format("Bearer %s", token));
+		return urlConn;
+	}
+
+	private static String generateSummaryURL(final String orcidId) {
+		return "https://api.orcid.org/v3.0/" + orcidId + "/record";
+	}
+
+	private static String generateWorksURL(final String orcidId) {
+		return "https://api.orcid.org/v3.0/" + orcidId + "/works";
+	}
+
+	private static String generateEmploymentsURL(final String orcidId) {
+		return "https://api.orcid.org/v3.0/" + orcidId + "/employments";
+	}
+
+	private static void writeResultToSequenceFile(String id, String url, String token, String orcidId,
+		SequenceFile.Writer file) throws IOException {
+		final String response = retrieveURL(id, url, token);
+		if (response != null) {
+			if (orcidId == null) {
+				log.error("Thread {}   {}   {}", id, orcidId, response);
+				throw new RuntimeException("null items ");
+			}
+
+			if (file == null) {
+				log.error("Thread {}   file is null for {}  URL:{}", id, url, orcidId);
+			} else {
+				file.append(new Text(orcidId), new Text(response));
+				file.hflush();
+			}
+
+		} else
+			log.error("Thread {} response is null for {}  URL:{}", id, url, orcidId);
+
+	}
+
+	@Override
+	public void run() {
+		final Text key = new Text();
+		final Text value = new Text();
+		long start;
+		long total_time;
+		String orcidId = "";
+		int requests = 0;
+		if (summary == null || employments == null || works == null)
+			throw new RuntimeException("Null files");
+
+		while (!hasComplete) {
+			try {
+
+				orcidId = queue.take();
+
+				if (orcidId.equalsIgnoreCase(JOB_COMPLETE)) {
+					hasComplete = true;
+				} else {
+					start = System.currentTimeMillis();
+					writeResultToSequenceFile(id, generateSummaryURL(orcidId), token, orcidId, summary);
+					total_time = System.currentTimeMillis() - start;
+					requests++;
+					if (total_time < 1000) {
+						// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
+						// hence
+						// the time between two http request in a thread must be 1 second
+						Thread.sleep(1000L - total_time);
+					}
+					start = System.currentTimeMillis();
+					writeResultToSequenceFile(id, generateWorksURL(orcidId), token, orcidId, works);
+					total_time = System.currentTimeMillis() - start;
+					requests++;
+					if (total_time < 1000) {
+						// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
+						// hence
+						// the time between two http request in a thread must be 1 second
+						Thread.sleep(1000L - total_time);
+					}
+					start = System.currentTimeMillis();
+					writeResultToSequenceFile(id, generateEmploymentsURL(orcidId), token, orcidId, employments);
+					total_time = System.currentTimeMillis() - start;
+					requests++;
+					if (total_time < 1000) {
+						// I know making a sleep on a thread is bad, but we need to stay to 24 requests per seconds,
+						// hence
+						// the time between two http request in a thread must be 1 second
+						Thread.sleep(1000L - total_time);
+					}
+					if (requests % 30 == 0) {
+						log.info("Thread {}   Downloaded {}", id, requests);
+					}
+				}
+
+			} catch (Throwable e) {
+
+				log.error("Thread {}  Unable to save ORICD: {} item error", id, orcidId, e);
+
+			}
+
+		}
+		try {
+			works.close();
+			summary.close();
+			employments.close();
+		} catch (Throwable e) {
+			throw new RuntimeException(e);
+		}
+
+		log.info("Thread {}  COMPLETE ", id);
+		log.info("Thread {}   Downloaded {}", id, requests);
+
+	}
+
+	public static class ORCIDWorkerBuilder {
+
+		private String id;
+		private SequenceFile.Writer employments;
+		private SequenceFile.Writer summary;
+		private SequenceFile.Writer works;
+		private BlockingQueue<String> queue;
+
+		private String token;
+
+		public ORCIDWorkerBuilder withId(final String id) {
+			this.id = id;
+			return this;
+		}
+
+		public ORCIDWorkerBuilder withEmployments(final SequenceFile.Writer sequenceFile) {
+			this.employments = sequenceFile;
+			return this;
+		}
+
+		public ORCIDWorkerBuilder withSummary(final SequenceFile.Writer sequenceFile) {
+			this.summary = sequenceFile;
+			return this;
+		}
+
+		public ORCIDWorkerBuilder withWorks(final SequenceFile.Writer sequenceFile) {
+			this.works = sequenceFile;
+			return this;
+		}
+
+		public ORCIDWorkerBuilder withAccessToken(final String accessToken) {
+			this.token = accessToken;
+			return this;
+		}
+
+		public ORCIDWorkerBuilder withBlockingQueue(final BlockingQueue<String> queue) {
+			this.queue = queue;
+			return this;
+		}
+
+		public ORCIDWorker build() {
+			if (this.summary == null || this.works == null || this.employments == null || StringUtils.isEmpty(token)
+				|| queue == null)
+				throw new RuntimeException("Unable to build missing required params");
+			return new ORCIDWorker(id, queue, employments, summary, works, token);
+		}
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java

@@ -0,0 +1,171 @@
+
+package eu.dnetlib.dhp.collection.orcid;
+
+import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
+
+import java.io.*;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+import java.util.concurrent.ArrayBlockingQueue;
+import java.util.concurrent.BlockingQueue;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.fs.FSDataInputStream;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class OrcidGetUpdatesFile {
+
+	private static Logger log = LoggerFactory.getLogger(OrcidGetUpdatesFile.class);
+
+	public static void main(String[] args) throws Exception {
+
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							OrcidGetUpdatesFile.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json")))
+
+		);
+		parser.parseArgument(args);
+
+		final String namenode = parser.get("namenode");
+		log.info("got variable namenode: {}", namenode);
+
+		final String master = parser.get("master");
+		log.info("got variable master: {}", master);
+
+		final String targetPath = parser.get("targetPath");
+		log.info("got variable targetPath: {}", targetPath);
+
+		final String apiURL = parser.get("apiURL");
+		log.info("got variable apiURL: {}", apiURL);
+
+		final String accessToken = parser.get("accessToken");
+		log.info("got variable accessToken: {}", accessToken);
+
+		final String graphPath = parser.get("graphPath");
+		log.info("got variable graphPath: {}", graphPath);
+
+		final SparkSession spark = SparkSession
+			.builder()
+			.appName(OrcidGetUpdatesFile.class.getName())
+			.master(master)
+			.getOrCreate();
+
+		final String latestDate = spark
+			.read()
+			.load(graphPath + "/Authors")
+			.selectExpr("max(lastModifiedDate)")
+			.first()
+			.getString(0);
+
+		log.info("latest date is {}", latestDate);
+
+		final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(namenode));
+
+		new OrcidGetUpdatesFile().readTar(fileSystem, accessToken, apiURL, targetPath, latestDate);
+
+	}
+
+	private SequenceFile.Writer createFile(Path aPath, FileSystem fileSystem) throws IOException {
+		return SequenceFile
+			.createWriter(
+				fileSystem.getConf(),
+				SequenceFile.Writer.file(aPath),
+				SequenceFile.Writer.keyClass(Text.class),
+				SequenceFile.Writer.valueClass(Text.class));
+	}
+
+	private ORCIDWorker createWorker(final String id, final String targetPath, final BlockingQueue<String> queue,
+		final String accessToken, FileSystem fileSystem) throws Exception {
+		return ORCIDWorker
+			.builder()
+			.withId(id)
+			.withEmployments(createFile(new Path(String.format("%s/employments_%s", targetPath, id)), fileSystem))
+			.withSummary(createFile(new Path(String.format("%s/summary_%s", targetPath, id)), fileSystem))
+			.withWorks(createFile(new Path(String.format("%s/works_%s", targetPath, id)), fileSystem))
+			.withAccessToken(accessToken)
+			.withBlockingQueue(queue)
+			.build();
+	}
+
+	public void readTar(FileSystem fileSystem, final String accessToken, final String apiURL, final String targetPath,
+		final String startDate) throws Exception {
+		final HttpURLConnection urlConn = (HttpURLConnection) new URL(apiURL).openConnection();
+		final HttpClientParams clientParams = new HttpClientParams();
+		urlConn.setInstanceFollowRedirects(false);
+		urlConn.setReadTimeout(clientParams.getReadTimeOut() * 1000);
+		urlConn.setConnectTimeout(clientParams.getConnectTimeOut() * 1000);
+		if (urlConn.getResponseCode() > 199 && urlConn.getResponseCode() < 300) {
+			InputStream input = urlConn.getInputStream();
+
+			Path hdfsWritePath = new Path("/tmp/orcid_updates.tar.gz");
+			final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true);
+			IOUtils.copy(input, fsDataOutputStream);
+			fsDataOutputStream.flush();
+			fsDataOutputStream.close();
+			FSDataInputStream updateFile = fileSystem.open(hdfsWritePath);
+			TarArchiveInputStream tais = new TarArchiveInputStream(new GzipCompressorInputStream(
+				new BufferedInputStream(
+					updateFile.getWrappedStream())));
+			TarArchiveEntry entry;
+
+			BlockingQueue<String> queue = new ArrayBlockingQueue<String>(3000);
+			final List<ORCIDWorker> workers = new ArrayList<>();
+			for (int i = 0; i < 22; i++) {
+				workers.add(createWorker("" + i, targetPath, queue, accessToken, fileSystem));
+			}
+			workers.forEach(Thread::start);
+
+			while ((entry = tais.getNextTarEntry()) != null) {
+
+				if (entry.isFile()) {
+
+					BufferedReader br = new BufferedReader(new InputStreamReader(tais));
+					System.out.println(br.readLine());
+					br
+						.lines()
+						.map(l -> l.split(","))
+						.filter(s -> StringUtils.compare(s[3].substring(0, 10), startDate) > 0)
+						.map(s -> s[0])
+						.forEach(s -> {
+							try {
+								queue.put(s);
+							} catch (InterruptedException e) {
+								throw new RuntimeException(e);
+							}
+						});
+
+				}
+			}
+
+			for (int i = 0; i < 22; i++) {
+				queue.put(ORCIDWorker.JOB_COMPLETE);
+			}
+			for (ORCIDWorker worker : workers) {
+				worker.join();
+			}
+		}
+
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java

@@ -1,11 +1,15 @@
 
 package eu.dnetlib.dhp.collection.orcid;
 
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
+import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
+import org.dom4j.Document;
+import org.dom4j.DocumentFactory;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Node;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -40,8 +44,8 @@ public class OrcidParser {
 	private static final String NS_ERROR = "error";
 	private static final String NS_HISTORY = "history";
 	private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history";
-	private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk";
-	private static final String NS_BULK = "bulk";
+	private static final String NS_EMPLOYMENT = "employment";
+	private static final String NS_EMPLOYMENT_URL = "http://www.orcid.org/ns/employment";
 	private static final String NS_EXTERNAL = "external-identifier";
 	private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier";
 
@@ -61,6 +65,7 @@ public class OrcidParser {
 		ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
 		ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL);
 		ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL);
+		ap.declareXPathNameSpace(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
 	}
 
 	public Author parseSummary(final String xml) {
@@ -70,13 +75,15 @@ public class OrcidParser {
 			generateParsedDocument(xml);
 			List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
 				.getTextValuesWithAttributes(
-					ap, vn, "//record:record", Arrays.asList("path"));
+					ap, vn, "//record:record", Collections.singletonList("path"));
 			if (!recordNodes.isEmpty()) {
 				final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
 				author.setOrcid(oid);
 			} else {
 				return null;
 			}
+			final String ltm = VtdUtilityParser.getSingleValue(ap, vn, "//common:last-modified-date");
+			author.setLastModifiedDate(ltm);
 			List<VtdUtilityParser.Node> personNodes = VtdUtilityParser
 				.getTextValuesWithAttributes(
 					ap, vn, "//person:name", Arrays.asList("visibility"));
@@ -129,6 +136,64 @@ public class OrcidParser {
 		}
 	}
 
+	public List<Work> parseWorks(final String xml) {
+
+		try {
+			String oid;
+
+			generateParsedDocument(xml);
+			List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
+				.getTextValuesWithAttributes(ap, vn, "//activities:works", Arrays.asList("path", "visibility"));
+			if (!workNodes.isEmpty()) {
+				oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
+
+			} else {
+				return null;
+			}
+			final List<Work> works = new ArrayList<>();
+			ap.selectXPath("//work:work-summary");
+
+			while (ap.evalXPath() != -1) {
+				final Work work = new Work();
+				work.setOrcid(oid);
+				final AutoPilot ap1 = new AutoPilot(ap.getNav());
+				ap1.selectXPath("./work:title/common:title");
+				while (ap1.evalXPath() != -1) {
+					int it = vn.getText();
+					work.setTitle(vn.toNormalizedString(it));
+				}
+				ap1.selectXPath(".//common:external-id");
+				while (ap1.evalXPath() != -1) {
+					final Pid pid = new Pid();
+
+					final AutoPilot ap2 = new AutoPilot(ap1.getNav());
+
+					ap2.selectXPath("./common:external-id-type");
+					while (ap2.evalXPath() != -1) {
+						int it = vn.getText();
+						pid.setSchema(vn.toNormalizedString(it));
+					}
+					ap2.selectXPath("./common:external-id-value");
+					while (ap2.evalXPath() != -1) {
+						int it = vn.getText();
+						pid.setValue(vn.toNormalizedString(it));
+					}
+
+					work.addPid(pid);
+				}
+
+				works.add(work);
+			}
+			return works;
+
+		} catch (Throwable e) {
+			log.error("Error on parsing {}", xml);
+			log.error(e.getMessage());
+			return null;
+		}
+
+	}
+
 	public Work parseWork(final String xml) {
 
 		try {
@@ -176,11 +241,15 @@ public class OrcidParser {
 	}
 
 	private String extractEmploymentDate(final String xpath) throws Exception {
+		return extractEmploymentDate(xpath, ap);
+	}
 
-		ap.selectXPath(xpath);
+	private String extractEmploymentDate(final String xpath, AutoPilot pp) throws Exception {
+
+		pp.selectXPath(xpath);
 		StringBuilder sb = new StringBuilder();
-		while (ap.evalXPath() != -1) {
-			final AutoPilot ap1 = new AutoPilot(ap.getNav());
+		while (pp.evalXPath() != -1) {
+			final AutoPilot ap1 = new AutoPilot(pp.getNav());
 			ap1.selectXPath("./common:year");
 			while (ap1.evalXPath() != -1) {
 				int it = vn.getText();
@@ -203,6 +272,104 @@ public class OrcidParser {
 
 	}
 
+	public List<Employment> parseEmployments(final String xml) {
+		try {
+			String oid;
+			Map<String, String> nsContext = getNameSpaceMap();
+			DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
+			Document doc = DocumentHelper.parseText(xml);
+			oid = doc.valueOf("//activities:employments/@path");
+			if (oid == null || StringUtils.isEmpty(oid))
+				return null;
+			final String orcid = oid.split("/")[1];
+
+			List<Node> nodes = doc.selectNodes("//employment:employment-summary");
+			return nodes.stream().map(n -> {
+				final Employment e = new Employment();
+				e.setOrcid(orcid);
+
+				final String depName = n.valueOf(".//common:department-name");
+				if (StringUtils.isNotBlank(depName))
+					e.setDepartmentName(depName);
+				final String roleTitle = n.valueOf(".//common:role-title");
+				e.setRoleTitle(roleTitle);
+				final String organizationName = n.valueOf(".//common:organization/common:name");
+				if (StringUtils.isEmpty(e.getDepartmentName()))
+					e.setDepartmentName(organizationName);
+				final Pid p = new Pid();
+				final String pid = n
+					.valueOf(
+						"./common:organization/common:disambiguated-organization/common:disambiguated-organization-identifier");
+				p.setValue(pid);
+				final String pidType = n
+					.valueOf("./common:organization/common:disambiguated-organization/common:disambiguation-source");
+				p.setSchema(pidType);
+				e.setAffiliationId(p);
+
+				final StringBuilder aDate = new StringBuilder();
+				final String sy = n.valueOf("./common:start-date/common:year");
+				if (StringUtils.isNotBlank(sy)) {
+					aDate.append(sy);
+					final String sm = n.valueOf("./common:start-date/common:month");
+					final String sd = n.valueOf("./common:start-date/common:day");
+					aDate.append("-");
+					if (StringUtils.isNotBlank(sm))
+						aDate.append(sm);
+					else
+						aDate.append("01");
+					aDate.append("-");
+					if (StringUtils.isNotBlank(sd))
+						aDate.append(sd);
+					else
+						aDate.append("01");
+					e.setEndDate(aDate.toString());
+				}
+
+				final String ey = n.valueOf("./common:end-date/common:year");
+				if (StringUtils.isNotBlank(ey)) {
+					aDate.append(ey);
+					final String em = n.valueOf("./common:end-date/common:month");
+					final String ed = n.valueOf("./common:end-date/common:day");
+					aDate.append("-");
+					if (StringUtils.isNotBlank(em))
+						aDate.append(em);
+					else
+						aDate.append("01");
+					aDate.append("-");
+					if (StringUtils.isNotBlank(ed))
+						aDate.append(ed);
+					else
+						aDate.append("01");
+					e.setEndDate(aDate.toString());
+				}
+
+				return e;
+
+			}).collect(Collectors.toList());
+		} catch (Throwable e) {
+			log.error("Error on parsing {}", xml);
+			log.error(e.getMessage());
+			return null;
+		}
+	}
+
+	@NotNull
+	private static Map<String, String> getNameSpaceMap() {
+		Map<String, String> nsContext = new HashMap<>();
+		nsContext.put(NS_COMMON, NS_COMMON_URL);
+		nsContext.put(NS_PERSON, NS_PERSON_URL);
+		nsContext.put(NS_DETAILS, NS_DETAILS_URL);
+		nsContext.put(NS_OTHER, NS_OTHER_URL);
+		nsContext.put(NS_RECORD, NS_RECORD_URL);
+		nsContext.put(NS_ERROR, NS_ERROR_URL);
+		nsContext.put(NS_HISTORY, NS_HISTORY_URL);
+		nsContext.put(NS_WORK, NS_WORK_URL);
+		nsContext.put(NS_EXTERNAL, NS_EXTERNAL_URL);
+		nsContext.put(NS_ACTIVITIES, NS_ACTIVITIES_URL);
+		nsContext.put(NS_EMPLOYMENT, NS_EMPLOYMENT_URL);
+		return nsContext;
+	}
+
 	public Employment parseEmployment(final String xml) {
 		try {
 			final Employment employment = new Employment();

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java

@@ -18,6 +18,8 @@ public class Author extends ORCIDItem {
 
 	private String biography;
 
+	private String lastModifiedDate;
+
 	public String getBiography() {
 		return biography;
 	}
@@ -74,6 +76,14 @@ public class Author extends ORCIDItem {
 		this.otherPids = otherPids;
 	}
 
+	public String getLastModifiedDate() {
+		return lastModifiedDate;
+	}
+
+	public void setLastModifiedDate(String lastModifiedDate) {
+		this.lastModifiedDate = lastModifiedDate;
+	}
+
 	public void addOtherPid(final Pid pid) {
 
 		if (otherPids == null)

