.gitignore

@@ -27,4 +27,3 @@ spark-warehouse
 /**/.factorypath
 /**/.scalafmt.conf
 /.java-version
-/dhp-shade-package/dependency-reduced-pom.xml

dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java

@@ -80,15 +80,7 @@ class WritePredefinedProjectPropertiesTest {
 		mojo.outputFile = testFolder;
 
 		// execute
-		try {
+		Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
-			mojo.execute();
-			Assertions.assertTrue(false); // not reached
-		} catch (Exception e) {
-			Assertions
-				.assertTrue(
-					MojoExecutionException.class.isAssignableFrom(e.getClass()) ||
-						IllegalArgumentException.class.isAssignableFrom(e.getClass()));
-		}
 	}
 
 	@Test

dhp-common/pom.xml

@@ -63,14 +63,15 @@
 
 	<dependencies>
 		<dependency>
-			<groupId>edu.cmu</groupId>
+			<groupId>eu.dnetlib.dhp</groupId>
-			<artifactId>secondstring</artifactId>
+			<artifactId>dhp-pace-core</artifactId>
-		</dependency>
+			<version>${project.version}</version>
-		<dependency>
-			<groupId>com.ibm.icu</groupId>
-			<artifactId>icu4j</artifactId>
 		</dependency>
 
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-common</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>com.github.sisyphsu</groupId>
 			<artifactId>dateparser</artifactId>
@@ -160,7 +161,7 @@
 
 		<dependency>
 			<groupId>eu.dnetlib.dhp</groupId>
-			<artifactId>dhp-schemas</artifactId>
+			<artifactId>${dhp-schemas.artifact}</artifactId>
 		</dependency>
 
 		<dependency>
@@ -169,23 +170,4 @@
 		</dependency>
 	</dependencies>
 
-	<!-- dependencies required on JDK9+ because J2EE has been removed -->
-	<profiles>
-		<profile>
-			<id>spark-34</id>
-			<dependencies>
-				<dependency>
-					<groupId>javax.xml.bind</groupId>
-					<artifactId>jaxb-api</artifactId>
-					<version>2.2.11</version>
-				</dependency>
-				<dependency>
-					<groupId>com.sun.xml.ws</groupId>
-					<artifactId>jaxws-ri</artifactId>
-					<version>2.3.3</version>
-					<type>pom</type>
-				</dependency>
-			</dependencies>
-		</profile>
-	</profiles>
 </project>

dhp-common/src/main/java/eu/dnetlib/dhp/common/DbClient.java

@@ -7,12 +7,12 @@ import java.sql.*;
 import java.util.function.Consumer;
 
 import org.apache.commons.lang3.StringUtils;
-import org.slf4j.Logger;
+import org.apache.commons.logging.Log;
-import org.slf4j.LoggerFactory;
+import org.apache.commons.logging.LogFactory;
 
 public class DbClient implements Closeable {
 
-	private static final Logger log = LoggerFactory.getLogger(DbClient.class);
+	private static final Log log = LogFactory.getLog(DbClient.class);
 
 	private final Connection connection;
 
@@ -37,8 +37,6 @@ public class DbClient implements Closeable {
 		try (final Statement stmt = connection.createStatement()) {
 			stmt.setFetchSize(100);
 
-			log.info("running SQL:\n\n{}\n\n", sql);
-
 			try (final ResultSet rs = stmt.executeQuery(sql)) {
 				while (rs.next()) {
 					consumer.accept(rs);

dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java

@@ -38,7 +38,7 @@ public class PacePerson {
 					PacePerson.class
 						.getResourceAsStream(
 							"/eu/dnetlib/dhp/common/name_particles.txt")));
-		} catch (Exception e) {
+		} catch (IOException e) {
 			throw new RuntimeException(e);
 		}
 	}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java

@@ -0,0 +1,53 @@
+
+package eu.dnetlib.dhp.common.api;
+
+import java.io.IOException;
+import java.io.InputStream;
+
+import okhttp3.MediaType;
+import okhttp3.RequestBody;
+import okhttp3.internal.Util;
+import okio.BufferedSink;
+import okio.Okio;
+import okio.Source;
+
+public class InputStreamRequestBody extends RequestBody {
+
+	private final InputStream inputStream;
+	private final MediaType mediaType;
+	private final long lenght;
+
+	public static RequestBody create(final MediaType mediaType, final InputStream inputStream, final long len) {
+
+		return new InputStreamRequestBody(inputStream, mediaType, len);
+	}
+
+	private InputStreamRequestBody(InputStream inputStream, MediaType mediaType, long len) {
+		this.inputStream = inputStream;
+		this.mediaType = mediaType;
+		this.lenght = len;
+	}
+
+	@Override
+	public MediaType contentType() {
+		return mediaType;
+	}
+
+	@Override
+	public long contentLength() {
+
+		return lenght;
+
+	}
+
+	@Override
+	public void writeTo(BufferedSink sink) throws IOException {
+		Source source = null;
+		try {
+			source = Okio.source(inputStream);
+			sink.writeAll(source);
+		} finally {
+			Util.closeQuietly(source);
+		}
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java