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

@@ -10,7 +10,8 @@ import eu.dnetlib.dhp.common.collection.CollectorException;
 public interface CollectorPlugin {
 
 	enum NAME {
-		oai, other, rest_json2xml, file, fileGzip;
+
+		oai, other, rest_json2xml, file, fileGzip, baseDump;
 
 		public enum OTHER_NAME {
 			mdstore_mongodb_dump, mdstore_mongodb

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIterator.java

@@ -0,0 +1,171 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import java.io.BufferedInputStream;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.Iterator;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.LinkedBlockingQueue;
+
+import javax.xml.stream.XMLEventReader;
+import javax.xml.stream.XMLEventWriter;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLOutputFactory;
+import javax.xml.stream.events.EndElement;
+import javax.xml.stream.events.StartElement;
+import javax.xml.stream.events.XMLEvent;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.compress.compressors.CompressorInputStream;
+import org.apache.commons.compress.compressors.CompressorStreamFactory;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+
+public class BaseCollectorIterator implements Iterator<String> {
+
+	private String nextElement;
+
+	private final BlockingQueue<String> queue = new LinkedBlockingQueue<>(100);
+
+	private static final Logger log = LoggerFactory.getLogger(BaseCollectorIterator.class);
+
+	private static final String END_ELEM = "__END__";
+
+	public BaseCollectorIterator(final FileSystem fs, final Path filePath, final AggregatorReport report) {
+		new Thread(() -> importHadoopFile(fs, filePath, report)).start();
+		try {
+			this.nextElement = this.queue.take();
+		} catch (final InterruptedException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	protected BaseCollectorIterator(final String resourcePath, final AggregatorReport report) {
+		new Thread(() -> importTestFile(resourcePath, report)).start();
+		try {
+			this.nextElement = this.queue.take();
+		} catch (final InterruptedException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	@Override
+	public synchronized boolean hasNext() {
+		return (this.nextElement != null) & !END_ELEM.equals(this.nextElement);
+	}
+
+	@Override
+	public synchronized String next() {
+		try {
+			return END_ELEM.equals(this.nextElement) ? null : this.nextElement;
+		} finally {
+			try {
+				this.nextElement = this.queue.take();
+			} catch (final InterruptedException e) {
+				throw new RuntimeException(e);
+			}
+		}
+
+	}
+
+	private void importHadoopFile(final FileSystem fs, final Path filePath, final AggregatorReport report) {
+		log.info("I start to read the TAR stream");
+
+		try (InputStream origInputStream = fs.open(filePath);
+			final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
+			importTarStream(tarInputStream, report);
+		} catch (final Throwable e) {
+			throw new RuntimeException("Error processing BASE records", e);
+		}
+	}
+
+	private void importTestFile(final String resourcePath, final AggregatorReport report) {
+		try (final InputStream origInputStream = BaseCollectorIterator.class.getResourceAsStream(resourcePath);
+			final TarArchiveInputStream tarInputStream = new TarArchiveInputStream(origInputStream)) {
+			importTarStream(tarInputStream, report);
+		} catch (final Throwable e) {
+			throw new RuntimeException("Error processing BASE records", e);
+		}
+	}
+
+	private void importTarStream(final TarArchiveInputStream tarInputStream, final AggregatorReport report) {
+		long count = 0;
+
+		final XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();
+		final XMLOutputFactory xmlOutputFactory = XMLOutputFactory.newInstance();
+
+		try {
+			TarArchiveEntry entry;
+			while ((entry = (TarArchiveEntry) tarInputStream.getNextEntry()) != null) {
+				final String name = entry.getName();
+
+				if (!entry.isDirectory() && name.contains("ListRecords") && name.endsWith(".bz2")) {
+
+					log.info("Processing file (BZIP): " + name);
+
+					final byte[] bzipData = new byte[(int) entry.getSize()];
+					IOUtils.readFully(tarInputStream, bzipData);
+
+					try (InputStream bzipIs = new ByteArrayInputStream(bzipData);
+						final BufferedInputStream bzipBis = new BufferedInputStream(bzipIs);
+						final CompressorInputStream bzipInput = new CompressorStreamFactory()
+							.createCompressorInputStream(bzipBis)) {
+
+						final XMLEventReader reader = xmlInputFactory.createXMLEventReader(bzipInput);
+
+						XMLEventWriter eventWriter = null;
+						StringWriter xmlWriter = null;
+
+						while (reader.hasNext()) {
+							final XMLEvent nextEvent = reader.nextEvent();
+
+							if (nextEvent.isStartElement()) {
+								final StartElement startElement = nextEvent.asStartElement();
+								if ("record".equals(startElement.getName().getLocalPart())) {
+									xmlWriter = new StringWriter();
+									eventWriter = xmlOutputFactory.createXMLEventWriter(xmlWriter);
+								}
+							}
+
+							if (eventWriter != null) {
+								eventWriter.add(nextEvent);
+							}
+
+							if (nextEvent.isEndElement()) {
+								final EndElement endElement = nextEvent.asEndElement();
+								if ("record".equals(endElement.getName().getLocalPart())) {
+									eventWriter.flush();
+									eventWriter.close();
+
+									this.queue.put(xmlWriter.toString());
+
+									eventWriter = null;
+									xmlWriter = null;
+									count++;
+								}
+							}
+
+						}
+					}
+				}
+			}
+
+			this.queue.put(END_ELEM); // TO INDICATE THE END OF THE QUEUE
+		} catch (final Throwable e) {
+			log.error("Error processing BASE records", e);
+			report.put(e.getClass().getName(), e.getMessage());
+			throw new RuntimeException("Error processing BASE records", e);
+		} finally {
+			log.info("Total records (written in queue): " + count);
+		}
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPlugin.java

@@ -0,0 +1,159 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Optional;
+import java.util.Set;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Node;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.file.AbstractSplittedRecordPlugin;
+import eu.dnetlib.dhp.common.DbClient;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class BaseCollectorPlugin implements CollectorPlugin {
+
+	private final FileSystem fs;
+
+	private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class);
+
+	// MAPPING AND FILTERING ARE DEFINED HERE:
+	// https://docs.google.com/document/d/1Aj-ZAV11b44MCrAAUCPiS2TUlXb6PnJEu1utCMAcCOU/edit
+
+	public BaseCollectorPlugin(final FileSystem fs) {
+		this.fs = fs;
+	}
+
+	@Override
+	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
+		// the path of the dump file on HDFS
+		// http://oai.base-search.net/initial_load/base_oaipmh_dump-current.tar
+		// it could be downloaded from iis-cdh5-test-gw.ocean.icm.edu.pl and then copied on HDFS
+		final Path filePath = Optional
+			.ofNullable(api.getBaseUrl())
+			.map(Path::new)
+			.orElseThrow(() -> new CollectorException("missing baseUrl"));
+
+		// get the parameters for the connection to the OpenAIRE database.
+		// the database is used to obtain the list of the datasources that the plugin will collect
+		final String dbUrl = api.getParams().get("dbUrl");
+		final String dbUser = api.getParams().get("dbUser");
+		final String dbPassword = api.getParams().get("dbPassword");
+
+		// the types(comma separated, empty value for all) that the plugin will collect,
+		// the types should be expressed in the format of the normalized types of BASE (for example 1,121,...)
+		final String acceptedNormTypesString = api.getParams().get("acceptedNormTypes");
+
+		log.info("baseUrl: {}", filePath);
+		log.info("dbUrl: {}", dbUrl);
+		log.info("dbUser: {}", dbUser);
+		log.info("dbPassword: {}", "***");
+		log.info("acceptedNormTypes: {}", acceptedNormTypesString);
+
+		try {
+			if (!this.fs.exists(filePath)) {
+				throw new CollectorException("path does not exist: " + filePath);
+			}
+		} catch (final Throwable e) {
+			throw new CollectorException(e);
+		}
+
+		final Set<String> acceptedOpendoarIds = findAcceptedOpendoarIds(dbUrl, dbUser, dbPassword);
+
+		final Set<String> acceptedNormTypes = new HashSet<>();
+		if (StringUtils.isNotBlank(acceptedNormTypesString)) {
+			for (final String s : StringUtils.split(acceptedNormTypesString, ",")) {
+				if (StringUtils.isNotBlank(s)) {
+					acceptedNormTypes.add(s.trim());
+				}
+			}
+		}
+
+		final Iterator<String> iterator = new BaseCollectorIterator(this.fs, filePath, report);
+		final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
+		return StreamSupport
+			.stream(spliterator, false)
+			.filter(doc -> filterXml(doc, acceptedOpendoarIds, acceptedNormTypes));
+	}
+
+	private Set<String> findAcceptedOpendoarIds(final String dbUrl, final String dbUser, final String dbPassword)
+		throws CollectorException {
+		final Set<String> accepted = new HashSet<>();
+
+		try (final DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
+
+			final String sql = IOUtils
+				.toString(
+					getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql"));
+
+			dbClient.processResults(sql, row -> {
+				try {
+					final String dsId = row.getString("id");
+					log.info("Accepted Datasource: " + dsId);
+					accepted.add(dsId);
+				} catch (final SQLException e) {
+					log.error("Error in SQL", e);
+					throw new RuntimeException("Error in SQL", e);
+				}
+			});
+
+		} catch (final IOException e) {
+			log.error("Error accessong SQL", e);
+			throw new CollectorException("Error accessong SQL", e);
+		}
+
+		log.info("Accepted Datasources (TOTAL): " + accepted.size());
+
+		return accepted;
+	}
+
+	protected static boolean filterXml(final String xml,
+		final Set<String> acceptedOpendoarIds,
+		final Set<String> acceptedNormTypes) {
+		try {
+
+			final Document doc = DocumentHelper.parseText(xml);
+
+			final String id = doc.valueOf("//*[local-name()='collection']/@opendoar_id").trim();
+
+			if (StringUtils.isBlank(id) || !acceptedOpendoarIds.contains("opendoar____::" + id)) {
+				return false;
+			}
+
+			if (acceptedNormTypes.isEmpty()) {
+				return true;
+			}
+
+			for (final Object s : doc.selectNodes("//*[local-name()='typenorm']")) {
+				if (acceptedNormTypes.contains(((Node) s).getText().trim())) {
+					return true;
+				}
+			}
+
+			return false;
+		} catch (final DocumentException e) {
+			log.error("Error parsing document", e);
+			throw new RuntimeException("Error parsing document", e);
+		}
+	}
+
+}

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

@@ -52,8 +52,6 @@ public class RestIterator implements Iterator<String> {
 
 	private final String BASIC = "basic";
 
-	private final JsonUtils jsonUtils;
-
 	private final String baseUrl;
 	private final String resumptionType;
 	private final String resumptionParam;
@@ -106,7 +104,6 @@ public class RestIterator implements Iterator<String> {
 		final String resultOutputFormat) {
 
 		this.clientParams = clientParams;
-		this.jsonUtils = new JsonUtils();
 		this.baseUrl = baseUrl;
 		this.resumptionType = resumptionType;
 		this.resumptionParam = resumptionParam;
@@ -126,6 +123,7 @@ public class RestIterator implements Iterator<String> {
 		} catch (Exception e) {
 			throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
 		}
+
 		initQueue();
 	}
 
@@ -190,7 +188,7 @@ public class RestIterator implements Iterator<String> {
 		String resultJson;
 		String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
 		String nextQuery = "";
-		String emptyXml = resultXml + "<" + JsonUtils.wrapName + "></" + JsonUtils.wrapName + ">";
+		String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
 		Node resultNode = null;
 		NodeList nodeList = null;
 		String qUrlArgument = "";
@@ -231,7 +229,7 @@ public class RestIterator implements Iterator<String> {
 			resultStream = theHttpInputStream;
 			if ("json".equals(resultOutputFormat)) {
 				resultJson = IOUtils.toString(resultStream, StandardCharsets.UTF_8);
-				resultXml = jsonUtils.convertToXML(resultJson);
+				resultXml = JsonUtils.convertToXML(resultJson);
 				resultStream = IOUtils.toInputStream(resultXml, UTF_8);
 			}
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java

@@ -3,82 +3,142 @@ package eu.dnetlib.dhp.collection.plugin.utils;
 
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
+import org.json.JSONArray;
+import org.json.JSONObject;
 
 public class JsonUtils {
+	public static final String XML_WRAP_TAG = "recordWrap";
+	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+	private static final String INVALID_XMLTAG_CHARS = "!\"#$%&'()*+,/;<=>?@[\\]^`{|}~,";
 
 	private static final Log log = LogFactory.getLog(JsonUtils.class);
 
-	public static final String wrapName = "recordWrap";
-
 	/**
-	 * convert in JSON-KeyName 'whitespace(s)' to '_' and '/' to '_', '(' and ')' to ''
+	 * cleanup in JSON-KeyName
 	 * check W3C XML syntax: https://www.w3.org/TR/2006/REC-xml11-20060816/#sec-starttags for valid tag names
 	 * and work-around for the JSON to XML converting of org.json.XML-package.
 	 *
-	 * known bugs:     doesn't prevent     "key name":" ["sexy name",": penari","erotic dance"],
-	 *
-	 * @param jsonInput
-	 * @return convertedJsonKeynameOutput
+	 * @param input
+	 * @return converted json object
 	 */
-	public String syntaxConvertJsonKeyNames(String jsonInput) {
-
-		log.trace("before convertJsonKeyNames: " + jsonInput);
-		// pre-clean json - rid spaces of element names (misinterpreted as elements with attributes in xml)
-		// replace ' 's in JSON Namens with '_'
-		while (jsonInput.matches(".*\"([^\"]*)\\s+([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*)\\s+([^\"]*)\":", "\"$1_$2\":");
+	public static JSONObject cleanJsonObject(final JSONObject input) {
+		if (null == input) {
+			return null;
 		}
 
-		// replace forward-slash (sign '/' ) in JSON Names with '_'
-		while (jsonInput.matches(".*\"([^\"]*)/([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*)/([^\"]*)\":", "\"$1_$2\":");
+		JSONObject result = new JSONObject();
+
+		for (String key : input.keySet()) {
+			Object value = input.opt(key);
+			if (value != null) {
+				result.put(cleanKey(key), cleanValue(value));
+			}
 		}
 
-		// replace '(' in JSON Names with ''
-		while (jsonInput.matches(".*\"([^\"]*)[(]([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*)[(]([^\"]*)\":", "\"$1$2\":");
+		return result;
 	}
 
-		// replace ')' in JSON Names with ''
-		while (jsonInput.matches(".*\"([^\"]*)[)]([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*)[)]([^\"]*)\":", "\"$1$2\":");
+	private static Object cleanValue(Object object) {
+		if (object instanceof JSONObject) {
+			return cleanJsonObject((JSONObject) object);
+		} else if (object instanceof JSONArray) {
+			JSONArray array = (JSONArray) object;
+			JSONArray res = new JSONArray();
+
+			for (int i = array.length() - 1; i >= 0; i--) {
+				res.put(i, cleanValue(array.opt(i)));
+			}
+			return res;
+		} else if (object instanceof String) {
+			String value = (String) object;
+
+			// XML 1.0 Allowed characters
+			// Char ::= #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
+
+			return value
+				.codePoints()
+				.filter(
+					cp -> cp == 0x9 || cp == 0xA || cp == 0xD || (cp >= 0x20 && cp <= 0xD7FF)
+						|| (cp >= 0xE000 && cp <= 0xFFFD)
+						|| (cp >= 0x10000 && cp <= 0x10FFFF))
+				.collect(
+					StringBuilder::new,
+					StringBuilder::appendCodePoint,
+					StringBuilder::append)
+				.toString();
 		}
 
-		// add prefix of startNumbers in JSON Keynames with 'n_'
-		while (jsonInput.matches(".*\"([^\"][0-9])([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"][0-9])([^\"]*)\":", "\"n_$1$2\":");
+		return object;
 	}
+
+	private static String cleanKey(String key) {
+		if (key == null || key.isEmpty()) {
+			return key;
+		}
+
+		// xml tag cannot begin with "-", ".", or a numeric digit.
+		switch (key.charAt(0)) {
+			case '-':
+			case '.':
+				key = "_" + key.substring(1);
+				break;
+		}
+
+		if (Character.isDigit(key.charAt(0))) {
+			if (key.matches("^[0-9]+$")) {
 				// add prefix of only numbers in JSON Keynames with 'm_'
-		while (jsonInput.matches(".*\"([0-9]+)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([0-9]+)\":", "\"m_$1\":");
+				key = "m_" + key;
+			} else {
+				// add prefix of startNumbers in JSON Keynames with 'n_'
+				key = "n_" + key;
+			}
 		}
 
-		// replace ':' between number like '2018-08-28T11:05:00Z' in JSON keynames with ''
-		while (jsonInput.matches(".*\"([^\"]*[0-9]):([0-9][^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*[0-9]):([0-9][^\"]*)\":", "\"$1$2\":");
+		StringBuilder res = new StringBuilder(key.length());
+		for (int i = 0; i < key.length(); i++) {
+			char c = key.charAt(i);
+
+			// sequence of whitespaces are rendered as a single '_'
+			if (Character.isWhitespace(c)) {
+				while (i + 1 < key.length() && Character.isWhitespace(key.charAt(i + 1))) {
+					i++;
+				}
+				res.append('_');
+			}
+			// remove invalid chars for xml tags with the expception of '=' and '/'
+			else if (INVALID_XMLTAG_CHARS.indexOf(c) >= 0) {
+				switch (c) {
+					case '=':
+						res.append('-');
+						break;
+					case '/':
+						res.append('_');
+						break;
+					default:
+						break;
+				}
+				// nothing
+			}
+			// all other chars are kept
+			else {
+				res.append(c);
+			}
 		}
 
-		// replace ',' in JSON Keynames with '.' to prevent , in xml tagnames.
-		// while (jsonInput.matches(".*\"([^\"]*),([^\"]*)\":.*")) {
-		// jsonInput = jsonInput.replaceAll("\"([^\"]*),([^\"]*)\":", "\"$1.$2\":");
-		// }
-
-		// replace '=' in JSON Keynames with '-'
-		while (jsonInput.matches(".*\"([^\"]*)=([^\"]*)\":.*")) {
-			jsonInput = jsonInput.replaceAll("\"([^\"]*)=([^\"]*)\":", "\"$1-$2\":");
+		return res.toString();
 	}
 
-		log.trace("after syntaxConvertJsonKeyNames: " + jsonInput);
-		return jsonInput;
+	static public String convertToXML(final String jsonRecord) {
+		if (log.isTraceEnabled()) {
+			log.trace("input json: " + jsonRecord);
 		}
 
-	public String convertToXML(final String jsonRecord) {
-		String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
-		org.json.JSONObject jsonObject = new org.json.JSONObject(syntaxConvertJsonKeyNames(jsonRecord));
-		resultXml += org.json.XML.toString(jsonObject, wrapName); // wrap xml in single root element
-		log.trace("before inputStream: " + resultXml);
-		resultXml = XmlCleaner.cleanAllEntities(resultXml);
-		log.trace("after cleaning: " + resultXml);
-		return resultXml;
+		JSONObject jsonObject = cleanJsonObject(new org.json.JSONObject(jsonRecord));
+		String res = XML_HEADER + org.json.XML.toString(jsonObject, XML_WRAP_TAG); // wrap xml in single root element
+
+		if (log.isTraceEnabled()) {
+			log.trace("outout xml: " + res);
+		}
+		return res;
 	}
 }

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json

@@ -17,6 +17,12 @@
     "paramDescription": "the path to get the input data from Pubmed",
     "paramRequired": true
   },
+  {
+    "paramName": "oip",
+    "paramLongName": "openapcInputPath",
+    "paramDescription": "the path to get the input data from OpenAPC",
+    "paramRequired": true
+  },
   {
     "paramName": "o",
     "paramLongName": "outputPath",

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties

@@ -31,6 +31,7 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
 # The following is needed as a property of a workflow
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
-crossrefInputPath=/data/bip-affiliations/data.json
+crossrefInputPath=/data/bip-affiliations/crossref-data.json
 pubmedInputPath=/data/bip-affiliations/pubmed-data.json
+openapcInputPath=/data/bip-affiliations/openapc-data.json
 outputPath=/tmp/crossref-affiliations-output-v5

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml

@@ -9,6 +9,10 @@
             <name>pubmedInputPath</name>
             <description>the path where to find the inferred affiliation relations from Pubmed</description>
         </property>
+        <property>
+            <name>openapcInputPath</name>
+            <description>the path where to find the inferred affiliation relations from OpenAPC</description>
+        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -102,6 +106,7 @@
             </spark-opts>
             <arg>--crossrefInputPath</arg><arg>${crossrefInputPath}</arg>
             <arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
+            <arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/as_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/input_read_parameters.json

@@ -0,0 +1,30 @@
+[
+
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+    "paramName": "d",
+    "paramLongName": "delimiter",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "if",
+    "paramLongName": "inputFile",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  }
+]
+
+
+

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/config-default.xml

@@ -0,0 +1,58 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>6G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>1</value>
+    </property>
+</configuration>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/download.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+curl -L $1  | hdfs dfs -put - $2

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml

@@ -0,0 +1,82 @@
+<workflow-app name="Transfomative Agreement Integration" xmlns="uri:oozie:workflow:0.5">
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+
+    <start to="resume_from"/>
+
+    <decision name="resume_from">
+        <switch>
+            <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
+            <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
+        </switch>
+    </decision>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="download">
+        <shell xmlns="uri:oozie:shell-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <configuration>
+                <property>
+                    <name>mapred.job.queue.name</name>
+                    <value>${queueName}</value>
+                </property>
+            </configuration>
+            <exec>download.sh</exec>
+            <argument>${inputFile}</argument>
+            <argument>${workingDir}/transformativeagreement/transformativeAgreement.json</argument>
+            <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
+            <file>download.sh</file>
+            <capture-output/>
+        </shell>
+        <ok to="create_actionset"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="create_actionset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the AS for the Transformative Agreement</name>
+            <class>eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${workingDir}/transformativeagreement/</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "m",
+    "paramLongName": "master",
+    "paramDescription": "the master name",
+    "paramRequired": true
+  },
+  {
+    "paramName": "t",
+    "paramLongName": "targetPath",
+    "paramDescription": "the target PATH of the DF tables",
+    "paramRequired": true
+  },
+  {
+    "paramName": "g",
+    "paramLongName": "graphPath",
+    "paramDescription": "the PATH of the current graph path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "u",
+    "paramLongName": "updatePath",
+    "paramDescription": "the PATH of the current graph update path",
+    "paramRequired": true
+  }
+  ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_update_parameter.json

@@ -0,0 +1,37 @@
+[ {
+    "paramName": "n",
+    "paramLongName": "namenode",
+    "paramDescription": "the Name Node URI",
+    "paramRequired": true
+  },
+  {
+    "paramName": "m",
+    "paramLongName": "master",
+    "paramDescription": "the master name",
+    "paramRequired": true
+  },
+  {
+    "paramName": "t",
+    "paramLongName": "targetPath",
+    "paramDescription": "the target PATH where download the files",
+    "paramRequired": true
+  },
+  {
+    "paramName": "a",
+    "paramLongName": "apiURL",
+    "paramDescription": "the URL  to download the tar file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "g",
+    "paramLongName": "graphPath",
+    "paramDescription": "the path of the input graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "at",
+    "paramLongName": "accessToken",
+    "paramDescription": "the accessToken to contact API",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json

@@ -16,6 +16,12 @@
     "paramLongName": "sourcePath",
     "paramDescription": "the PATH of the ORCID sequence file",
     "paramRequired": true
+  },
+  {
+    "paramName": "fu",
+    "paramLongName": "fromUpdate",
+    "paramDescription": "whether we have to generate table from dump or from update",
+    "paramRequired": false
   }
 
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml

@@ -0,0 +1,23 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml

@@ -0,0 +1,114 @@
+<workflow-app name="download_Update_ORCID" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>graphPath</name>
+            <description>the  path  to store the original ORCID dump</description>
+        </property>
+        <property>
+            <name>targetPath</name>
+            <description>the  path  to store the original ORCID dump</description>
+        </property>
+        <property>
+            <name>apiURL</name>
+            <value>http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar</value>
+            <description>The URL of the update CSV list </description>
+        </property>
+        <property>
+            <name>accessToken</name>
+            <description>The access token</description>
+        </property>
+
+
+    </parameters>
+
+    <start to="startUpdate"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="startUpdate">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Check Latest Orcid and Download updates</name>
+            <class>eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=2g
+                --conf spark.sql.shuffle.partitions=3000
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--master</arg><arg>yarn</arg>
+            <arg>--namenode</arg><arg>${nameNode}</arg>
+            <arg>--graphPath</arg><arg>${graphPath}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
+            <arg>--apiURL</arg><arg>${apiURL}</arg>
+            <arg>--accessToken</arg><arg>${accessToken}</arg>
+        </spark>
+        <ok to="generateTables"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="generateTables">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Generate ORCID Tables</name>
+            <class>eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=2g
+                --conf spark.sql.shuffle.partitions=3000
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${targetPath}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}/updateTable</arg>
+            <arg>--fromUpdate</arg><arg>true</arg>
+            <arg>--master</arg><arg>yarn</arg>
+        </spark>
+        <ok to="updateTable"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="updateTable">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Update ORCID Tables</name>
+            <class>eu.dnetlib.dhp.collection.orcid.SparkApplyUpdate</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=2g
+                --conf spark.sql.shuffle.partitions=3000
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--graphPath</arg><arg>${graphPath}</arg>
+            <arg>--updatePath</arg><arg>${targetPath}/updateTable</arg>
+            <arg>--targetPath</arg><arg>${targetPath}/newTable</arg>
+            <arg>--master</arg><arg>yarn</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/base.sql

@@ -0,0 +1,114 @@
+BEGIN;
+
+INSERT INTO dsm_services(
+	_dnet_resource_identifier_, 
+	id,
+	officialname,
+	englishname,
+	namespaceprefix,
+	websiteurl,
+	logourl,
+	platform,
+	contactemail,
+	collectedfrom,
+	provenanceaction,
+	_typology_to_remove_,
+	eosc_type,
+	eosc_datasource_type,
+	research_entity_types,
+	thematic
+) VALUES (
+	'openaire____::base_search',
+	'openaire____::base_search',
+	'Bielefeld Academic Search Engine (BASE)',
+	'Bielefeld Academic Search Engine (BASE)',
+	'base_search_',
+	'https://www.base-search.net',
+	'https://www.base-search.net/about/download/logo_224x57_white.gif',
+	'BASE',
+	'openaire-helpdesk@uni-bielefeld.de',
+	'infrastruct_::openaire',
+	'user:insert',
+	'aggregator::pubsrepository::unknown',
+	'Data Source',
+	'Aggregator',
+	ARRAY['Research Products'],
+	false
+);
+
+INSERT INTO dsm_service_organization(
+	_dnet_resource_identifier_,
+	organization,
+	service
+) VALUES (
+	'fairsharing_::org::214@@openaire____::base_search',
+	'fairsharing_::org::214',
+	'openaire____::base_search'
+);
+
+INSERT INTO dsm_api(
+	_dnet_resource_identifier_,
+	id,
+	service,
+	protocol,
+	baseurl,
+	metadata_identifier_path
+) VALUES (
+	'api_________::openaire____::base_search::dump',
+	'api_________::openaire____::base_search::dump',
+	'openaire____::base_search',
+	'baseDump',
+	'/user/michele.artini/base-import/base_oaipmh_dump-current.tar',
+	'//*[local-name()=''header'']/*[local-name()=''identifier'']'
+);
+
+
+INSERT INTO dsm_apiparams(
+	_dnet_resource_identifier_, 
+	api, 
+	param, 
+	value
+) VALUES (
+	'api_________::openaire____::base_search::dump@@dbUrl',
+	'api_________::openaire____::base_search::dump',
+	'dbUrl',
+	'jdbc:postgresql://postgresql.services.openaire.eu:5432/dnet_openaireplus'
+);
+
+INSERT INTO dsm_apiparams(
+	_dnet_resource_identifier_, 
+	api, 
+	param, 
+	value
+) VALUES (
+	'api_________::openaire____::base_search::dump@@dbUser',
+	'api_________::openaire____::base_search::dump',
+	'dbUser',
+	'dnet'
+);
+
+INSERT INTO dsm_apiparams(
+	_dnet_resource_identifier_, 
+	api, 
+	param, 
+	value
+) VALUES (
+	'api_________::openaire____::base_search::dump@@dbPassword',
+	'api_________::openaire____::base_search::dump',
+	'dbPassword',
+	'***'
+);
+
+INSERT INTO dsm_apiparams(
+	_dnet_resource_identifier_, 
+	api, 
+	param, 
+	value
+) VALUES (
+	'api_________::openaire____::base_search::dump@@acceptedNormTypes',
+	'api_________::openaire____::base_search::dump',
+	'acceptedNormTypes',
+	'1,11,111,121,14,15,18,181,182,183,1A,6,7'
+);
+
+COMMIT;

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-accepted.sql

@@ -0,0 +1,9 @@
+select s.id as id 
+from dsm_services s 
+where collectedfrom = 'openaire____::opendoar' 
+and jurisdiction = 'Institutional'
+and s.id in (
+	select service from dsm_api where coalesce(compatibility_override, compatibility) = 'driver' or coalesce(compatibility_override, compatibility) = 'UNKNOWN'
+) and s.id not in (
+	select service from dsm_api where coalesce(compatibility_override, compatibility) like '%openaire%'
+);

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/sql/opendoar-aggregation-status.sql

@@ -0,0 +1,11 @@
+select 
+	s.id           as id, 
+	s.jurisdiction as jurisdiction, 
+	array_remove(array_agg(a.id || ' (compliance: ' || coalesce(a.compatibility_override, a.compatibility, 'UNKNOWN') || ')@@@' || coalesce(a.last_collection_total, 0)), NULL) as aggregations
+from 
+	dsm_services s 
+	join dsm_api a on (s.id = a.service) 
+where 
+	collectedfrom = 'openaire____::opendoar'
+group by 
+	s.id;

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base-types.vocabulary.xml

@@ -0,0 +1,180 @@
+<RESOURCE_PROFILE>
+	<HEADER>
+		<RESOURCE_IDENTIFIER value="c67911d6-9988-4a3b-b965-7d39bdd4a31d_Vm9jYWJ1bGFyeURTUmVzb3VyY2VzL1ZvY2FidWxhcnlEU1Jlc291cmNlVHlwZQ==" />
+		<RESOURCE_TYPE value="VocabularyDSResourceType" />
+		<RESOURCE_KIND value="VocabularyDSResources" />
+		<RESOURCE_URI value="" />
+		<DATE_OF_CREATION value="2024-02-13T11:15:48+00:00" />
+	</HEADER>
+	<BODY>
+		<CONFIGURATION>
+			<VOCABULARY_NAME code="base:normalized_types">base:normalized_types</VOCABULARY_NAME>
+			<VOCABULARY_DESCRIPTION>base:normalized_types</VOCABULARY_DESCRIPTION>
+			<TERMS>
+				<TERM native_name="Text" code="Text" english_name="Text" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="1" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Book" code="Book" english_name="Book" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="11" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Book part" code="Book part" english_name="Book part" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="111" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Journal/Newspaper" code="Journal/Newspaper" english_name="Journal/Newspaper" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="12" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Article contribution" code="Article contribution" english_name="Article contribution" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="121" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Other non-article" code="Other non-article" english_name="Other non-article" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="122" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Conference object" code="Conference object" english_name="Conference object" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="13" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Report" code="Report" english_name="Report" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="14" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Review" code="Review" english_name="Review" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="15" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Course material" code="Course material" english_name="Course material" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="16" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Lecture" code="Lecture" english_name="Lecture" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="17" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Thesis" code="Thesis" english_name="Thesis" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="18" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Bachelor's thesis" code="Bachelor's thesis" english_name="Bachelor's thesis" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="181" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Master's thesis" code="Master's thesis" english_name="Master's thesis" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="182" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Doctoral and postdoctoral thesis" code="Doctoral and postdoctoral thesis" english_name="Doctoral and postdoctoral thesis" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="183" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Manuscript" code="Manuscript" english_name="Manuscript" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="19" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Patent" code="Patent" english_name="Patent" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="1A" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Musical notation" code="Musical notation" english_name="Musical notation" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="2" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Map" code="Map" english_name="Map" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="3" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Audio" code="Audio" english_name="Audio" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="4" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Image/Video" code="Image/Video" english_name="Image/Video" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="5" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Still image" code="Still image" english_name="Still image" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="51" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Moving image/Video" code="Moving image/Video" english_name="Moving image/Video" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="52" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Software" code="Software" english_name="Software" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="6" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Dataset" code="Dataset" english_name="Dataset" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="7" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+				<TERM native_name="Unknown" code="Unknown" english_name="Unknown" encoding="BASE">
+					<SYNONYMS>
+						<SYNONYM term="F" encoding="BASE" />
+					</SYNONYMS>
+					<RELATIONS />
+				</TERM>
+
+			</TERMS>
+		</CONFIGURATION>
+		<STATUS>
+			<LAST_UPDATE value="2013-11-18T10:46:36Z" />
+		</STATUS>
+		<SECURITY_PARAMETERS>String</SECURITY_PARAMETERS>
+	</BODY>
+</RESOURCE_PROFILE>
+
+                

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2oaf.transformationRule.xml

@@ -0,0 +1,432 @@
+<RESOURCE_PROFILE>
+	<HEADER>
+		<RESOURCE_IDENTIFIER value="" />
+		<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
+		<RESOURCE_KIND value="TransformationRuleDSResources" />
+		<RESOURCE_URI value="" />
+		<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
+	</HEADER>
+	<BODY>
+		<CONFIGURATION>
+			<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
+			<SINK_METADATA_FORMAT name="oaf_hbase" />
+			<IMPORTED />
+			<SCRIPT>
+				<TITLE>xslt_base2oaf_hadoop</TITLE>
+				<CODE>
+					<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
+						xmlns:base_dc="http://oai.base-search.net/base_dc/"
+						xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+						xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
+						xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
+						exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" version="2.0">
+						<xsl:param name="varOfficialName" />
+						<xsl:param name="varDataSourceId" />
+						<xsl:param name="varFP7" select="'corda_______::'" />
+						<xsl:param name="varH2020" select="'corda__h2020::'" />
+						<xsl:param name="repoCode" select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
+						<xsl:param name="index" select="0" />
+						<xsl:param name="transDate" select="current-dateTime()" />
+
+						<xsl:template name="terminate">
+							<xsl:message terminate="yes">
+								record is not compliant, transformation is interrupted.
+							</xsl:message>
+						</xsl:template>
+
+						<xsl:template match="/">
+							<record>
+								<xsl:apply-templates select="//*[local-name() = 'header']" />
+
+
+<!-- TO EVALUATE
+base_dc:authod_id
+base_dc:authod_id/base_dc:creator_id
+base_dc:authod_id/base_dc:creator_name
+
+example:
+
+<dc:creator>ALBU, Svetlana</dc:creator>
+
+<base_dc:authod_id>
+	<base_dc:creator_name>ALBU, Svetlana</base_dc:creator_name>
+    <base_dc:creator_id>https://orcid.org/0000-0002-8648-950X</base_dc:creator_id>
+</base_dc:authod_id>
+-->
+
+<!-- NOT USED 
+base_dc:global_id (I used oai:identifier)
+base_dc:collection/text()
+
+base_dc:continent
+base_dc:country
+base_dc:year (I used dc:date)
+dc:coverage
+dc:language (I used base_dc:lang)
+base_dc:link (I used dc:identifier)
+-->
+
+								<metadata>
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:title" />
+										<xsl:with-param name="targetElement" select="'dc:title'" />
+									</xsl:call-template>
+
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:creator/replace(., '^(.*)\|.*$', '$1')" />
+										<xsl:with-param name="targetElement" select="'dc:creator'" />
+									</xsl:call-template>
+
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:contributor" />
+										<xsl:with-param name="targetElement" select="'dc:contributor'" />
+									</xsl:call-template>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:description" />
+										<xsl:with-param name="targetElement" select="'dc:description'" />
+									</xsl:call-template>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:subject" />
+										<xsl:with-param name="targetElement" select="'dc:subject'" />
+									</xsl:call-template>
+									
+									<!-- TODO: I'm not sure if this is the correct encoding -->
+									<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
+										<dc:subject><xsl:value-of select="concat(@type, ':', .)" /></dc:subject>
+									</xsl:for-each>
+									<!-- END TODO -->
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:publisher" />
+										<xsl:with-param name="targetElement" select="'dc:publisher'" />
+									</xsl:call-template>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:format" />
+										<xsl:with-param name="targetElement" select="'dc:format'" />
+									</xsl:call-template>
+									
+									
+									<xsl:for-each select="//base_dc:typenorm">
+										<dc:type>
+											<xsl:value-of select="vocabulary:clean(., 'base:normalized_types')" />
+										</dc:type>
+									</xsl:for-each>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:type" />
+										<xsl:with-param name="targetElement" select="'dc:type'" />
+									</xsl:call-template>
+									
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:source" />
+										<xsl:with-param name="targetElement" select="'dc:source'" />
+									</xsl:call-template>
+									
+									<dc:language>
+										<xsl:value-of select="vocabulary:clean( //base_dc:lang, 'dnet:languages')" />
+									</dc:language>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:rights" />
+										<xsl:with-param name="targetElement" select="'dc:rights'" />
+									</xsl:call-template>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:relation" />
+										<xsl:with-param name="targetElement" select="'dc:relation'" />
+									</xsl:call-template>
+									
+									<xsl:if test="not(//dc:identifier[starts-with(., 'http')])">
+										<xsl:call-template name="terminate" />
+									</xsl:if>
+									
+									<xsl:call-template name="allElements">
+										<xsl:with-param name="sourceElement" select="//dc:identifier[starts-with(., 'http')]" />
+										<xsl:with-param name="targetElement" select="'dc:identifier'" />
+									</xsl:call-template>
+									
+									<xsl:for-each select="//dc:relation">
+										<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
+											<oaf:projectid>
+												<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+											</oaf:projectid>
+										</xsl:if>
+										<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
+											<oaf:projectid>
+												<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+											</oaf:projectid>
+										</xsl:if>
+									</xsl:for-each>
+
+									<xsl:choose>
+										<!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority  -->
+										
+										<!-- Book part -->
+										<xsl:when test="//base_dc:typenorm = '111'">
+											<dr:CobjCategory type="publication">0013</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Book -->
+										<xsl:when test="//base_dc:typenorm = '11'">
+											<dr:CobjCategory type="publication">0002</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Article contribution -->
+										<xsl:when test="//base_dc:typenorm = '121'">
+											<dr:CobjCategory type="publication">0001</dr:CobjCategory>
+										</xsl:when>
+										
+																				
+										<!-- Journal/Newspaper -->
+										<xsl:when test="//base_dc:typenorm = '12'">
+											<dr:CobjCategory type="publication">0043</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Report -->
+										<xsl:when test="//base_dc:typenorm = '14'">
+											<dr:CobjCategory type="publication">0017</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Review -->
+										<xsl:when test="//base_dc:typenorm = '15'">
+											<dr:CobjCategory type="publication">0015</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Lecture -->
+										<xsl:when test="//base_dc:typenorm = '17'">
+											<dr:CobjCategory type="publication">0010</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Bachelor's thesis -->
+										<xsl:when test="//base_dc:typenorm = '181'">
+											<dr:CobjCategory type="publication">0008</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Master's thesis -->
+										<xsl:when test="//base_dc:typenorm = '182'">
+											<dr:CobjCategory type="publication">0007</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Doctoral and postdoctoral thesis -->
+										<xsl:when test="//base_dc:typenorm = '183'">
+											<dr:CobjCategory type="publication">0006</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Thesis -->
+										<xsl:when test="//base_dc:typenorm = '18'">
+											<dr:CobjCategory type="publication">0044</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Patent -->
+										<xsl:when test="//base_dc:typenorm = '1A'">
+											<dr:CobjCategory type="publication">0019</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Text -->
+										<xsl:when test="//base_dc:typenorm = '1'">
+											<dr:CobjCategory type="publication">0001</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Software -->
+										<xsl:when test="//base_dc:typenorm = '6'">
+											<dr:CobjCategory type="software">0029</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Dataset -->										
+										<xsl:when test="//base_dc:typenorm = '7'">
+											<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
+										</xsl:when>										
+																				
+										<!-- Still image -->
+										<xsl:when test="//base_dc:typenorm = '51'">
+											<dr:CobjCategory type="other">0025</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Moving image/Video -->										
+										<xsl:when test="//base_dc:typenorm = '52'">
+											<dr:CobjCategory type="other">0024</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Image/Video -->
+										<xsl:when test="//base_dc:typenorm = '5'">
+											<dr:CobjCategory type="other">0033</dr:CobjCategory>
+										</xsl:when>
+
+										<!-- Audio -->
+										<xsl:when test="//base_dc:typenorm = '4'">
+											<dr:CobjCategory type="other">0030</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Musical notation -->
+										<xsl:when test="//base_dc:typenorm = '2'">
+											<dr:CobjCategory type="other">0020</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Map -->
+										<xsl:when test="//base_dc:typenorm = '3'">
+											<dr:CobjCategory type="other">0020</dr:CobjCategory>
+										</xsl:when>										
+										
+										<!-- Other non-article -->
+										<xsl:when test="//base_dc:typenorm = '122'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Course material -->
+										<xsl:when test="//base_dc:typenorm = '16'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Manuscript -->
+										<xsl:when test="//base_dc:typenorm = '19'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Conference object -->
+										<xsl:when test="//base_dc:typenorm = '13'">
+											<dr:CobjCategory type="publication">0004</dr:CobjCategory>
+										</xsl:when>
+
+										<!-- Unknown -->
+										<xsl:when test="//base_dc:typenorm = 'F'">
+											<dr:CobjCategory type="other">0000</dr:CobjCategory>
+										</xsl:when>
+										<xsl:otherwise>
+											<dr:CobjCategory type="other">0000</dr:CobjCategory>
+										</xsl:otherwise>
+									</xsl:choose>
+									
+									
+									<oaf:accessrights>
+										<xsl:choose>
+											<xsl:when test="//base_dc:oa[.='0']">CLOSED</xsl:when>
+											<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
+											<xsl:when test="//base_dc:oa[.='2']">UNKNOWN</xsl:when>
+											<xsl:when test="//base_dc:rightsnorm">
+												<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
+											</xsl:when>
+											<xsl:when test="//dc:rights">
+												<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
+											</xsl:when>
+											<xsl:otherwise>UNKNOWN</xsl:otherwise>
+										</xsl:choose>
+									</oaf:accessrights>
+									
+									<xsl:for-each select="//base_dc:doi">
+										<oaf:identifier identifierType="doi">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
+										<oaf:identifier identifierType="url">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
+										<oaf:identifier identifierType="handle">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>									
+
+									<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
+										<oaf:identifier identifierType='urn'>
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+									
+									<oaf:identifier identifierType="oai-original">
+										<xsl:value-of
+											select="//oai:header/oai:identifier" />
+									</oaf:identifier>
+									
+									<oaf:hostedBy>
+										<xsl:attribute name="name">
+											<xsl:value-of select="//base_dc:collname" />
+										</xsl:attribute>
+										<xsl:attribute name="id">
+											<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
+										</xsl:attribute>
+									</oaf:hostedBy>
+									
+									<oaf:collectedFrom>
+										<xsl:attribute name="name">
+											<xsl:value-of select="$varOfficialName" />
+										</xsl:attribute>
+										<xsl:attribute name="id">
+											<xsl:value-of select="$varDataSourceId" />
+										</xsl:attribute>
+									</oaf:collectedFrom>
+									
+									<oaf:dateAccepted>
+										<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
+									</oaf:dateAccepted>
+									
+									<xsl:if test="//base_dc:oa[.='1']">
+										<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
+											<oaf:fulltext>
+												<xsl:value-of select="normalize-space(.)" />
+											</oaf:fulltext>
+										</xsl:for-each>
+									</xsl:if>
+									
+									<xsl:for-each select="//base_dc:collection/@ror_id">
+										<oaf:relation relType="resultOrganization"
+										 	subRelType="affiliation"
+										 	relClass="hasAuthorInstitution"
+											targetType="organization">
+											<xsl:choose>
+												<xsl:when test="contains(.,'https://ror.org/')">
+													<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
+												</xsl:when>
+												<xsl:otherwise>
+													<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
+												</xsl:otherwise>
+											</xsl:choose>
+										</oaf:relation>
+									</xsl:for-each>
+								</metadata>
+								<xsl:copy-of select="//*[local-name() = 'about']" />
+							</record>
+						</xsl:template>
+
+						<xsl:template name="allElements">
+							<xsl:param name="sourceElement" />
+							<xsl:param name="targetElement" />
+							<xsl:for-each select="$sourceElement">
+								<xsl:element name="{$targetElement}">
+									<xsl:value-of select="normalize-space(.)" />
+								</xsl:element>
+							</xsl:for-each>
+						</xsl:template>
+
+						<xsl:template match="//*[local-name() = 'header']">
+							<xsl:if test="//oai:header/@status='deleted'">
+								<xsl:call-template name="terminate" />
+							</xsl:if>
+							<xsl:copy>
+								<xsl:apply-templates select="node()|@*" />
+								<xsl:element name="dr:dateOfTransformation">
+									<xsl:value-of select="$transDate" />
+								</xsl:element>
+							</xsl:copy>
+						</xsl:template>
+
+						<xsl:template match="node()|@*">
+							<xsl:copy>
+								<xsl:apply-templates select="node()|@*" />
+							</xsl:copy>
+						</xsl:template>
+					</xsl:stylesheet>
+				</CODE>
+			</SCRIPT>
+		</CONFIGURATION>
+		<STATUS />
+		<SECURITY_PARAMETERS />
+	</BODY>
+</RESOURCE_PROFILE>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/plugin/base/xml/base2odf.transformationRule.xml