@@ -0,0 +1,8 @@
+
+package eu.dnetlib.dhp.common.api;
+
+public class MissingConceptDoiException extends Throwable {
+	public MissingConceptDoiException(String message) {
+		super(message);
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -0,0 +1,365 @@
+
+package eu.dnetlib.dhp.common.api;
+
+import java.io.*;
+import java.io.IOException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.http.HttpHeaders;
+import org.apache.http.entity.ContentType;
+import org.jetbrains.annotations.NotNull;
+
+import com.google.gson.Gson;
+
+import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
+import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList;
+import okhttp3.*;
+
+public class ZenodoAPIClient implements Serializable {
+
+	String urlString;
+	String bucket;
+
+	String deposition_id;
+	String access_token;
+
+	public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8");
+
+	private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip");
+
+	public String getUrlString() {
+		return urlString;
+	}
+
+	public void setUrlString(String urlString) {
+		this.urlString = urlString;
+	}
+
+	public String getBucket() {
+		return bucket;
+	}
+
+	public void setBucket(String bucket) {
+		this.bucket = bucket;
+	}
+
+	public void setDeposition_id(String deposition_id) {
+		this.deposition_id = deposition_id;
+	}
+
+	public ZenodoAPIClient(String urlString, String access_token) {
+
+		this.urlString = urlString;
+		this.access_token = access_token;
+	}
+
+	/**
+	 * Brand new deposition in Zenodo. It sets the deposition_id and the bucket where to store the files to upload
+	 *
+	 * @return response code
+	 * @throws IOException
+	 */
+	public int newDeposition() throws IOException {
+		String json = "{}";
+
+		URL url = new URL(urlString);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setRequestMethod("POST");
+		conn.setDoOutput(true);
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+		conn.disconnect();
+
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
+		this.bucket = newSubmission.getLinks().getBucket();
+		this.deposition_id = newSubmission.getId();
+
+		return responseCode;
+	}
+
+	/**
+	 * Upload files in Zenodo.
+	 *
+	 * @param is the inputStream for the file to upload
+	 * @param file_name the name of the file as it will appear on Zenodo
+	 * @return the response code
+	 */
+	public int uploadIS(InputStream is, String file_name) throws IOException {
+
+		URL url = new URL(bucket + "/" + file_name);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/zip");
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("PUT");
+
+		byte[] buf = new byte[8192];
+		int length;
+		try (OutputStream os = conn.getOutputStream()) {
+			while ((length = is.read(buf)) != -1) {
+				os.write(buf, 0, length);
+			}
+
+		}
+		int responseCode = conn.getResponseCode();
+		if (!checkOKStatus(responseCode)) {
+			throw new IOException("Unexpected code " + responseCode + getBody(conn));
+		}
+
+		return responseCode;
+	}
+
+	@NotNull
+	private String getBody(HttpURLConnection conn) throws IOException {
+		String body = "{}";
+		try (BufferedReader br = new BufferedReader(
+			new InputStreamReader(conn.getInputStream(), "utf-8"))) {
+			StringBuilder response = new StringBuilder();
+			String responseLine = null;
+			while ((responseLine = br.readLine()) != null) {
+				response.append(responseLine.trim());
+			}
+
+			body = response.toString();
+
+		}
+		return body;
+	}
+
+	/**
+	 * Associates metadata information to the current deposition
+	 *
+	 * @param metadata the metadata
+	 * @return response code
+	 * @throws IOException
+	 */
+	public int sendMretadata(String metadata) throws IOException {
+
+		URL url = new URL(urlString + "/" + deposition_id);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("PUT");
+
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = metadata.getBytes("utf-8");
+			os.write(input, 0, input.length);
+
+		}
+
+		final int responseCode = conn.getResponseCode();
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + getBody(conn));
+
+		return responseCode;
+
+	}
+
+	private boolean checkOKStatus(int responseCode) {
+
+		if (HttpURLConnection.HTTP_OK != responseCode ||
+			HttpURLConnection.HTTP_CREATED != responseCode)
+			return true;
+		return false;
+	}
+
+	/**
+	 * To publish the current deposition. It works for both new deposition or new version of an old deposition
+	 *
+	 * @return response code
+	 * @throws IOException
+	 */
+	@Deprecated
+	public int publish() throws IOException {
+
+		String json = "{}";
+
+		OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
+
+		RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
+
+		Request request = new Request.Builder()
+			.url(urlString + "/" + deposition_id + "/actions/publish")
+			.addHeader("Authorization", "Bearer " + access_token)
+			.post(body)
+			.build();
+
+		try (Response response = httpClient.newCall(request).execute()) {
+
+			if (!response.isSuccessful())
+				throw new IOException("Unexpected code " + response + response.body().string());
+
+			return response.code();
+
+		}
+	}
+
+	/**
+	 * To create a new version of an already published deposition. It sets the deposition_id and the bucket to be used
+	 * for the new version.
+	 *
+	 * @param concept_rec_id the concept record id of the deposition for which to create a new version. It is the last
+	 *            part of the url for the DOI Zenodo suggests to use to cite all versions: DOI: 10.xxx/zenodo.656930
+	 *            concept_rec_id = 656930
+	 * @return response code
+	 * @throws IOException
+	 * @throws MissingConceptDoiException
+	 */
+	public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
+		setDepositionId(concept_rec_id, 1);
+		String json = "{}";
+
+		URL url = new URL(urlString + "/" + deposition_id + "/actions/newversion");
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("POST");
+
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+		String latest_draft = zenodoModel.getLinks().getLatest_draft();
+		deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1);
+		bucket = getBucket(latest_draft);
+
+		return responseCode;
+
+	}
+
+	/**
+	 * To finish uploading a version or new deposition not published
+	 * It sets the deposition_id and the bucket to be used
+	 *
+	 *
+	 * @param deposition_id the deposition id of the not yet published upload
+	 *            concept_rec_id = 656930
+	 * @return response code
+	 * @throws IOException
+	 * @throws MissingConceptDoiException
+	 */
+	public int uploadOpenDeposition(String deposition_id) throws IOException, MissingConceptDoiException {
+
+		this.deposition_id = deposition_id;
+
+		String json = "{}";
+
+		URL url = new URL(urlString + "/" + deposition_id);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setRequestMethod("POST");
+		conn.setDoOutput(true);
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+		conn.disconnect();
+
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+		bucket = zenodoModel.getLinks().getBucket();
+
+		return responseCode;
+
+	}
+
+	private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException {
+
+		ZenodoModelList zenodoModelList = new Gson()
+			.fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class);
+
+		for (ZenodoModel zm : zenodoModelList) {
+			if (zm.getConceptrecid().equals(concept_rec_id)) {
+				deposition_id = zm.getId();
+				return;
+			}
+		}
+		if (zenodoModelList.size() == 0)
+			throw new MissingConceptDoiException(
+				"The concept record id specified was missing in the list of depositions");
+		setDepositionId(concept_rec_id, page + 1);
+
+	}
+
+	private String getPrevDepositions(String page) throws IOException {
+
+		HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder();
+		urlBuilder.addQueryParameter("page", page);
+
+		URL url = new URL(urlBuilder.build().toString());
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("GET");
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		return body;
+
+	}
+
+	private String getBucket(String inputUurl) throws IOException {
+
+		URL url = new URL(inputUurl);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("GET");
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+
+		return zenodoModel.getLinks().getBucket();
+
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java