@@ -0,0 +1,461 @@
+<RESOURCE_PROFILE>
+	<HEADER>
+		<RESOURCE_IDENTIFIER value="2ad0cdd9-c96c-484c-8b0e-ed56d86891fe_VHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZXMvVHJhbnNmb3JtYXRpb25SdWxlRFNSZXNvdXJjZVR5cGU=" />
+		<RESOURCE_TYPE value="TransformationRuleDSResourceType" />
+		<RESOURCE_KIND value="TransformationRuleDSResources" />
+		<RESOURCE_URI value="" />
+		<DATE_OF_CREATION value="2024-03-05T11:23:00+00:00" />
+	</HEADER>
+	<BODY>
+		<CONFIGURATION>
+			<SOURCE_METADATA_FORMAT interpretation="cleaned" layout="store" name="dc" />
+			<SINK_METADATA_FORMAT name="odf_hbase" />
+			<IMPORTED />
+			<SCRIPT>
+				<TITLE>xslt_base2odf_hadoop</TITLE>
+				<CODE>
+					<xsl:stylesheet xmlns:oaire="http://namespace.openaire.eu/schema/oaire/" xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO" xmlns:base_dc="http://oai.base-search.net/base_dc/"
+						xmlns:datacite="http://datacite.org/schema/kernel-4" xmlns:dr="http://www.driver-repository.eu/namespace/dr" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+						xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xmlns:vocabulary="http://eu/dnetlib/transform/clean" xmlns:oaf="http://namespace.openaire.eu/oaf"
+						xmlns:oai="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:dc="http://purl.org/dc/elements/1.1/"
+						exclude-result-prefixes="xsl vocabulary dateCleaner base_dc" version="2.0">
+						<xsl:param name="varOfficialName" />
+						<xsl:param name="varDataSourceId" />
+						<xsl:param name="varFP7" select="'corda_______::'" />
+						<xsl:param name="varH2020" select="'corda__h2020::'" />
+						<xsl:param name="repoCode" select="substring-before(//*[local-name() = 'header']/*[local-name()='recordIdentifier'], ':')" />
+						<xsl:param name="index" select="0" />
+						<xsl:param name="transDate" select="current-dateTime()" />
+
+						<xsl:template name="terminate">
+							<xsl:message terminate="yes">
+								record is not compliant, transformation is interrupted.
+							</xsl:message>
+						</xsl:template>
+
+						<xsl:template match="/">
+							<record>
+								<xsl:apply-templates select="//*[local-name() = 'header']" />
+
+
+								<!-- NOT USED 
+									base_dc:global_id (I used oai:identifier) 
+									base_dc:collection/text() 
+									base_dc:continent 
+									base_dc:country  
+									dc:coverage
+									dc:source
+									dc:relation
+									dc:type (I used //base_dc:typenorm)
+									dc:language (I used base_dc:lang) 
+									base_dc:link (I used dc:identifier)
+								 -->
+
+								<metadata>
+									<datacite:resource>
+
+										<xsl:for-each select="//base_dc:doi">
+											<datacite:identifier identifierType="DOI">
+												<xsl:value-of select="." />
+											</datacite:identifier>
+										</xsl:for-each>										
+
+										<datacite:alternateIdentifiers>
+											<xsl:for-each
+												select="distinct-values(//dc:identifier[starts-with(., 'http') and (not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
+												<datacite:identifier alternateIdentifierType="url">
+													<xsl:value-of select="." />
+												</datacite:identifier>
+											</xsl:for-each>
+
+											<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
+												<datacite:identifier alternateIdentifierType="handle">
+													<xsl:value-of select="." />
+												</datacite:identifier>
+											</xsl:for-each>
+
+											<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
+												<datacite:identifier alternateIdentifierType='urn'>
+													<xsl:value-of select="." />
+												</datacite:identifier>
+											</xsl:for-each>
+
+											<datacite:identifier alternateIdentifierType="oai-original">
+												<xsl:value-of
+													select="//oai:header/oai:identifier" />
+											</datacite:identifier>
+											
+										</datacite:alternateIdentifiers>
+
+										<datacite:relatedIdentifiers />
+
+
+										<xsl:for-each select="//base_dc:typenorm">
+											<datacite:resourceType><xsl:value-of select="vocabulary:clean(., 'base:normalized_types')" /></datacite:resourceType>
+										</xsl:for-each>
+
+										<datacite:titles>
+											<xsl:for-each select="//dc:title">
+												<datacite:title>
+													<xsl:value-of select="normalize-space(.)" />
+												</datacite:title>
+											</xsl:for-each>
+										</datacite:titles>
+
+										<datacite:creators>
+											<xsl:for-each select="//dc:creator">
+												<xsl:variable name="author" select="normalize-space(.)" />
+												<datacite:creator>
+													<datacite:creatorName>
+														<xsl:value-of select="$author" />
+													</datacite:creatorName>
+													<xsl:for-each select="//base_dc:authod_id[normalize-space(./base_dc:creator_name) = $author]/base_dc:creator_id ">
+														<xsl:if test="contains(.,'https://orcid.org/')">
+															<nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">
+																<xsl:value-of select="substring-after(., 'https://orcid.org/')" />
+															</nameIdentifier>
+														</xsl:if>
+													</xsl:for-each>
+												</datacite:creator>
+											</xsl:for-each>
+										</datacite:creators>
+
+										<datacite:contributors>
+											<xsl:for-each select="//dc:contributor">
+												<datacite:contributor>
+													<datacite:contributorName>
+														<xsl:value-of select="normalize-space(.)" />
+													</datacite:contributorName>
+												</datacite:contributor>
+											</xsl:for-each>
+										</datacite:contributors>
+
+										<datacite:descriptions>
+											<xsl:for-each select="//dc:description">
+												<datacite:description descriptionType="Abstract">
+													<xsl:value-of select="normalize-space(.)" />
+												</datacite:description>
+											</xsl:for-each>
+										</datacite:descriptions>
+
+										<datacite:subjects>
+											<xsl:for-each select="//dc:subject">
+												<datacite:subject>
+													<xsl:value-of select="normalize-space(.)" />
+												</datacite:subject>
+											</xsl:for-each>
+											
+											<xsl:for-each select="//base_dc:classcode|//base_dc:autoclasscode">
+												<datacite:subject subjectScheme="{@type}" classificationCode="{normalize-space(.)}">
+													<!-- TODO the value should be obtained by the Code -->
+													<xsl:value-of select="normalize-space(.)" />
+												</datacite:subject>
+											</xsl:for-each>
+										</datacite:subjects>
+										
+										<xsl:for-each select="//dc:publisher">
+											<datacite:publisher>
+												<xsl:value-of select="normalize-space(.)" />
+											</datacite:publisher>
+										</xsl:for-each>
+										
+										<xsl:for-each select="//base_dc:year">
+											<datacite:publicationYear>
+												<xsl:value-of select="normalize-space(.)" />
+											</datacite:publicationYear>
+										</xsl:for-each>
+																				
+										<datacite:formats>
+											<xsl:for-each select="//dc:format">
+												<datacite:format>
+													<xsl:value-of select="normalize-space(.)" />
+												</datacite:format>
+											</xsl:for-each>
+										</datacite:formats>
+										
+										<datacite:language>
+											<xsl:value-of select="vocabulary:clean( //base_dc:lang, 'dnet:languages')" />
+										</datacite:language>
+
+										<oaf:accessrights>
+											<xsl:if test="//base_dc:oa[.='0']">
+												<datacite:rights rightsURI="http://purl.org/coar/access_right/c_16ec">restricted access</datacite:rights>
+											</xsl:if>
+											<xsl:if test="//base_dc:oa[.='1']">
+												<datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
+											</xsl:if>
+											<xsl:for-each select="//dc:rights|//base_dc:rightsnorm">
+												<datacite:rights><xsl:value-of select="vocabulary:clean(., 'dnet:access_modes')" /></datacite:rights>	
+											</xsl:for-each>
+										</oaf:accessrights>
+
+									</datacite:resource>
+
+									<xsl:for-each select="//dc:relation">
+										<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', 'i')">
+											<oaf:projectid>
+												<xsl:value-of select="concat($varFP7, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/fp7/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+											</oaf:projectid>
+										</xsl:if>
+										<xsl:if test="matches(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', 'i')">
+											<oaf:projectid>
+												<xsl:value-of select="concat($varH2020, replace(normalize-space(.), '(info:eu-repo/grantagreement/ec/h2020/)(\d\d\d\d\d\d)(.*)', '$2', 'i'))" />
+											</oaf:projectid>
+										</xsl:if>
+									</xsl:for-each>
+
+									<xsl:choose>
+										<!-- I used an inline mapping because the field typenorm could be repeated and I have to specify a list of priority  -->
+										
+										<!-- Book part -->
+										<xsl:when test="//base_dc:typenorm = '111'">
+											<dr:CobjCategory type="publication">0013</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Book -->
+										<xsl:when test="//base_dc:typenorm = '11'">
+											<dr:CobjCategory type="publication">0002</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Article contribution -->
+										<xsl:when test="//base_dc:typenorm = '121'">
+											<dr:CobjCategory type="publication">0001</dr:CobjCategory>
+										</xsl:when>
+										
+																				
+										<!-- Journal/Newspaper -->
+										<xsl:when test="//base_dc:typenorm = '12'">
+											<dr:CobjCategory type="publication">0043</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Report -->
+										<xsl:when test="//base_dc:typenorm = '14'">
+											<dr:CobjCategory type="publication">0017</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Review -->
+										<xsl:when test="//base_dc:typenorm = '15'">
+											<dr:CobjCategory type="publication">0015</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Lecture -->
+										<xsl:when test="//base_dc:typenorm = '17'">
+											<dr:CobjCategory type="publication">0010</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Bachelor's thesis -->
+										<xsl:when test="//base_dc:typenorm = '181'">
+											<dr:CobjCategory type="publication">0008</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Master's thesis -->
+										<xsl:when test="//base_dc:typenorm = '182'">
+											<dr:CobjCategory type="publication">0007</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Doctoral and postdoctoral thesis -->
+										<xsl:when test="//base_dc:typenorm = '183'">
+											<dr:CobjCategory type="publication">0006</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Thesis -->
+										<xsl:when test="//base_dc:typenorm = '18'">
+											<dr:CobjCategory type="publication">0044</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Patent -->
+										<xsl:when test="//base_dc:typenorm = '1A'">
+											<dr:CobjCategory type="publication">0019</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Text -->
+										<xsl:when test="//base_dc:typenorm = '1'">
+											<dr:CobjCategory type="publication">0001</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Software -->
+										<xsl:when test="//base_dc:typenorm = '6'">
+											<dr:CobjCategory type="software">0029</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Dataset -->										
+										<xsl:when test="//base_dc:typenorm = '7'">
+											<dr:CobjCategory type="dataset">0021</dr:CobjCategory>
+										</xsl:when>										
+																				
+										<!-- Still image -->
+										<xsl:when test="//base_dc:typenorm = '51'">
+											<dr:CobjCategory type="other">0025</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Moving image/Video -->										
+										<xsl:when test="//base_dc:typenorm = '52'">
+											<dr:CobjCategory type="other">0024</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Image/Video -->
+										<xsl:when test="//base_dc:typenorm = '5'">
+											<dr:CobjCategory type="other">0033</dr:CobjCategory>
+										</xsl:when>
+
+										<!-- Audio -->
+										<xsl:when test="//base_dc:typenorm = '4'">
+											<dr:CobjCategory type="other">0030</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Musical notation -->
+										<xsl:when test="//base_dc:typenorm = '2'">
+											<dr:CobjCategory type="other">0020</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Map -->
+										<xsl:when test="//base_dc:typenorm = '3'">
+											<dr:CobjCategory type="other">0020</dr:CobjCategory>
+										</xsl:when>										
+										
+										<!-- Other non-article -->
+										<xsl:when test="//base_dc:typenorm = '122'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Course material -->
+										<xsl:when test="//base_dc:typenorm = '16'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Manuscript -->
+										<xsl:when test="//base_dc:typenorm = '19'">
+											<dr:CobjCategory type="publication">0038</dr:CobjCategory>
+										</xsl:when>
+										
+										<!-- Conference object -->
+										<xsl:when test="//base_dc:typenorm = '13'">
+											<dr:CobjCategory type="publication">0004</dr:CobjCategory>
+										</xsl:when>
+
+										<!-- Unknown -->
+										<xsl:when test="//base_dc:typenorm = 'F'">
+											<dr:CobjCategory type="other">0000</dr:CobjCategory>
+										</xsl:when>
+										<xsl:otherwise>
+											<dr:CobjCategory type="other">0000</dr:CobjCategory>
+										</xsl:otherwise>
+									</xsl:choose>
+									
+									<oaf:accessrights>
+										<xsl:choose>
+											<xsl:when test="//base_dc:oa[.='0']">CLOSED</xsl:when>
+											<xsl:when test="//base_dc:oa[.='1']">OPEN</xsl:when>
+											<xsl:when test="//base_dc:oa[.='2']">UNKNOWN</xsl:when>
+											<xsl:when test="//base_dc:rightsnorm">
+												<xsl:value-of select="vocabulary:clean(//base_dc:rightsnorm, 'dnet:access_modes')" />
+											</xsl:when>
+											<xsl:when test="//dc:rights">
+												<xsl:value-of select="vocabulary:clean( //dc:rights, 'dnet:access_modes')" />
+											</xsl:when>
+											<xsl:otherwise>UNKNOWN</xsl:otherwise>
+										</xsl:choose>
+									</oaf:accessrights>
+
+									<xsl:for-each select="//base_dc:doi">
+										<oaf:identifier identifierType="doi">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<xsl:for-each
+										select="distinct-values(//dc:identifier[starts-with(., 'http') and ( not(contains(., '://dx.doi.org/') or contains(., '://doi.org/') or contains(., '://hdl.handle.net/')))])">
+										<oaf:identifier identifierType="url">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'http') and contains(., '://hdl.handle.net/')]/substring-after(., 'hdl.handle.net/'))">
+										<oaf:identifier identifierType="handle">
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<xsl:for-each select="distinct-values(//dc:identifier[starts-with(., 'urn:nbn:nl:') or starts-with(., 'URN:NBN:NL:')])">
+										<oaf:identifier identifierType='urn'>
+											<xsl:value-of select="." />
+										</oaf:identifier>
+									</xsl:for-each>
+
+									<oaf:identifier identifierType="oai-original">
+										<xsl:value-of
+											select="//oai:header/oai:identifier" />
+									</oaf:identifier>
+
+									<oaf:hostedBy>
+										<xsl:attribute name="name">
+											<xsl:value-of select="//base_dc:collname" />
+										</xsl:attribute>
+										<xsl:attribute name="id">
+											<xsl:value-of select="concat('opendoar____::', //base_dc:collection/@opendoar_id)" />
+										</xsl:attribute>
+									</oaf:hostedBy>
+
+									<oaf:collectedFrom>
+										<xsl:attribute name="name">
+											<xsl:value-of select="$varOfficialName" />
+										</xsl:attribute>
+										<xsl:attribute name="id">
+											<xsl:value-of select="$varDataSourceId" />
+										</xsl:attribute>
+									</oaf:collectedFrom>
+
+									<oaf:dateAccepted>
+										<xsl:value-of select="dateCleaner:dateISO( //dc:date[1] )" />
+									</oaf:dateAccepted>
+
+									<xsl:if test="//base_dc:oa[.='1']">
+										<xsl:for-each select="//dc:relation[starts-with(., 'http')]">
+											<oaf:fulltext>
+												<xsl:value-of select="normalize-space(.)" />
+											</oaf:fulltext>
+										</xsl:for-each>
+									</xsl:if>
+
+									<xsl:for-each select="//base_dc:collection/@ror_id">
+										<oaf:relation relType="resultOrganization" subRelType="affiliation" relClass="hasAuthorInstitution" targetType="organization">
+											<xsl:choose>
+												<xsl:when test="contains(.,'https://ror.org/')">
+													<xsl:value-of select="concat('ror_________::', normalize-space(.))" />
+												</xsl:when>
+												<xsl:otherwise>
+													<xsl:value-of select="concat('ror_________::https://ror.org/', normalize-space(.))" />
+												</xsl:otherwise>
+											</xsl:choose>
+										</oaf:relation>
+									</xsl:for-each>
+								</metadata>
+								<xsl:copy-of select="//*[local-name() = 'about']" />
+							</record>
+						</xsl:template>
+
+						<xsl:template match="//*[local-name() = 'header']">
+							<xsl:if test="//oai:header/@status='deleted'">
+								<xsl:call-template name="terminate" />
+							</xsl:if>
+							<xsl:copy>
+								<xsl:apply-templates select="node()|@*" />
+								<xsl:element name="dr:dateOfTransformation">
+									<xsl:value-of select="$transDate" />
+								</xsl:element>
+							</xsl:copy>
+						</xsl:template>
+
+						<xsl:template match="node()|@*">
+							<xsl:copy>
+								<xsl:apply-templates select="node()|@*" />
+							</xsl:copy>
+						</xsl:template>
+					</xsl:stylesheet>
+				</CODE>
+			</SCRIPT>
+		</CONFIGURATION>
+		<STATUS />
+		<SECURITY_PARAMETERS />
+	</BODY>
+</RESOURCE_PROFILE>

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkApplyUpdate.scala

@@ -0,0 +1,120 @@
+package eu.dnetlib.dhp.collection.orcid
+
+import eu.dnetlib.dhp.application.AbstractScalaApplication
+import org.apache.spark.sql.{DataFrame, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+class SparkApplyUpdate(propertyPath: String, args: Array[String], log: Logger)
+    extends AbstractScalaApplication(propertyPath, args, log: Logger) {
+
+  /** Here all the spark applications runs this method
+    * where the whole logic of the spark node is defined
+    */
+  override def run(): Unit = {
+
+    val graphPath: String = parser.get("graphPath")
+    log.info("found parameters graphPath: {}", graphPath)
+    val updatePath: String = parser.get("updatePath")
+    log.info("found parameters updatePath: {}", updatePath)
+    val targetPath: String = parser.get("targetPath")
+    log.info("found parameters targetPath: {}", targetPath)
+    applyTableUpdate(spark, graphPath, updatePath, targetPath)
+    checkUpdate(spark, graphPath, targetPath)
+    moveTable(spark, graphPath, targetPath)
+
+  }
+
+  private def moveTable(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
+    spark.read
+      .load(s"$updatePath/Authors")
+      .repartition(1000)
+      .write
+      .mode(SaveMode.Overwrite)
+      .save(s"$graphPath/Authors")
+    spark.read
+      .load(s"$updatePath/Works")
+      .repartition(1000)
+      .write
+      .mode(SaveMode.Overwrite)
+      .save(s"$graphPath/Works")
+    spark.read
+      .load(s"$updatePath/Employments")
+      .repartition(1000)
+      .write
+      .mode(SaveMode.Overwrite)
+      .save(s"$graphPath/Employments")
+
+  }
+
+  private def updateDataset(
+    inputDataset: DataFrame,
+    idUpdate: DataFrame,
+    updateDataframe: DataFrame,
+    targetPath: String
+  ): Unit = {
+    inputDataset
+      .join(idUpdate, inputDataset("orcid").equalTo(idUpdate("orcid")), "leftanti")
+      .select(inputDataset("*"))
+      .unionByName(updateDataframe)
+      .write
+      .mode(SaveMode.Overwrite)
+      .save(targetPath)
+  }
+
+  private def checkUpdate(spark: SparkSession, graphPath: String, updatePath: String): Unit = {
+    val totalOriginalAuthors = spark.read.load(s"$graphPath/Authors").count
+    val totalOriginalWorks = spark.read.load(s"$graphPath/Works").count
+    val totalOriginalEmployments = spark.read.load(s"$graphPath/Employments").count
+    val totalUpdateAuthors = spark.read.load(s"$updatePath/Authors").count
+    val totalUpdateWorks = spark.read.load(s"$updatePath/Works").count
+    val totalUpdateEmployments = spark.read.load(s"$updatePath/Employments").count
+
+    log.info("totalOriginalAuthors: {}", totalOriginalAuthors)
+    log.info("totalOriginalWorks: {}", totalOriginalWorks)
+    log.info("totalOriginalEmployments: {}", totalOriginalEmployments)
+    log.info("totalUpdateAuthors: {}", totalUpdateAuthors)
+    log.info("totalUpdateWorks: {}", totalUpdateWorks)
+    log.info("totalUpdateEmployments: {}", totalUpdateEmployments)
+    if (
+      totalUpdateAuthors < totalOriginalAuthors || totalUpdateEmployments < totalOriginalEmployments || totalUpdateWorks < totalOriginalWorks
+    )
+      throw new RuntimeException("The updated Graph contains less elements of the original one")
+
+  }
+
+  private def applyTableUpdate(spark: SparkSession, graphPath: String, updatePath: String, targetPath: String): Unit = {
+    val orcidIDUpdate = spark.read.load(s"$updatePath/Authors").select("orcid")
+    updateDataset(
+      spark.read.load(s"$graphPath/Authors"),
+      orcidIDUpdate,
+      spark.read.load(s"$updatePath/Authors"),
+      s"$targetPath/Authors"
+    )
+    updateDataset(
+      spark.read.load(s"$graphPath/Employments"),
+      orcidIDUpdate,
+      spark.read.load(s"$updatePath/Employments"),
+      s"$targetPath/Employments"
+    )
+    updateDataset(
+      spark.read.load(s"$graphPath/Works"),
+      orcidIDUpdate,
+      spark.read.load(s"$updatePath/Works"),
+      s"$targetPath/Works"
+    )
+  }
+
+}
+
+object SparkApplyUpdate {
+
+  val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass)
+
+  def main(args: Array[String]): Unit = {
+
+    new SparkApplyUpdate("/eu/dnetlib/dhp/collection/orcid/apply_orcid_table_parameter.json", args, log)
+      .initialize()
+      .run()
+
+  }
+}

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala

@@ -6,6 +6,7 @@ import org.apache.hadoop.io.Text
 import org.apache.spark.SparkContext
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
+import scala.collection.JavaConverters._
 
 class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger)
     extends AbstractScalaApplication(propertyPath, args, log: Logger) {
@@ -18,12 +19,16 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
     log.info("found parameters sourcePath: {}", sourcePath)
     val targetPath: String = parser.get("targetPath")
     log.info("found parameters targetPath: {}", targetPath)
-    extractORCIDTable(spark, sourcePath, targetPath)
-    extractORCIDEmploymentsTable(spark, sourcePath, targetPath)
-    extractORCIDWorksTable(spark, sourcePath, targetPath)
+    val fromUpdate = "true".equals(parser.get("fromUpdate"))
+    val sourceSummaryPath = if (fromUpdate) s"$sourcePath/summary*" else sourcePath
+    val sourceEmploymentsPath = if (fromUpdate) s"$sourcePath/employments*" else sourcePath
+    val sourceWorksPath = if (fromUpdate) s"$sourcePath/works*" else sourcePath
+    extractORCIDTable(spark, sourceSummaryPath, targetPath, fromUpdate)
+    extractORCIDEmploymentsTable(spark, sourceEmploymentsPath, targetPath, fromUpdate)
+    extractORCIDWorksTable(spark, sourceWorksPath, targetPath, fromUpdate)
   }
 
-  def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
+  def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String, skipFilterByKey: Boolean): Unit = {
     val sc: SparkContext = spark.sparkContext
     import spark.implicits._
     val df = sc
@@ -32,8 +37,8 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
       .toDF
       .as[(String, String)]
     implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author])
-//    implicit  val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid])
-    df.filter(r => r._1.contains("summaries"))
+    val newDf = if (!skipFilterByKey) df.filter(r => r._1.contains("summaries")) else df
+    newDf
       .map { r =>
         val p = new OrcidParser
         p.parseSummary(r._2)
@@ -44,7 +49,12 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
       .save(s"$targetPath/Authors")
   }
 
-  def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
+  def extractORCIDWorksTable(
+    spark: SparkSession,
+    sourcePath: String,
+    targetPath: String,
+    skipFilterByKey: Boolean
+  ): Unit = {
     val sc: SparkContext = spark.sparkContext
     import spark.implicits._
     val df = sc
@@ -53,7 +63,19 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
       .toDF
       .as[(String, String)]
     implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work])
-    implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
+
+    //We are in the case of parsing ORCID UPDATE
+    if (skipFilterByKey) {
+      df.flatMap { r =>
+        val p = new OrcidParser
+        p.parseWorks(r._2).asScala
+      }.filter(p => p != null)
+        .write
+        .mode(SaveMode.Overwrite)
+        .save(s"$targetPath/Works")
+    }
+    //We are in the case of parsing ORCID DUMP
+    else {
       df.filter(r => r._1.contains("works"))
         .map { r =>
           val p = new OrcidParser
@@ -64,8 +86,14 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
         .mode(SaveMode.Overwrite)
         .save(s"$targetPath/Works")
     }
+  }
 
-  def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = {
+  def extractORCIDEmploymentsTable(
+    spark: SparkSession,
+    sourcePath: String,
+    targetPath: String,
+    skipFilterByKey: Boolean
+  ): Unit = {
     val sc: SparkContext = spark.sparkContext
     import spark.implicits._
     val df = sc
@@ -74,7 +102,17 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
       .toDF
       .as[(String, String)]
     implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment])
-    implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid])
+    if (skipFilterByKey) {
+      df.flatMap { r =>
+        val p = new OrcidParser
+        p.parseEmployments(r._2).asScala
+      }.filter(p => p != null)
+        .write
+        .mode(SaveMode.Overwrite)
+        .save(s"$targetPath/Employments")
+    }
+    //We are in the case of parsing ORCID DUMP
+    else {
       df.filter(r => r._1.contains("employments"))
         .map { r =>
           val p = new OrcidParser
@@ -85,6 +123,7 @@ class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Lo
         .mode(SaveMode.Overwrite)
         .save(s"$targetPath/Employments")
     }
+  }
 }
 
 object SparkGenerateORCIDTable {

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java

@@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest {
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
-		String pubmedAffiliationRelationsPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
-			.getPath();
-
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
@@ -89,7 +85,8 @@ public class PrepareAffiliationRelationsTest {
 				new String[] {
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
 					"-crossrefInputPath", crossrefAffiliationRelationPath,
-					"-pubmedInputPath", pubmedAffiliationRelationsPath,
+					"-pubmedInputPath", crossrefAffiliationRelationPath,
+					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -106,7 +103,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(40, tmp.count());
+		assertEquals(60, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -117,7 +114,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				20, execVerification
+				30, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -125,7 +122,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				20, execVerification
+				30, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java

@@ -0,0 +1,324 @@
+
+package eu.dnetlib.dhp.actionmanager.transformativeagreement;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+
+/**
+ * @author miriam.baglioni
+ * @Date 13/02/24
+ */
+public class CreateTAActionSetTest {
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(CreateOpenCitationsASTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(CreateTAActionSetTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CreateTAActionSetTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(CreateTAActionSetTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void createActionSet() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/transformativeagreement/facts.json")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.transformativeagreement.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet1"
+				});
+
+	}
+
+	@Test
+	void testNumberofRelations2() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet2"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		assertEquals(23, tmp.count());
+
+		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+
+	}
+
+	@Test
+	void testRelationsCollectedFrom() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet3"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
+			assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
+		});
+
+	}
+
+	@Test
+	void testRelationsDataInfo() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet4"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(false, r.getDataInfo().getInferred());
+			assertEquals(false, r.getDataInfo().getDeletedbyinference());
+			assertEquals("0.91", r.getDataInfo().getTrust());
+			assertEquals(
+				eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSID,
+				r.getDataInfo().getProvenanceaction().getClassid());
+			assertEquals(
+				eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME,
+				r.getDataInfo().getProvenanceaction().getClassname());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
+		});
+
+	}
+
+	@Test
+	void testRelationsSemantics() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet5"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("citation", r.getSubRelType());
+			assertEquals("resultResult", r.getRelType());
+		});
+		assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
+		assertEquals(0, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
+
+	}
+
+	@Test
+	void testRelationsSourceTargetPrefix() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet6"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("50|doi_________::", r.getSource().substring(0, 17));
+			assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
+		});
+
+	}
+
+	@Test
+	void testRelationsSourceTargetCouple() throws Exception {
+		final String doi1 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
+		final String doi2 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
+		final String doi3 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
+		final String doi4 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
+		final String doi5 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
+		final String doi6 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet7"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
+
+		assertEquals(5, check.count());
+
+//		check.foreach(r -> {
+//			if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
+//				r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
+//				assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
+//				assertEquals(doi1, r.getTarget());
+//			}
+//		});
+
+		assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
+		check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.collection.orcid;
 
 import java.io.IOException;
+import java.net.URI;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Objects;
@@ -9,7 +10,12 @@ import java.util.Objects;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.CompressionCodec;
+import org.apache.hadoop.io.compress.CompressionCodecFactory;
 import org.apache.spark.SparkContext;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.Encoders;
@@ -27,6 +33,7 @@ import com.ximpleware.XPathParseException;
 
 import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem;
+import eu.dnetlib.dhp.collection.orcid.model.Work;
 import eu.dnetlib.dhp.parser.utility.VtdException;
 
 public class DownloadORCIDTest {
@@ -82,6 +89,34 @@ public class DownloadORCIDTest {
 		});
 	}
 
+	@Test
+	public void testParsingOrcidUpdateEmployments() throws Exception {
+		final String xml = IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_employments.xml")));
+
+		final OrcidParser parser = new OrcidParser();
+		final ObjectMapper mapper = new ObjectMapper();
+		System.out.println(mapper.writeValueAsString(parser.parseEmployments(xml)));
+	}
+
+	@Test
+	public void testParsingOrcidUpdateWorks() throws Exception {
+		final String xml = IOUtils
+			.toString(
+				Objects
+					.requireNonNull(
+						getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/update_work.xml")));
+
+		final OrcidParser parser = new OrcidParser();
+		final List<Work> works = parser.parseWorks(xml);
+
+		final ObjectMapper mapper = new ObjectMapper();
+		System.out.println(mapper.writeValueAsString(works));
+	}
+
 	@Test
 	public void testParsingEmployments() throws Exception {
 

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectionInfo.java

@@ -0,0 +1,38 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import java.io.Serializable;
+
+public class BaseCollectionInfo implements Serializable {
+
+	private static final long serialVersionUID = 5766333937429419647L;
+
+	private String id;
+	private String opendoarId;
+	private String rorId;
+
+	public String getId() {
+		return this.id;
+	}
+
+	public void setId(final String id) {
+		this.id = id;
+	}
+
+	public String getOpendoarId() {
+		return this.opendoarId;
+	}
+
+	public void setOpendoarId(final String opendoarId) {
+		this.opendoarId = opendoarId;
+	}
+
+	public String getRorId() {
+		return this.rorId;
+	}
+
+	public void setRorId(final String rorId) {
+		this.rorId = rorId;
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorIteratorTest.java

@@ -0,0 +1,184 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicInteger;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.dom4j.Attribute;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Element;
+import org.dom4j.Node;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+
+@Disabled
+public class BaseCollectorIteratorTest {
+
+	@Test
+	void testImportFile() throws Exception {
+
+		long count = 0;
+
+		final BaseCollectorIterator iterator = new BaseCollectorIterator("base-sample.tar", new AggregatorReport());
+
+		final Map<String, Map<String, String>> collections = new HashMap<>();
+		final Map<String, AtomicInteger> fields = new HashMap<>();
+		final Set<String> types = new HashSet<>();
+
+		while (iterator.hasNext()) {
+
+			final Document record = DocumentHelper.parseText(iterator.next());
+
+			count++;
+
+			if ((count % 1000) == 0) {
+				System.out.println("# Read records: " + count);
+			}
+
+			// System.out.println(record.asXML());
+
+			for (final Object o : record.selectNodes("//*|//@*")) {
+				final String path = ((Node) o).getPath();
+
+				if (fields.containsKey(path)) {
+					fields.get(path).incrementAndGet();
+				} else {
+					fields.put(path, new AtomicInteger(1));
+				}
+
+				if (o instanceof Element) {
+					final Element n = (Element) o;
+
+					if ("collection".equals(n.getName())) {
+						final String collName = n.getText().trim();
+						if (StringUtils.isNotBlank(collName) && !collections.containsKey(collName)) {
+							final Map<String, String> collAttrs = new HashMap<>();
+							for (final Object ao : n.attributes()) {
+								collAttrs.put(((Attribute) ao).getName(), ((Attribute) ao).getValue());
+							}
+							collections.put(collName, collAttrs);
+						}
+					} else if ("type".equals(n.getName())) {
+						types.add(n.getText().trim());
+					}
+
+				}
+			}
+
+		}
+
+		final ObjectMapper mapper = new ObjectMapper();
+		for (final Entry<String, Map<String, String>> e : collections.entrySet()) {
+			System.out.println(e.getKey() + ": " + mapper.writeValueAsString(e.getValue()));
+
+		}
+
+		for (final Entry<String, AtomicInteger> e : fields.entrySet()) {
+			System.out.println(e.getKey() + ": " + e.getValue().get());
+
+		}
+
+		System.out.println("TYPES: ");
+		for (final String s : types) {
+			System.out.println(s);
+
+		}
+
+		assertEquals(30000, count);
+	}
+
+	@Test
+	public void testParquet() throws Exception {
+
+		final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
+
+		final SparkSession spark = SparkSession.builder().master("local[*]").getOrCreate();
+
+		final List<BaseRecordInfo> ls = new ArrayList<>();
+
+		for (int i = 0; i < 10; i++) {
+			ls.add(extractInfo(xml));
+		}
+
+		final JavaRDD<BaseRecordInfo> rdd = JavaSparkContext
+			.fromSparkContext(spark.sparkContext())
+			.parallelize(ls);
+
+		final Dataset<BaseRecordInfo> df = spark
+			.createDataset(rdd.rdd(), Encoders.bean(BaseRecordInfo.class));
+
+		df.printSchema();
+
+		df.show(false);
+	}
+
+	private BaseRecordInfo extractInfo(final String s) {
+		try {
+			final Document record = DocumentHelper.parseText(s);
+
+			final BaseRecordInfo info = new BaseRecordInfo();
+
+			final Set<String> paths = new LinkedHashSet<>();
+			final Set<String> types = new LinkedHashSet<>();
+			final List<BaseCollectionInfo> colls = new ArrayList<>();
+
+			for (final Object o : record.selectNodes("//*|//@*")) {
+				paths.add(((Node) o).getPath());
+
+				if (o instanceof Element) {
+					final Element n = (Element) o;
+
+					final String nodeName = n.getName();
+
+					if ("collection".equals(nodeName)) {
+						final String collName = n.getText().trim();
+
+						if (StringUtils.isNotBlank(collName)) {
+							final BaseCollectionInfo coll = new BaseCollectionInfo();
+							coll.setId(collName);
+							coll.setOpendoarId(n.valueOf("@opendoar_id").trim());
+							coll.setRorId(n.valueOf("@ror_id").trim());
+							colls.add(coll);
+						}
+					} else if ("type".equals(nodeName)) {
+						types.add("TYPE: " + n.getText().trim());
+					} else if ("typenorm".equals(nodeName)) {
+						types.add("TYPE_NORM: " + n.getText().trim());
+					}
+				}
+			}
+
+			info.setId(record.valueOf("//*[local-name() = 'header']/*[local-name() = 'identifier']").trim());
+			info.getTypes().addAll(types);
+			info.getPaths().addAll(paths);
+			info.setCollections(colls);
+
+			return info;
+		} catch (final DocumentException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseCollectorPluginTest.java

@@ -0,0 +1,32 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Test;
+
+class BaseCollectorPluginTest {
+
+	@Test
+	void testFilterXml() throws Exception {
+		final String xml = IOUtils.toString(getClass().getResourceAsStream("record.xml"));
+
+		final Set<String> validIds = new HashSet<>(Arrays.asList("opendoar____::1234", "opendoar____::4567"));
+		final Set<String> validTypes = new HashSet<>(Arrays.asList("1", "121"));
+		final Set<String> validTypes2 = new HashSet<>(Arrays.asList("1", "11"));
+
+		assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, validTypes));
+		assertTrue(BaseCollectorPlugin.filterXml(xml, validIds, new HashSet<>()));
+
+		assertFalse(BaseCollectorPlugin.filterXml(xml, new HashSet<>(), validTypes));
+		assertFalse(BaseCollectorPlugin.filterXml(xml, validIds, validTypes2));
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseRecordInfo.java

@@ -0,0 +1,49 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+public class BaseRecordInfo implements Serializable {
+
+	private static final long serialVersionUID = -8848232018350074593L;
+
+	private String id;
+	private List<BaseCollectionInfo> collections = new ArrayList<>();
+	private List<String> paths = new ArrayList<>();
+	private List<String> types = new ArrayList<>();
+
+	public String getId() {
+		return this.id;
+	}
+
+	public void setId(final String id) {
+		this.id = id;
+	}
+
+	public List<String> getPaths() {
+		return this.paths;
+	}
+
+	public void setPaths(final List<String> paths) {
+		this.paths = paths;
+	}
+
+	public List<String> getTypes() {
+		return this.types;
+	}
+
+	public void setTypes(final List<String> types) {
+		this.types = types;
+	}
+
+	public List<BaseCollectionInfo> getCollections() {
+		return this.collections;
+	}
+
+	public void setCollections(final List<BaseCollectionInfo> collections) {
+		this.collections = collections;
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/base/BaseTransfomationTest.java