@@ -0,0 +1,14 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+public class Community {
+	private String identifier;
+
+	public String getIdentifier() {
+		return identifier;
+	}
+
+	public void setIdentifier(String identifier) {
+		this.identifier = identifier;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java

@@ -0,0 +1,47 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+public class Creator {
+	private String affiliation;
+	private String name;
+	private String orcid;
+
+	public String getAffiliation() {
+		return affiliation;
+	}
+
+	public void setAffiliation(String affiliation) {
+		this.affiliation = affiliation;
+	}
+
+	public String getName() {
+		return name;
+	}
+
+	public void setName(String name) {
+		this.name = name;
+	}
+
+	public String getOrcid() {
+		return orcid;
+	}
+
+	public void setOrcid(String orcid) {
+		this.orcid = orcid;
+	}
+
+	public static Creator newInstance(String name, String affiliation, String orcid) {
+		Creator c = new Creator();
+		if (name != null) {
+			c.name = name;
+		}
+		if (affiliation != null) {
+			c.affiliation = affiliation;
+		}
+		if (orcid != null) {
+			c.orcid = orcid;
+		}
+
+		return c;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java

@@ -0,0 +1,44 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+
+public class File implements Serializable {
+	private String checksum;
+	private String filename;
+	private long filesize;
+	private String id;
+
+	public String getChecksum() {
+		return checksum;
+	}
+
+	public void setChecksum(String checksum) {
+		this.checksum = checksum;
+	}
+
+	public String getFilename() {
+		return filename;
+	}
+
+	public void setFilename(String filename) {
+		this.filename = filename;
+	}
+
+	public long getFilesize() {
+		return filesize;
+	}
+
+	public void setFilesize(long filesize) {
+		this.filesize = filesize;
+	}
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java

@@ -0,0 +1,23 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+
+public class Grant implements Serializable {
+	private String id;
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public static Grant newInstance(String id) {
+		Grant g = new Grant();
+		g.id = id;
+
+		return g;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java

@@ -0,0 +1,92 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+
+public class Links implements Serializable {
+
+	private String bucket;
+
+	private String discard;
+
+	private String edit;
+	private String files;
+	private String html;
+	private String latest_draft;
+	private String latest_draft_html;
+	private String publish;
+
+	private String self;
+
+	public String getBucket() {
+		return bucket;
+	}
+
+	public void setBucket(String bucket) {
+		this.bucket = bucket;
+	}
+
+	public String getDiscard() {
+		return discard;
+	}
+
+	public void setDiscard(String discard) {
+		this.discard = discard;
+	}
+
+	public String getEdit() {
+		return edit;
+	}
+
+	public void setEdit(String edit) {
+		this.edit = edit;
+	}
+
+	public String getFiles() {
+		return files;
+	}
+
+	public void setFiles(String files) {
+		this.files = files;
+	}
+
+	public String getHtml() {
+		return html;
+	}
+
+	public void setHtml(String html) {
+		this.html = html;
+	}
+
+	public String getLatest_draft() {
+		return latest_draft;
+	}
+
+	public void setLatest_draft(String latest_draft) {
+		this.latest_draft = latest_draft;
+	}
+
+	public String getLatest_draft_html() {
+		return latest_draft_html;
+	}
+
+	public void setLatest_draft_html(String latest_draft_html) {
+		this.latest_draft_html = latest_draft_html;
+	}
+
+	public String getPublish() {
+		return publish;
+	}
+
+	public void setPublish(String publish) {
+		this.publish = publish;
+	}
+
+	public String getSelf() {
+		return self;
+	}
+
+	public void setSelf(String self) {
+		this.self = self;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java