@@ -0,0 +1,94 @@
+
+package eu.dnetlib.dhp.collection.plugin.base;
+
+import static org.junit.jupiter.api.Assertions.assertThrows;
+
+import java.io.IOException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.util.LongAccumulator;
+import org.dom4j.io.SAXReader;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
+
+import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest;
+import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
+import eu.dnetlib.dhp.schema.mdstore.MetadataRecord;
+import eu.dnetlib.dhp.schema.mdstore.Provenance;
+import eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+
+// @Disabled
+@ExtendWith(MockitoExtension.class)
+public class BaseTransfomationTest extends AbstractVocabularyTest {
+
+	private SparkConf sparkConf;
+
+	@BeforeEach
+	public void setUp() throws IOException, ISLookUpException {
+		setUpVocabulary();
+
+		this.sparkConf = new SparkConf();
+		this.sparkConf.setMaster("local[*]");
+		this.sparkConf.set("spark.driver.host", "localhost");
+		this.sparkConf.set("spark.ui.enabled", "false");
+	}
+
+	@Test
+	void testBase2ODF() throws Exception {
+
+		final MetadataRecord mr = new MetadataRecord();
+		mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
+		mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml")));
+
+		final XSLTTransformationFunction tr = loadTransformationRule("xml/base2odf.transformationRule.xml");
+
+		final MetadataRecord result = tr.call(mr);
+
+		System.out.println(result.getBody());
+	}
+
+	@Test
+	void testBase2OAF() throws Exception {
+
+		final MetadataRecord mr = new MetadataRecord();
+		mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
+		mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record.xml")));
+
+		final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml");
+
+		final MetadataRecord result = tr.call(mr);
+
+		System.out.println(result.getBody());
+	}
+
+	@Test
+	void testBase2ODF_wrong_date() throws Exception {
+
+		final MetadataRecord mr = new MetadataRecord();
+		mr.setProvenance(new Provenance("DSID", "DSNAME", "PREFIX"));
+		mr.setBody(IOUtils.toString(getClass().getResourceAsStream("record_wrong_1.xml")));
+
+		final XSLTTransformationFunction tr = loadTransformationRule("xml/base2oaf.transformationRule.xml");
+
+		assertThrows(NullPointerException.class, () -> {
+			final MetadataRecord result = tr.call(mr);
+			System.out.println(result.getBody());
+		});
+	}
+
+	private XSLTTransformationFunction loadTransformationRule(final String path) throws Exception {
+		final String xslt = new SAXReader()
+				.read(this.getClass().getResourceAsStream(path))
+				.selectSingleNode("//CODE/*")
+				.asXML();
+
+		final LongAccumulator la = new LongAccumulator();
+
+		return new XSLTTransformationFunction(new AggregationCounter(la, la, la), xslt, 0, this.vocabularies);
+	}
+
+}

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

@@ -9,6 +9,7 @@ import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
 /**
@@ -37,7 +38,7 @@ public class RestIteratorTest {
 
 	@Disabled
 	@Test
-	public void test() {
+	public void test() throws CollectorException {
 
 		HttpClientParams clientParams = new HttpClientParams();
 

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtilsTest.java

@@ -0,0 +1,48 @@
+
+package eu.dnetlib.dhp.collection.plugin.utils;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import org.junit.jupiter.api.Test;
+
+class JsonUtilsTest {
+
+	static private String wrapped(String xml) {
+		return "<?xml version=\"1.0\" encoding=\"UTF-8\"?><recordWrap>" + xml + "</recordWrap>";
+	}
+
+	@Test
+	void keyStartWithDigit() {
+		assertEquals(
+			wrapped("<m_100><n_200v>null</n_200v></m_100>"),
+			JsonUtils.convertToXML("{\"100\" : {\"200v\" : null}}"));
+	}
+
+	@Test
+	void keyStartWithSpecialchars() {
+		assertEquals(
+			wrapped("<_parent><_nest1><_nest2>null</_nest2></_nest1></_parent>"),
+			JsonUtils.convertToXML("{\"   parent\" : {\"-nest1\" : {\".nest2\" : null}}}"));
+	}
+
+	@Test
+	void encodeArray() {
+		assertEquals(
+			wrapped("<_parent.child>1</_parent.child><_parent.child>2</_parent.child>"),
+			JsonUtils.convertToXML("{\" parent.child\":[1, 2]}"));
+	}
+
+	@Test
+	void arrayOfObjects() {
+		assertEquals(
+			wrapped("<parent><id>1</id></parent><parent><id>2</id></parent>"),
+			JsonUtils.convertToXML("{\"parent\": [{\"id\": 1}, {\"id\": 2}]}"));
+	}
+
+	@Test
+	void removeControlCharacters() {
+		assertEquals(
+			wrapped("<m_100><n_200v>Test</n_200v></m_100>"),
+			JsonUtils.convertToXML("{\"100\" : {\"200v\" : \"\\u0000\\u000cTest\"}}"));
+	}
+}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary2.xml

@@ -0,0 +1,966 @@
+<record:record path="/0000-0001-6816-8350" xmlns:internal="http://www.orcid.org/ns/internal" xmlns:education="http://www.orcid.org/ns/education" xmlns:distinction="http://www.orcid.org/ns/distinction" xmlns:deprecated="http://www.orcid.org/ns/deprecated" xmlns:other-name="http://www.orcid.org/ns/other-name" xmlns:membership="http://www.orcid.org/ns/membership" xmlns:error="http://www.orcid.org/ns/error" xmlns:common="http://www.orcid.org/ns/common" xmlns:record="http://www.orcid.org/ns/record" xmlns:personal-details="http://www.orcid.org/ns/personal-details" xmlns:keyword="http://www.orcid.org/ns/keyword" xmlns:email="http://www.orcid.org/ns/email" xmlns:external-identifier="http://www.orcid.org/ns/external-identifier" xmlns:funding="http://www.orcid.org/ns/funding" xmlns:preferences="http://www.orcid.org/ns/preferences" xmlns:address="http://www.orcid.org/ns/address" xmlns:invited-position="http://www.orcid.org/ns/invited-position" xmlns:work="http://www.orcid.org/ns/work" xmlns:history="http://www.orcid.org/ns/history" xmlns:employment="http://www.orcid.org/ns/employment" xmlns:qualification="http://www.orcid.org/ns/qualification" xmlns:service="http://www.orcid.org/ns/service" xmlns:person="http://www.orcid.org/ns/person" xmlns:activities="http://www.orcid.org/ns/activities" xmlns:researcher-url="http://www.orcid.org/ns/researcher-url" xmlns:peer-review="http://www.orcid.org/ns/peer-review" xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:research-resource="http://www.orcid.org/ns/research-resource">
+    <common:orcid-identifier>
+        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+        <common:path>0000-0001-6816-8350</common:path>
+        <common:host>orcid.org</common:host>
+    </common:orcid-identifier>
+    <preferences:preferences>
+        <preferences:locale>en</preferences:locale>
+    </preferences:preferences>
+    <history:history>
+        <history:creation-method>Direct</history:creation-method>
+        <history:submission-date>2016-01-06T05:08:45.720Z</history:submission-date>
+        <common:last-modified-date>2024-01-02T20:07:05.186Z</common:last-modified-date>
+        <history:claimed>true</history:claimed>
+        <history:verified-email>true</history:verified-email>
+        <history:verified-primary-email>true</history:verified-primary-email>
+    </history:history>
+    <person:person path="/0000-0001-6816-8350/person">
+        <common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
+        <other-name:other-names path="/0000-0001-6816-8350/other-names"/>
+        <researcher-url:researcher-urls path="/0000-0001-6816-8350/researcher-urls">
+            <common:last-modified-date>2016-02-09T09:18:18.417Z</common:last-modified-date>
+            <researcher-url:researcher-url put-code="633431" visibility="public" path="/0000-0001-6816-8350/researcher-urls/633431" display-index="0">
+                <common:created-date>2016-02-09T09:18:18.416Z</common:created-date>
+                <common:last-modified-date>2016-02-09T09:18:18.417Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <researcher-url:url-name>Dr Michael Muchiri</researcher-url:url-name>
+                <researcher-url:url>http://www.rmit.edu.au/contact/staff-contacts/academic-staff/m/muchiri-dr-michael</researcher-url:url>
+            </researcher-url:researcher-url>
+        </researcher-url:researcher-urls>
+        <email:emails path="/0000-0001-6816-8350/email"/>
+        <address:addresses path="/0000-0001-6816-8350/address">
+            <common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
+            <address:address put-code="897528" visibility="public" path="/0000-0001-6816-8350/address/897528" display-index="2">
+                <common:created-date>2018-02-13T02:32:04.094Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:32:05.269Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <address:country>AU</address:country>
+            </address:address>
+            <address:address put-code="3191142" visibility="public" path="/0000-0001-6816-8350/address/3191142" display-index="1">
+                <common:created-date>2023-12-02T13:32:05.260Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:32:05.260Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <address:country>SA</address:country>
+            </address:address>
+        </address:addresses>
+        <keyword:keywords path="/0000-0001-6816-8350/keywords">
+            <common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
+            <keyword:keyword put-code="368304" visibility="public" path="/0000-0001-6816-8350/keywords/368304" display-index="4">
+                <common:created-date>2016-02-09T09:16:44.001Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <keyword:content>Organizational Behavior</keyword:content>
+            </keyword:keyword>
+            <keyword:keyword put-code="368303" visibility="public" path="/0000-0001-6816-8350/keywords/368303" display-index="3">
+                <common:created-date>2016-02-09T09:16:27.374Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <keyword:content>Organizational Leadership</keyword:content>
+            </keyword:keyword>
+            <keyword:keyword put-code="368306" visibility="public" path="/0000-0001-6816-8350/keywords/368306" display-index="2">
+                <common:created-date>2016-02-09T09:17:08.998Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:31:16.269Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <keyword:content>Organizational performance</keyword:content>
+            </keyword:keyword>
+            <keyword:keyword put-code="3590814" visibility="public" path="/0000-0001-6816-8350/keywords/3590814" display-index="1">
+                <common:created-date>2023-12-02T13:31:16.259Z</common:created-date>
+                <common:last-modified-date>2023-12-02T13:31:16.259Z</common:last-modified-date>
+                <common:source>
+                    <common:source-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-orcid>
+                </common:source>
+                <keyword:content>Thriving at work</keyword:content>
+            </keyword:keyword>
+        </keyword:keywords>
+        <external-identifier:external-identifiers path="/0000-0001-6816-8350/external-identifiers">
+            <common:last-modified-date>2018-04-10T00:49:55.386Z</common:last-modified-date>
+            <external-identifier:external-identifier put-code="998076" visibility="public" path="/0000-0001-6816-8350/external-identifiers/998076" display-index="0">
+                <common:created-date>2018-04-10T00:49:55.385Z</common:created-date>
+                <common:last-modified-date>2018-04-10T00:49:55.386Z</common:last-modified-date>
+                <common:source>
+                    <common:source-client-id>
+                        <common:uri>https://orcid.org/client/0000-0003-1377-5676</common:uri>
+                        <common:path>0000-0003-1377-5676</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:source-client-id>
+                    <common:source-name>ResearcherID</common:source-name>
+                    <common:assertion-origin-orcid>
+                        <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                        <common:path>0000-0001-6816-8350</common:path>
+                        <common:host>orcid.org</common:host>
+                    </common:assertion-origin-orcid>
+                </common:source>
+                <common:external-id-type>ResearcherID</common:external-id-type>
+                <common:external-id-value>D-1929-2018</common:external-id-value>
+                <common:external-id-url>http://www.researcherid.com/rid/D-1929-2018</common:external-id-url>
+                <common:external-id-relationship>self</common:external-id-relationship>
+            </external-identifier:external-identifier>
+        </external-identifier:external-identifiers>
+    </person:person>
+    <activities:activities-summary path="/0000-0001-6816-8350/activities">
+        <common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
+        <activities:distinctions path="/0000-0001-6816-8350/distinctions"/>
+        <activities:educations path="/0000-0001-6816-8350/educations">
+            <common:last-modified-date>2018-02-13T02:33:38.225Z</common:last-modified-date>
+            <activities:affiliation-group>
+                <common:last-modified-date>2016-02-09T06:55:21.838Z</common:last-modified-date>
+                <common:external-ids/>
+                <education:education-summary put-code="1549986" display-index="0" path="/0000-0001-6816-8350/education/1549986" visibility="public">
+                    <common:created-date>2016-02-09T06:54:39.199Z</common:created-date>
+                    <common:last-modified-date>2016-02-09T06:55:21.838Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-orcid>
+                            <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                            <common:path>0000-0001-6816-8350</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-orcid>
+                    </common:source>
+                    <common:department-name>Management</common:department-name>
+                    <common:role-title>PhD</common:role-title>
+                    <common:start-date>
+                        <common:year>2021</common:year>
+                    </common:start-date>
+                    <common:end-date>
+                        <common:year>2022</common:year>
+                        <common:month>02</common:month>
+                        <common:day>12</common:day>
+                    </common:end-date>
+                    <common:start-date>
+                        <common:year>2003</common:year>
+                        <common:month>03</common:month>
+                    </common:start-date>
+                    <common:end-date>
+                        <common:year>2007</common:year>
+                        <common:month>03</common:month>
+                    </common:end-date>
+                    <common:organization>
+                        <common:name>University of New England</common:name>
+                        <common:address>
+                            <common:city>Armidale</common:city>
+                            <common:region>NSW</common:region>
+                            <common:country>AU</common:country>
+                        </common:address>
+                        <common:disambiguated-organization>
+                            <common:disambiguated-organization-identifier>1319</common:disambiguated-organization-identifier>
+                            <common:disambiguation-source>RINGGOLD</common:disambiguation-source>
+                        </common:disambiguated-organization>
+                    </common:organization>
+                </education:education-summary>
+            </activities:affiliation-group>
+            <activities:affiliation-group>
+                <common:last-modified-date>2018-02-13T02:33:38.225Z</common:last-modified-date>
+                <common:external-ids/>
+                <education:education-summary put-code="1549990" display-index="0" path="/0000-0001-6816-8350/education/1549990" visibility="public">
+                    <common:created-date>2016-02-09T06:57:04.181Z</common:created-date>
+                    <common:last-modified-date>2018-02-13T02:33:38.225Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-orcid>
+                            <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                            <common:path>0000-0001-6816-8350</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-orcid>
+                    </common:source>
+                    <common:department-name>Psychology</common:department-name>
+                    <common:role-title>Master of Science (Industrial and Organizational) Psychology</common:role-title>
+                    <common:start-date>
+                        <common:year>1998</common:year>
+                        <common:month>01</common:month>
+                    </common:start-date>
+                    <common:end-date>
+                        <common:year>2000</common:year>
+                        <common:month>01</common:month>
+                    </common:end-date>
+                    <common:organization>
+                        <common:name>Universitas Gadjah Mada</common:name>
+                        <common:address>
+                            <common:city>Yogyakarta</common:city>
+                            <common:region>Daerah Istimewa Yogyakart</common:region>
+                            <common:country>ID</common:country>
+                        </common:address>
+                        <common:disambiguated-organization>
+                            <common:disambiguated-organization-identifier>59166</common:disambiguated-organization-identifier>
+                            <common:disambiguation-source>RINGGOLD</common:disambiguation-source>
+                        </common:disambiguated-organization>
+                    </common:organization>
+                </education:education-summary>
+            </activities:affiliation-group>
+            <activities:affiliation-group>
+                <common:last-modified-date>2018-02-13T02:33:35.821Z</common:last-modified-date>
+                <common:external-ids/>
+                <education:education-summary put-code="1549998" display-index="0" path="/0000-0001-6816-8350/education/1549998" visibility="public">
+                    <common:created-date>2016-02-09T06:58:59.869Z</common:created-date>
+                    <common:last-modified-date>2018-02-13T02:33:35.821Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-orcid>
+                            <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                            <common:path>0000-0001-6816-8350</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-orcid>
+                    </common:source>
+                    <common:department-name>Education</common:department-name>
+                    <common:role-title>Bachelor of Education (Honors)</common:role-title>
+                    <common:start-date>
+                        <common:year>1988</common:year>
+                        <common:month>03</common:month>
+                    </common:start-date>
+                    <common:end-date>
+                        <common:year>1991</common:year>
+                        <common:month>03</common:month>
+                    </common:end-date>
+                    <common:organization>
+                        <common:name>Kenyatta University</common:name>
+                        <common:address>
+                            <common:city>Nairobi</common:city>
+                            <common:region>Nairobi</common:region>
+                            <common:country>KE</common:country>
+                        </common:address>
+                        <common:disambiguated-organization>
+                            <common:disambiguated-organization-identifier>107864</common:disambiguated-organization-identifier>
+                            <common:disambiguation-source>RINGGOLD</common:disambiguation-source>
+                        </common:disambiguated-organization>
+                    </common:organization>
+                </education:education-summary>
+            </activities:affiliation-group>
+        </activities:educations>
+        <activities:employments path="/0000-0001-6816-8350/employments">
+            <common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
+            <activities:affiliation-group>
+                <common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
+                <common:external-ids/>
+                <employment:employment-summary put-code="21884863" display-index="1" path="/0000-0001-6816-8350/employment/21884863" visibility="public">
+                    <common:created-date>2023-12-02T13:28:26.051Z</common:created-date>
+                    <common:last-modified-date>2023-12-02T13:28:26.051Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-orcid>
+                            <common:uri>https://orcid.org/0000-0001-6816-8350</common:uri>
+                            <common:path>0000-0001-6816-8350</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-orcid>
+                    </common:source>
+                    <common:department-name>Management</common:department-name>
+                    <common:role-title>Associate Professor in Management</common:role-title>
+                    <common:start-date>
+                        <common:year>2023</common:year>
+                        <common:month>08</common:month>
+                        <common:day>20</common:day>
+                    </common:start-date>
+                    <common:organization>
+                        <common:name>Alfaisal University</common:name>
+                        <common:address>
+                            <common:city>Riyadh</common:city>
+                            <common:country>SA</common:country>
+                        </common:address>
+                        <common:disambiguated-organization>
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+                                <common:path>APP-945VYTN20C7BZXYT</common:path>
+                                <common:host>orcid.org</common:host>
+                            </common:source-client-id>
+                            <common:source-name>Springer Nature @ Editorial Manager</common:source-name>
+                        </common:source>
+                        <peer-review:reviewer-role>reviewer</peer-review:reviewer-role>
+                        <common:external-ids>
+                            <common:external-id>
+                                <common:external-id-type>source-work-id</common:external-id-type>
+                                <common:external-id-value>c9bdf086-cfee-4cd9-bcfb-268cc5423248</common:external-id-value>
+                                <common:external-id-normalized transient="true">c9bdf086-cfee-4cd9-bcfb-268cc5423248</common:external-id-normalized>
+                                <common:external-id-url></common:external-id-url>
+                                <common:external-id-relationship>self</common:external-id-relationship>
+                            </common:external-id>
+                        </common:external-ids>
+                        <peer-review:review-type>review</peer-review:review-type>
+                        <peer-review:completion-date>
+                            <common:year>2023</common:year>
+                        </peer-review:completion-date>
+                        <peer-review:review-group-id>issn:0167-4544</peer-review:review-group-id>
+                        <peer-review:convening-organization>
+                            <common:name>Springer Nature</common:name>
+                            <common:address>
+                                <common:city>New York</common:city>
+                                <common:country>US</common:country>
+                            </common:address>
+                            <common:disambiguated-organization>
+                                <common:disambiguated-organization-identifier>grid.467660.5</common:disambiguated-organization-identifier>
+                                <common:disambiguation-source>GRID</common:disambiguation-source>
+                            </common:disambiguated-organization>
+                        </peer-review:convening-organization>
+                    </peer-review:peer-review-summary>
+                </activities:peer-review-group>
+                <activities:peer-review-group>
+                    <common:last-modified-date>2023-05-31T05:53:44.542Z</common:last-modified-date>
+                    <common:external-ids>
+                        <common:external-id>
+                            <common:external-id-type>source-work-id</common:external-id-type>
+                            <common:external-id-value>c442840b-5807-459d-802a-303d8ba4e25e</common:external-id-value>
+                            <common:external-id-normalized transient="true">c442840b-5807-459d-802a-303d8ba4e25e</common:external-id-normalized>
+                            <common:external-id-url></common:external-id-url>
+                            <common:external-id-relationship>self</common:external-id-relationship>
+                        </common:external-id>
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+                        <common:last-modified-date>2023-05-31T05:53:44.542Z</common:last-modified-date>
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+                                <common:path>APP-945VYTN20C7BZXYT</common:path>
+                                <common:host>orcid.org</common:host>
+                            </common:source-client-id>
+                            <common:source-name>Springer Nature @ Editorial Manager</common:source-name>
+                        </common:source>
+                        <peer-review:reviewer-role>reviewer</peer-review:reviewer-role>
+                        <common:external-ids>
+                            <common:external-id>
+                                <common:external-id-type>source-work-id</common:external-id-type>
+                                <common:external-id-value>c442840b-5807-459d-802a-303d8ba4e25e</common:external-id-value>
+                                <common:external-id-normalized transient="true">c442840b-5807-459d-802a-303d8ba4e25e</common:external-id-normalized>
+                                <common:external-id-url></common:external-id-url>
+                                <common:external-id-relationship>self</common:external-id-relationship>
+                            </common:external-id>
+                        </common:external-ids>
+                        <peer-review:review-type>review</peer-review:review-type>
+                        <peer-review:completion-date>
+                            <common:year>2023</common:year>
+                        </peer-review:completion-date>
+                        <peer-review:review-group-id>issn:0167-4544</peer-review:review-group-id>
+                        <peer-review:convening-organization>
+                            <common:name>Springer Nature</common:name>
+                            <common:address>
+                                <common:city>New York</common:city>
+                                <common:country>US</common:country>
+                            </common:address>
+                            <common:disambiguated-organization>
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+                                <common:disambiguation-source>GRID</common:disambiguation-source>
+                            </common:disambiguated-organization>
+                        </peer-review:convening-organization>
+                    </peer-review:peer-review-summary>
+                </activities:peer-review-group>
+            </activities:group>
+        </activities:peer-reviews>
+        <activities:qualifications path="/0000-0001-6816-8350/qualifications"/>
+        <activities:research-resources path="/0000-0001-6816-8350/research-resources"/>
+        <activities:services path="/0000-0001-6816-8350/services"/>
+        <activities:works path="/0000-0001-6816-8350/works">
+            <common:last-modified-date>2023-06-02T20:12:00.338Z</common:last-modified-date>
+            <activities:group>
+                <common:last-modified-date>2023-06-02T20:12:00.338Z</common:last-modified-date>
+                <common:external-ids>
+                    <common:external-id>
+                        <common:external-id-type>doi</common:external-id-type>
+                        <common:external-id-value>10.4337/9781800881945.00020</common:external-id-value>
+                        <common:external-id-normalized transient="true">10.4337/9781800881945.00020</common:external-id-normalized>
+                        <common:external-id-url>https://doi.org/10.4337/9781800881945.00020</common:external-id-url>
+                        <common:external-id-relationship>self</common:external-id-relationship>
+                    </common:external-id>
+                </common:external-ids>
+                <work:work-summary put-code="134891279" path="/0000-0001-6816-8350/work/134891279" visibility="public" display-index="0">
+                    <common:created-date>2023-05-11T21:05:54.188Z</common:created-date>
+                    <common:last-modified-date>2023-06-02T20:12:00.338Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-client-id>
+                            <common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
+                            <common:path>0000-0001-9884-1913</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-client-id>
+                        <common:source-name>Crossref</common:source-name>
+                    </common:source>
+                    <work:title>
+                        <common:title>Ethical leadership as workplace innovation and enabler for employee commitment and innovative work behaviours in Vietnam</common:title>
+                    </work:title>
+                    <common:external-ids>
+                        <common:external-id>
+                            <common:external-id-type>doi</common:external-id-type>
+                            <common:external-id-value>10.4337/9781800881945.00020</common:external-id-value>
+                            <common:external-id-normalized transient="true">10.4337/9781800881945.00020</common:external-id-normalized>
+                            <common:external-id-url>https://doi.org/10.4337/9781800881945.00020</common:external-id-url>
+                            <common:external-id-relationship>self</common:external-id-relationship>
+                        </common:external-id>
+                    </common:external-ids>
+                    <common:url>https://doi.org/10.4337/9781800881945.00020</common:url>
+                    <work:type>book-chapter</work:type>
+                    <common:publication-date>
+                        <common:year>2023</common:year>
+                        <common:month>05</common:month>
+                        <common:day>26</common:day>
+                    </common:publication-date>
+                </work:work-summary>
+            </activities:group>
+            <activities:group>
+                <common:last-modified-date>2023-03-01T11:30:31.972Z</common:last-modified-date>
+                <common:external-ids>
+                    <common:external-id>
+                        <common:external-id-type>doi</common:external-id-type>
+                        <common:external-id-value>10.1007/s10551-022-05081-6</common:external-id-value>
+                        <common:external-id-normalized transient="true">10.1007/s10551-022-05081-6</common:external-id-normalized>
+                        <common:external-id-url>https://doi.org/10.1007/s10551-022-05081-6</common:external-id-url>
+                        <common:external-id-relationship>self</common:external-id-relationship>
+                    </common:external-id>
+                </common:external-ids>
+                <work:work-summary put-code="110048777" path="/0000-0001-6816-8350/work/110048777" visibility="public" display-index="0">
+                    <common:created-date>2022-03-18T03:36:55.927Z</common:created-date>
+                    <common:last-modified-date>2023-03-01T11:30:31.972Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-client-id>
+                            <common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
+                            <common:path>0000-0001-9884-1913</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-client-id>
+                        <common:source-name>Crossref</common:source-name>
+                    </common:source>
+                    <work:title>
+                        <common:title>Unethical Leadership: Review, Synthesis and Directions for Future Research</common:title>
+                    </work:title>
+                    <common:external-ids>
+                        <common:external-id>
+                            <common:external-id-type>doi</common:external-id-type>
+                            <common:external-id-value>10.1007/s10551-022-05081-6</common:external-id-value>
+                            <common:external-id-normalized transient="true">10.1007/s10551-022-05081-6</common:external-id-normalized>
+                            <common:external-id-url>https://doi.org/10.1007/s10551-022-05081-6</common:external-id-url>
+                            <common:external-id-relationship>self</common:external-id-relationship>
+                        </common:external-id>
+                    </common:external-ids>
+                    <common:url>https://doi.org/10.1007/s10551-022-05081-6</common:url>
+                    <work:type>journal-article</work:type>
+                    <common:publication-date>
+                        <common:year>2023</common:year>
+                        <common:month>03</common:month>
+                    </common:publication-date>
+                    <work:journal-title>Journal of Business Ethics</work:journal-title>
+                </work:work-summary>
+            </activities:group>
+            <activities:group>
+                <common:last-modified-date>2022-05-28T18:16:16.575Z</common:last-modified-date>
+                <common:external-ids>
+                    <common:external-id>
+                        <common:external-id-type>doi</common:external-id-type>
+                        <common:external-id-value>10.1017/jmo.2019.33</common:external-id-value>
+                        <common:external-id-normalized transient="true">10.1017/jmo.2019.33</common:external-id-normalized>
+                        <common:external-id-url>https://doi.org/10.1017/jmo.2019.33</common:external-id-url>
+                        <common:external-id-relationship>self</common:external-id-relationship>
+                    </common:external-id>
+                </common:external-ids>
+                <work:work-summary put-code="57272180" path="/0000-0001-6816-8350/work/57272180" visibility="public" display-index="0">
+                    <common:created-date>2019-05-10T07:23:14.608Z</common:created-date>
+                    <common:last-modified-date>2022-05-28T18:16:16.575Z</common:last-modified-date>
+                    <common:source>
+                        <common:source-client-id>
+                            <common:uri>https://orcid.org/client/0000-0001-9884-1913</common:uri>
+                            <common:path>0000-0001-9884-1913</common:path>
+                            <common:host>orcid.org</common:host>
+                        </common:source-client-id>
+                        <common:source-name>Crossref</common:source-name>
+                    </common:source>
+                    <work:title>
+                        <common:title>And now for something completely different: Reframing social processes of leadership theory using positive organisational behaviour</common:title>
+                    </work:title>
+                    <common:external-ids>
+                        <common:external-id>
+                            <common:external-id-type>doi</common:external-id-type>
+                            <common:external-id-value>10.1017/jmo.2019.33</common:external-id-value>
+                            <common:external-id-normalized transient="true">10.1017/jmo.2019.33</common:external-id-normalized>
+                            <common:external-id-url>https://doi.org/10.1017/jmo.2019.33</common:external-id-url>
+                            <common:external-id-relationship>self</common:external-id-relationship>
+                        </common:external-id>
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+                    <common:url>https://doi.org/10.1017/jmo.2019.33</common:url>
+                    <work:type>journal-article</work:type>
+                    <common:publication-date>
+                        <common:year>2019</common:year>
+                        <common:month>05</common:month>
+                        <common:day>09</common:day>
+                    </common:publication-date>
+                    <work:journal-title>Journal of Management &amp; Organization</work:journal-title>
+                </work:work-summary>
+            </activities:group>
+        </activities:works>
+    </activities:activities-summary>
+</record:record>

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/update_employments.xml

@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<activities:employments path="/0000-0002-0456-1185/employments" xmlns:internal="http://www.orcid.org/ns/internal" xmlns:education="http://www.orcid.org/ns/education" xmlns:distinction="http://www.orcid.org/ns/distinction" xmlns:deprecated="http://www.orcid.org/ns/deprecated" xmlns:other-name="http://www.orcid.org/ns/other-name" xmlns:membership="http://www.orcid.org/ns/membership" xmlns:error="http://www.orcid.org/ns/error" xmlns:common="http://www.orcid.org/ns/common" xmlns:record="http://www.orcid.org/ns/record" xmlns:personal-details="http://www.orcid.org/ns/personal-details" xmlns:keyword="http://www.orcid.org/ns/keyword" xmlns:email="http://www.orcid.org/ns/email" xmlns:external-identifier="http://www.orcid.org/ns/external-identifier" xmlns:funding="http://www.orcid.org/ns/funding" xmlns:preferences="http://www.orcid.org/ns/preferences" xmlns:address="http://www.orcid.org/ns/address" xmlns:invited-position="http://www.orcid.org/ns/invited-position" xmlns:work="http://www.orcid.org/ns/work" xmlns:history="http://www.orcid.org/ns/history" xmlns:employment="http://www.orcid.org/ns/employment" xmlns:qualification="http://www.orcid.org/ns/qualification" xmlns:service="http://www.orcid.org/ns/service" xmlns:person="http://www.orcid.org/ns/person" xmlns:activities="http://www.orcid.org/ns/activities" xmlns:researcher-url="http://www.orcid.org/ns/researcher-url" xmlns:peer-review="http://www.orcid.org/ns/peer-review" xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:research-resource="http://www.orcid.org/ns/research-resource">
+    <common:last-modified-date>2024-01-07T23:59:38.869Z</common:last-modified-date>
+    <activities:affiliation-group>
+        <common:last-modified-date>2024-01-07T23:59:38.869Z</common:last-modified-date>
+        <common:external-ids/>
+        <employment:employment-summary put-code="22127142" display-index="0" path="/0000-0002-0456-1185/employment/22127142" visibility="public">
+            <common:created-date>2024-01-07T23:59:38.869Z</common:created-date>
+            <common:last-modified-date>2024-01-07T23:59:38.869Z</common:last-modified-date>
+            <common:source>
+                <common:source-client-id>
+                    <common:uri>https://orcid.org/client/APP-N0TAO4G9BBK9PWHT</common:uri>
+                    <common:path>APP-N0TAO4G9BBK9PWHT</common:path>
+                    <common:host>orcid.org</common:host>
+                </common:source-client-id>
+                <common:source-name>Tampere University</common:source-name>
+            </common:source>
+            <common:organization>
+                <common:name>Tampere University</common:name>
+                <common:address>
+                    <common:city>Tampere</common:city>
+                    <common:country>FI</common:country>
+                </common:address>
+                <common:disambiguated-organization>
+                    <common:disambiguated-organization-identifier>https://ror.org/033003e23</common:disambiguated-organization-identifier>
+                    <common:disambiguation-source>ROR</common:disambiguation-source>
+                </common:disambiguated-organization>
+            </common:organization>
+        </employment:employment-summary>
+    </activities:affiliation-group>
+    <activities:affiliation-group>
+        <common:last-modified-date>2019-01-03T17:00:05.658Z</common:last-modified-date>
+        <common:external-ids/>
+        <employment:employment-summary put-code="3291239" display-index="1" path="/0000-0002-0456-1185/employment/3291239" visibility="public">
+            <common:created-date>2017-02-26T04:46:20.917Z</common:created-date>
+            <common:last-modified-date>2019-01-03T17:00:05.658Z</common:last-modified-date>
+            <common:source>
+                <common:source-orcid>
+                    <common:uri>https://orcid.org/0000-0002-0456-1185</common:uri>
+                    <common:path>0000-0002-0456-1185</common:path>
+                    <common:host>orcid.org</common:host>
+                </common:source-orcid>
+                <common:source-name>Tiina Manninen</common:source-name>
+            </common:source>
+            <common:department-name> Faculty of Medicine and Health Technology</common:department-name>
+            <common:role-title>Academy Research Fellow</common:role-title>
+            <common:organization>
+                <common:name>Tampere University</common:name>
+                <common:address>
+                    <common:city>Tampere</common:city>
+                    <common:country>FI</common:country>
+                </common:address>
+                <common:disambiguated-organization>
+                    <common:disambiguated-organization-identifier>7839</common:disambiguated-organization-identifier>
+                    <common:disambiguation-source>RINGGOLD</common:disambiguation-source>
+                </common:disambiguated-organization>
+            </common:organization>
+        </employment:employment-summary>
+    </activities:affiliation-group>
+</activities:employments>

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record.xml

@@ -0,0 +1,58 @@
+<record>
+  <header xmlns="http://www.openarchives.org/OAI/2.0/">
+    <identifier>ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1</identifier>
+    <datestamp>2022-12-31T11:48:55Z</datestamp>
+  </header>
+  <metadata xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:base_dc="http://oai.base-search.net/base_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/">
+    <base_dc:dc xsi:schemaLocation="http://oai.base-search.net/base_dc/ http://oai.base-search.net/base_dc/base_dc.xsd">
+      <base_dc:global_id>ftdoajarticles:oai:doaj.org/article:e2d5b5126b2d4e479933cc7f9a9ae0c1</base_dc:global_id>
+      <base_dc:continent>cww</base_dc:continent>
+      <base_dc:country>org</base_dc:country>
+      <base_dc:collection opendoar_id="1234" ror_id="ror1234">ftdoajarticles</base_dc:collection>
+      <base_dc:collname>TEST REPO</base_dc:collname>
+      <dc:title>Assessment of cultural heritage: the legislative and methodological framework of Russian Federation</dc:title>
+      <dc:creator>ALBU, Svetlana</dc:creator>
+      <dc:creator>LEȘAN, Anna</dc:creator>
+      <dc:subject>architectural heritage</dc:subject>
+      <dc:subject>evaluation of architectural heritage</dc:subject>
+      <dc:subject>types of values</dc:subject>
+      <dc:subject>experience of russian federation</dc:subject>
+      <dc:subject>Social Sciences</dc:subject>
+      <dc:subject>H</dc:subject>
+      <dc:description>Architectural heritage is the real estate inheritance by population of a country becoming an extremely valuable and specific category, preserving and capitalizing on those assets requires considerable effort. The state does not have sufficient means to maintain and preserve cultural heritage, as a result it is included in the civil circuit. The transfer of property right or of some partial rights over the architectural patrimony is accompanied by the necessity to estimate the value of goods. In this article, the authors examine the experience of Russian Federation (one of the largest countries with a huge architectural heritage) on the legislative framework of architectural and methodological heritage of architectural heritage assessment. The particularities of cultural assets valuation compared to other categories of real estate are examined, as well as the methodological aspects (types of values, methods applied in valuation, approaches according to the purpose of valuation) regarding the valuation of real estate with architectural value in Russian Federation.</dc:description>
+      <dc:publisher>Technical University of Moldova</dc:publisher>
+      <dc:date>2020-09-01T00:00:00Z</dc:date>
+      <base_dc:year>2020</base_dc:year>
+      <dc:type>article</dc:type>
+      <base_dc:typenorm>121</base_dc:typenorm>
+      <dc:identifier>https://doi.org/10.5281/zenodo.3971988</dc:identifier>
+      <dc:identifier>https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1</dc:identifier>
+      <base_dc:link>https://doi.org/10.5281/zenodo.3971988</base_dc:link>
+      <dc:source>Journal of Social Sciences, Vol 3, Iss 3, Pp 134-143 (2020)</dc:source>
+      <dc:language>EN</dc:language>
+      <dc:language>FR</dc:language>
+      <dc:language>RO</dc:language>
+      <dc:relation>http://ibn.idsi.md/sites/default/files/imag_file/JSS-3-2020_134-143.pdf</dc:relation>
+      <dc:relation>https://doaj.org/toc/2587-3490</dc:relation>
+      <dc:relation>https://doaj.org/toc/2587-3504</dc:relation>
+      <dc:relation>doi:10.5281/zenodo.3971988</dc:relation>
+      <dc:relation>2587-3490</dc:relation>
+      <dc:relation>2587-3504</dc:relation>
+      <dc:relation>https://doaj.org/article/e2d5b5126b2d4e479933cc7f9a9ae0c1</dc:relation>
+      <base_dc:autoclasscode type="ddc">720</base_dc:autoclasscode>
+      <base_dc:authod_id>
+        <base_dc:creator_name>ALBU, Svetlana</base_dc:creator_name>
+        <base_dc:creator_id>https://orcid.org/0000-0002-8648-950X</base_dc:creator_id>
+      </base_dc:authod_id>
+      <base_dc:authod_id>
+        <base_dc:creator_name>LEȘAN, Anna</base_dc:creator_name>
+        <base_dc:creator_id>https://orcid.org/0000-0003-3284-0525</base_dc:creator_id>
+      </base_dc:authod_id>
+      <base_dc:doi>https://doi.org/10.5281/zenodo.3971988</base_dc:doi>
+      <base_dc:oa>1</base_dc:oa>
+      <base_dc:lang>eng</base_dc:lang>
+      <base_dc:lang>fre</base_dc:lang>
+      <base_dc:lang>rum</base_dc:lang>
+    </base_dc:dc>
+  </metadata>
+</record>

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/base/record_wrong_1.xml

@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>                                          
+<record>
+  <header xmlns="http://www.openarchives.org/OAI/2.0/">
+    <identifier>ftunivminnesdc:oai:conservancy.umn.edu:11299/109914</identifier>
+    <datestamp>2023-07-18T20:05:40Z</datestamp>
+  </header>
+  <metadata xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:base_dc="http://oai.base-search.net/base_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/">
+    <base_dc:dc xsi:schemaLocation="http://oai.base-search.net/base_dc/ http://oai.base-search.net/base_dc/base_dc.xsd">
+      <base_dc:global_id>ftunivminnesdc:oai:conservancy.umn.edu:11299/109914</base_dc:global_id>
+      <base_dc:continent>cna</base_dc:continent>
+      <base_dc:country>us</base_dc:country>
+      <base_dc:collection opendoar_id="1008">ftunivminnesdc</base_dc:collection>
+      <base_dc:collname>University of Minnesota Digital Conservancy</base_dc:collname>
+      <dc:title>An Experimental Investigation of the influence of an air bubble layer on radiated noise and surface pressure fluctuations in a turbulent boundary layer</dc:title>
+      <dc:creator>Killen, John M.</dc:creator>
+      <dc:subject>Boundary layer noise</dc:subject>
+      <dc:subject>Kinetic energy dissipation</dc:subject>
+      <dc:subject>Air bubble layer</dc:subject>
+      <dc:subject>Maximum stable bubble size</dc:subject>
+      <dc:subject>bubble noise spectra</dc:subject>
+      <dc:description>between the noise spectra of a layer of air bubbles in a turbulent flow and' a maximum stable bubble size which can exist in the same flow. An air bubbie layer with individual bubble sizes greater than a maximum stable size was introduced into the boundary layer of water flowing along a smooth flat plate. It was found that the maximum stable bubble size was related to the turbulent kinetic energy dissipation as had been previously shown by other investigators ; Office of Naval Research Arlington, Virginia 22217</dc:description>
+      <dc:date>1981-09-31T21:42:52Z</dc:date>
+      <base_dc:year>1981</base_dc:year>
+      <dc:type>Report</dc:type>
+      <base_dc:typenorm>14</base_dc:typenorm>
+      <dc:identifier>http://purl.umn.edu/109914</dc:identifier>
+      <base_dc:link>http://purl.umn.edu/109914</base_dc:link>
+      <dc:language>en_US</dc:language>
+      <dc:relation>Project Reports</dc:relation>
+      <dc:relation>202</dc:relation>
+      <dc:relation>http://purl.umn.edu/109914</dc:relation>
+      <base_dc:oa>2</base_dc:oa>
+      <base_dc:lang>eng</base_dc:lang>
+    </base_dc:dc>
+  </metadata>
+</record>

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/synonyms.txt

@@ -1497,3 +1497,29 @@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ CDS132
 cnr:institutes @=@ https://ror.org/0263zy895 @=@ SCITEC - Istituto di Scienze e Tecnologie Chimiche \"Giulio Natta\"
 cnr:institutes @=@ __CDS133__ @=@ CDS133
 cnr:institutes @=@ __CDS133__ @=@ STEMS - Istituto di Scienze e Tecnologie per l'Energia e la Mobilità Sostenibili
+base:normalized_types @=@ Text @=@ 1
+base:normalized_types @=@ Book @=@ 11
+base:normalized_types @=@ Book part @=@ 111
+base:normalized_types @=@ Journal/Newspaper @=@ 12
+base:normalized_types @=@ Article contribution @=@ 121
+base:normalized_types @=@ Other non-article @=@ 122
+base:normalized_types @=@ Conference object @=@ 13
+base:normalized_types @=@ Report @=@ 14
+base:normalized_types @=@ Review @=@ 15
+base:normalized_types @=@ Course material @=@ 16
+base:normalized_types @=@ Lecture @=@ 17
+base:normalized_types @=@ Thesis @=@ 18
+base:normalized_types @=@ Bachelor's thesis @=@ 181
+base:normalized_types @=@ Master's thesis @=@ 182
+base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ 183
+base:normalized_types @=@ Manuscript @=@ 19
+base:normalized_types @=@ Patent @=@ 1A
+base:normalized_types @=@ Musical notation @=@ 2
+base:normalized_types @=@ Map @=@ 3
+base:normalized_types @=@ Audio @=@ 4
+base:normalized_types @=@ Image/Video @=@ 5
+base:normalized_types @=@ Still image @=@ 51
+base:normalized_types @=@ Moving image/Video @=@ 52
+base:normalized_types @=@ Software @=@ 6
+base:normalized_types @=@ Dataset @=@ 7
+base:normalized_types @=@ Unknown @=@ F

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt

@@ -1210,4 +1210,29 @@ cnr:institutes @=@ cnr:institutes @=@ __CDS130__ @=@ __CDS130__
 cnr:institutes @=@ cnr:institutes @=@ __CDS131__ @=@ __CDS131__
 cnr:institutes @=@ cnr:institutes @=@ https://ror.org/0263zy895 @=@ https://ror.org/0263zy895
 cnr:institutes @=@ cnr:institutes @=@ __CDS133__ @=@ __CDS133__
-
+base:normalized_types @=@ base:normalized_types @=@ Text @=@ Text
+base:normalized_types @=@ base:normalized_types @=@ Book @=@ Book
+base:normalized_types @=@ base:normalized_types @=@ Book part @=@ Book part
+base:normalized_types @=@ base:normalized_types @=@ Journal/Newspaper @=@ Journal/Newspaper
+base:normalized_types @=@ base:normalized_types @=@ Article contribution @=@ Article contribution
+base:normalized_types @=@ base:normalized_types @=@ Other non-article @=@ Other non-article
+base:normalized_types @=@ base:normalized_types @=@ Conference object @=@ Conference object
+base:normalized_types @=@ base:normalized_types @=@ Report @=@ Report
+base:normalized_types @=@ base:normalized_types @=@ Review @=@ Review
+base:normalized_types @=@ base:normalized_types @=@ Course material @=@ Course material
+base:normalized_types @=@ base:normalized_types @=@ Lecture @=@ Lecture
+base:normalized_types @=@ base:normalized_types @=@ Thesis @=@ Thesis
+base:normalized_types @=@ base:normalized_types @=@ Bachelor's thesis @=@ Bachelor's thesis
+base:normalized_types @=@ base:normalized_types @=@ Master's thesis @=@ Master's thesis
+base:normalized_types @=@ base:normalized_types @=@ Doctoral and postdoctoral thesis @=@ Doctoral and postdoctoral thesis
+base:normalized_types @=@ base:normalized_types @=@ Manuscript @=@ Manuscript
+base:normalized_types @=@ base:normalized_types @=@ Patent @=@ Patent
+base:normalized_types @=@ base:normalized_types @=@ Musical notation @=@ Musical notation
+base:normalized_types @=@ base:normalized_types @=@ Map @=@ Map
+base:normalized_types @=@ base:normalized_types @=@ Audio @=@ Audio
+base:normalized_types @=@ base:normalized_types @=@ Image/Video @=@ Image/Video
+base:normalized_types @=@ base:normalized_types @=@ Still image @=@ Still image
+base:normalized_types @=@ base:normalized_types @=@ Moving image/Video @=@ Moving image/Video
+base:normalized_types @=@ base:normalized_types @=@ Software @=@ Software
+base:normalized_types @=@ base:normalized_types @=@ Dataset @=@ Dataset
+base:normalized_types @=@ base:normalized_types @=@ Unknown @=@ Unknown

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

@@ -1,26 +1,29 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import eu.dnetlib.dhp.oa.dedup.model.Identifier;
-import eu.dnetlib.dhp.oa.merge.AuthorMerger;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Author;
-import eu.dnetlib.dhp.schema.oaf.DataInfo;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Result;
+import java.util.*;
+import java.util.stream.Stream;
+
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
+
+import eu.dnetlib.dhp.oa.dedup.model.Identifier;
+import eu.dnetlib.dhp.oa.merge.AuthorMerger;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
+import eu.dnetlib.dhp.schema.oaf.Author;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
 import scala.Tuple2;
 import scala.Tuple3;
 import scala.collection.JavaConversions;
 
-import java.util.*;
-import java.util.stream.Stream;
-
 public class DedupRecordFactory {
     public static final class DedupRecordReduceState {
         public final String dedupId;
@@ -39,7 +42,8 @@ public class DedupRecordFactory {
             } else {
                 if (Result.class.isAssignableFrom(entity.getClass())) {
                     Result result = (Result) entity;
-                    if (result.getDateofacceptance() != null && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
+                    if (result.getDateofacceptance() != null
+                            && StringUtils.isNotBlank(result.getDateofacceptance().getValue())) {
                         acceptanceDate.add(result.getDateofacceptance().getValue());
                     }
                 }
@@ -50,6 +54,7 @@ public class DedupRecordFactory {
             return dedupId;
         }
     }
+
     private static final int MAX_ACCEPTANCE_DATE = 20;
 
     private DedupRecordFactory() {
@@ -90,8 +95,12 @@ public class DedupRecordFactory {
                 .join(entities, JavaConversions.asScalaBuffer(Collections.singletonList("id")), "left")
                 .select("dedupId", "id", "kryoObject")
                 .as(Encoders.tuple(Encoders.STRING(), Encoders.STRING(), kryoEncoder))
-                .map((MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(t._1(), t._2(), t._3()), Encoders.kryo(DedupRecordReduceState.class))
-                .groupByKey((MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
+                .map(
+                        (MapFunction<Tuple3<String, String, OafEntity>, DedupRecordReduceState>) t -> new DedupRecordReduceState(
+                                t._1(), t._2(), t._3()),
+                        Encoders.kryo(DedupRecordReduceState.class))
+                .groupByKey(
+                        (MapFunction<DedupRecordReduceState, String>) DedupRecordReduceState::getDedupId, Encoders.STRING())
                 .reduceGroups(
                         (ReduceFunction<DedupRecordReduceState>) (t1, t2) -> {
                             if (t1.entity == null) {
@@ -105,10 +114,8 @@ public class DedupRecordFactory {
                             t1.entity = reduceEntity(t1.entity, t2.entity);
 
                             return t1;
-                        }
-                )
-                .flatMap
-                        ((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
+                        })
+                .flatMap((FlatMapFunction<Tuple2<String, DedupRecordReduceState>, OafEntity>) t -> {
                     String dedupId = t._1();
                     DedupRecordReduceState agg = t._2();
 
@@ -116,10 +123,21 @@ public class DedupRecordFactory {
                         return Collections.emptyIterator();
                     }
 
-                            return Stream.concat(Stream.of(agg.getDedupId()), agg.aliases.stream())
-                                    .map(id -> {
+                    return Stream
+                            .concat(
+                                    Stream
+                                            .of(agg.getDedupId())
+                                            .map(id -> createDedupOafEntity(id, agg.entity, dataInfo, ts)),
+                                    agg.aliases
+                                            .stream()
+                                            .map(id -> createMergedDedupAliasOafEntity(id, agg.entity, dataInfo, ts)))
+                            .iterator();
+                }, beanEncoder);
+    }
+
+    private static OafEntity createDedupOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
         try {
-                                            OafEntity res = (OafEntity) BeanUtils.cloneBean(agg.entity);
+            OafEntity res = (OafEntity) BeanUtils.cloneBean(base);
             res.setId(id);
             res.setDataInfo(dataInfo);
             res.setLastupdatetimestamp(ts);
@@ -127,8 +145,18 @@ public class DedupRecordFactory {
         } catch (Exception e) {
             throw new RuntimeException(e);
         }
-                                    }).iterator();
-                        }, beanEncoder);
+    }
+
+    private static OafEntity createMergedDedupAliasOafEntity(String id, OafEntity base, DataInfo dataInfo, long ts) {
+        try {
+            OafEntity res = createDedupOafEntity(id, base, dataInfo, ts);
+            DataInfo ds = (DataInfo) BeanUtils.cloneBean(dataInfo);
+            ds.setDeletedbyinference(true);
+            res.setDataInfo(ds);
+            return res;
+        } catch (Exception e) {
+            throw new RuntimeException(e);
+        }
     }
 
     private static OafEntity reduceEntity(OafEntity entity, OafEntity duplicate) {
@@ -137,7 +165,6 @@ public class DedupRecordFactory {
             return entity;
         }
 
-
         int compare = new IdentifierComparator<>()
                 .compare(Identifier.newInstance(entity), Identifier.newInstance(duplicate));
 
@@ -147,7 +174,7 @@ public class DedupRecordFactory {
             entity = swap;
         }
 
-        entity.mergeFrom(duplicate);
+        entity = MergeUtils.checkedMerge(entity, duplicate);
 
         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

@@ -242,13 +242,14 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 
 						// this was a pivot in a previous graph but it has been merged into a new group with different
 						// pivot
-						if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id) && !dedupId.equals(pivotDedupId)) {
+						if (!r.isNullAt(r.fieldIndex("lastUsage")) && !pivot.equals(id)
+							&& !dedupId.equals(pivotDedupId)) {
 							// materialize the previous dedup record as a merge relation with the new one
 							res.add(new Tuple3<>(dedupId, pivotDedupId, null));
 						}
 
 						// add merge relations
-						if (cut <=0 || r.<Integer>getAs("position") <= cut) {
+						if (cut <= 0 || r.<Integer> getAs("position") <= cut) {
 							res.add(new Tuple3<>(id, pivotDedupId, pivot));
 						}
 

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

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static org.apache.spark.sql.functions.col;
 
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
@@ -127,10 +128,8 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 				(MapFunction<Relation, String>) r -> String
 					.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
 				Encoders.STRING())
-			.reduceGroups((ReduceFunction<Relation>) (b, a) -> {
-				b.mergeFrom(a);
-				return b;
-			})
+			.reduceGroups((ReduceFunction<Relation>) MergeUtils::mergeRelation
+			)
 			.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
 
 		final String outputRelationPath = graphOutputPath + "/relation";

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/config-default.xml

@@ -0,0 +1,26 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>sparkSqlWarehouseDir</name>
+        <value>/user/hive/warehouse</value>
+    </property>
+</configuration>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql

@@ -0,0 +1,62 @@
+
+CREATE TABLE `${pivot_history_db}`.`dataset_new` STORED AS PARQUET AS
+WITH pivots (
+    SELECT property.value AS id, '${new_graph_date}' AS usedIn  FROM `${new_graph_db}`.`relation`
+    LEFT SEMI JOIN `${new_graph_db}`.`dataset` ON relation.source = dataset.id
+    LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
+UNION
+    SELECT id, usedIn FROM `${pivot_history_db}`.`dataset` LATERAL VIEW EXPLODE(usages) AS usedIn
+)
+SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
+    FROM pivots
+    GROUP BY id; /*EOS*/
+CREATE TABLE `${pivot_history_db}`.`publication_new` STORED AS PARQUET AS
+WITH pivots (
+    SELECT property.value AS id, '${new_graph_date}' AS usedIn  FROM `${new_graph_db}`.`relation`
+    LEFT SEMI JOIN `${new_graph_db}`.`publication` ON relation.source = publication.id
+    LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
+UNION
+    SELECT id, usedIn FROM `${pivot_history_db}`.`publication` LATERAL VIEW EXPLODE(usages) AS usedIn
+)
+SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
+    FROM pivots
+    GROUP BY id; /*EOS*/
+CREATE TABLE `${pivot_history_db}`.`software_new` STORED AS PARQUET AS
+WITH pivots (
+    SELECT property.value AS id, '${new_graph_date}' AS usedIn  FROM `${new_graph_db}`.`relation`
+    LEFT SEMI JOIN `${new_graph_db}`.`software` ON relation.source = software.id
+    LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
+UNION
+    SELECT id, usedIn FROM `${pivot_history_db}`.`software` LATERAL VIEW EXPLODE(usages) AS usedIn
+)
+SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
+    FROM pivots
+    GROUP BY id; /*EOS*/
+CREATE TABLE `${pivot_history_db}`.`otherresearchproduct_new` STORED AS PARQUET AS
+WITH pivots (
+    SELECT property.value AS id, '${new_graph_date}' AS usedIn  FROM `${new_graph_db}`.`relation`
+     LEFT SEMI JOIN `${new_graph_db}`.`otherresearchproduct` ON relation.source = otherresearchproduct.id
+     LATERAL VIEW EXPLODE(properties) AS property WHERE relClass = 'isMergedIn' AND property.key = 'pivot'
+UNION
+    SELECT id, usedIn FROM `${pivot_history_db}`.`otherresearchproduct` LATERAL VIEW EXPLODE(usages) AS usedIn
+)
+SELECT id, min(usedIn) as firstUsage, max(usedIn) as lastUsage, collect_set(usedIn) as usages
+    FROM pivots
+    GROUP BY id; /*EOS*/
+
+
+DROP TABLE IF EXISTS `${pivot_history_db}`.`dataset_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`dataset` RENAME TO `${pivot_history_db}`.`dataset_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`dataset_new` RENAME TO `${pivot_history_db}`.`dataset`; /*EOS*/
+
+DROP TABLE IF EXISTS `${pivot_history_db}`.`publication_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`publication` RENAME TO `${pivot_history_db}`.`publication_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`publication_new` RENAME TO `${pivot_history_db}`.`publication`; /*EOS*/
+
+DROP TABLE IF EXISTS `${pivot_history_db}`.`software_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`software` RENAME TO `${pivot_history_db}`.`software_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`software_new` RENAME TO `${pivot_history_db}`.`software`; /*EOS*/
+
+DROP TABLE IF EXISTS `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`otherresearchproduct` RENAME TO `${pivot_history_db}`.`otherresearchproduct_old`; /*EOS*/
+ALTER TABLE `${pivot_history_db}`.`otherresearchproduct_new` RENAME TO `${pivot_history_db}`.`otherresearchproduct`; /*EOS*/

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

@@ -0,0 +1,95 @@
+<workflow-app name="Update pivot history" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <!-- properties used in SQL -->
+        <property>
+            <name>pivot_history_db</name>
+            <!-- <value>openaire_beta_pivots_test</value> -->
+            <description>Pivot history DB on hive</description>
+        </property>
+        <property>
+            <name>new_graph_db</name>
+            <!--<value>openaire_beta_20231208</value> -->
+            <description>New graph DB on hive</description>
+    </property>
+    <property>
+        <name>new_graph_date</name>
+        <!-- <value>20231208</value> -->
+        <description>Creation date of new graph db</description>
+    </property>
+
+    <!-- RunSQLSparkJob properties -->
+        <property>
+            <name>hiveMetastoreUris</name>
+            <description>hive server metastore URIs</description>
+        </property>
+        <property>
+            <name>sparkSqlWarehouseDir</name>
+        </property>
+        <!-- General oozie workflow properties -->
+        <property>
+            <name>sparkClusterOpts</name>
+            <value>--conf spark.network.timeout=600 --conf spark.extraListeners= --conf spark.sql.queryExecutionListeners= --conf spark.yarn.historyServer.address=http://iis-cdh5-test-m3.ocean.icm.edu.pl:18088 --conf spark.eventLog.dir=hdfs://nameservice1/user/spark/applicationHistory</value>
+            <description>spark cluster-wide options</description>
+        </property>
+        <property>
+            <name>sparkResourceOpts</name>
+            <value>--executor-memory=3G --conf spark.executor.memoryOverhead=3G --executor-cores=6 --driver-memory=8G --driver-cores=4</value>
+            <description>spark resource options</description>
+        </property>
+        <property>
+            <name>sparkApplicationOpts</name>
+            <value>--conf spark.sql.shuffle.partitions=3840</value>
+            <description>spark resource options</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="UpgradePivotHistory"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="UpgradePivotHistory">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Upgrade Pivot History</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/dedup/pivothistory/oozie_app/sql.sql</arg>
+            <arg>--pivot_history_db</arg><arg>${pivot_history_db}</arg>
+            <arg>--new_graph_db</arg><arg>${new_graph_db}</arg>
+            <arg>--new_graph_date</arg><arg>${new_graph_date}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -3,17 +3,18 @@ package eu.dnetlib.doiboost
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.oa.merge.AuthorMerger
 import eu.dnetlib.dhp.schema.common.ModelConstants
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils
 import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
 import eu.dnetlib.doiboost.mag.ConversionUtil
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
-import org.apache.spark.sql.expressions.Aggregator
 import org.apache.spark.sql.functions.col
 import org.apache.spark.sql._
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse
 import org.slf4j.{Logger, LoggerFactory}
+
 import scala.collection.JavaConverters._
 
 object SparkGenerateDoiBoost {
@@ -78,8 +79,10 @@ object SparkGenerateDoiBoost {
       if (item._2 != null) {
         val otherPub = item._2._2
         if (otherPub != null) {
-          crossrefPub.mergeFrom(otherPub)
-          crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor))
+          val mergedAuthor = AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)
+          val res = MergeUtils.mergePublication(crossrefPub, otherPub)
+          res.setAuthor(mergedAuthor);
+          return res
         }
       }
       crossrefPub
@@ -130,14 +133,13 @@ object SparkGenerateDoiBoost {
             // So we have to merge
             val b1 = left._2
             val b2 = right._2
-            b1.mergeFrom(b2)
-            b1.mergeOAFDataInfo(b2)
             val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
-            b1.setAuthor(authors)
+            val merged = MergeUtils.mergePublication(b1, b2);
+            merged.setAuthor(authors)
             if (b2.getId != null && b2.getId.nonEmpty)
-              b1.setId(b2.getId)
+              merged.setId(b2.getId)
             //Return publication Merged
-            (b1.getId, b1)
+            (merged.getId, merged)
           }
         } else {
           // Left is Null so we return right

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -25,7 +25,7 @@ case class mappingAffiliation(name: String) {}
 
 case class mappingAuthor(
   given: Option[String],
-  family: String,
+  family: Option[String],
   sequence: Option[String],
   ORCID: Option[String],
   affiliation: Option[mappingAffiliation]
@@ -226,14 +226,14 @@ case object Crossref2Oaf {
 
     //Mapping Author
     val authorList: List[mappingAuthor] =
-      (json \ "author").extractOrElse[List[mappingAuthor]](List())
+      (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
 
     val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) =>
       a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first")
     )
 
     result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
-      generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull, index)
+      generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index)
     }.asJava)
 
     // Mapping instance