@@ -0,0 +1,153 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class Metadata implements Serializable {
+
+	private String access_right;
+	private List<Community> communities;
+	private List<Creator> creators;
+	private String description;
+	private String doi;
+	private List<Grant> grants;
+	private List<String> keywords;
+	private String language;
+	private String license;
+	private PrereserveDoi prereserve_doi;
+	private String publication_date;
+	private List<String> references;
+	private List<RelatedIdentifier> related_identifiers;
+	private String title;
+	private String upload_type;
+	private String version;
+
+	public String getUpload_type() {
+		return upload_type;
+	}
+
+	public void setUpload_type(String upload_type) {
+		this.upload_type = upload_type;
+	}
+
+	public String getVersion() {
+		return version;
+	}
+
+	public void setVersion(String version) {
+		this.version = version;
+	}
+
+	public String getAccess_right() {
+		return access_right;
+	}
+
+	public void setAccess_right(String access_right) {
+		this.access_right = access_right;
+	}
+
+	public List<Community> getCommunities() {
+		return communities;
+	}
+
+	public void setCommunities(List<Community> communities) {
+		this.communities = communities;
+	}
+
+	public List<Creator> getCreators() {
+		return creators;
+	}
+
+	public void setCreators(List<Creator> creators) {
+		this.creators = creators;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
+
+	public List<Grant> getGrants() {
+		return grants;
+	}
+
+	public void setGrants(List<Grant> grants) {
+		this.grants = grants;
+	}
+
+	public List<String> getKeywords() {
+		return keywords;
+	}
+
+	public void setKeywords(List<String> keywords) {
+		this.keywords = keywords;
+	}
+
+	public String getLanguage() {
+		return language;
+	}
+
+	public void setLanguage(String language) {
+		this.language = language;
+	}
+
+	public String getLicense() {
+		return license;
+	}
+
+	public void setLicense(String license) {
+		this.license = license;
+	}
+
+	public PrereserveDoi getPrereserve_doi() {
+		return prereserve_doi;
+	}
+
+	public void setPrereserve_doi(PrereserveDoi prereserve_doi) {
+		this.prereserve_doi = prereserve_doi;
+	}
+
+	public String getPublication_date() {
+		return publication_date;
+	}
+
+	public void setPublication_date(String publication_date) {
+		this.publication_date = publication_date;
+	}
+
+	public List<String> getReferences() {
+		return references;
+	}
+
+	public void setReferences(List<String> references) {
+		this.references = references;
+	}
+
+	public List<RelatedIdentifier> getRelated_identifiers() {
+		return related_identifiers;
+	}
+
+	public void setRelated_identifiers(List<RelatedIdentifier> related_identifiers) {
+		this.related_identifiers = related_identifiers;
+	}
+
+	public String getTitle() {
+		return title;
+	}
+
+	public void setTitle(String title) {
+		this.title = title;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java

@@ -0,0 +1,25 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+
+public class PrereserveDoi implements Serializable {
+	private String doi;
+	private String recid;
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
+
+	public String getRecid() {
+		return recid;
+	}
+
+	public void setRecid(String recid) {
+		this.recid = recid;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java

@@ -0,0 +1,43 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+
+public class RelatedIdentifier implements Serializable {
+	private String identifier;
+	private String relation;
+	private String resource_type;
+	private String scheme;
+
+	public String getIdentifier() {
+		return identifier;
+	}
+
+	public void setIdentifier(String identifier) {
+		this.identifier = identifier;
+	}
+
+	public String getRelation() {
+		return relation;
+	}
+
+	public void setRelation(String relation) {
+		this.relation = relation;
+	}
+
+	public String getResource_type() {
+		return resource_type;
+	}
+
+	public void setResource_type(String resource_type) {
+		this.resource_type = resource_type;
+	}
+
+	public String getScheme() {
+		return scheme;
+	}
+
+	public void setScheme(String scheme) {
+		this.scheme = scheme;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java

@@ -0,0 +1,118 @@
+
+package eu.dnetlib.dhp.common.api.zenodo;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class ZenodoModel implements Serializable {
+
+	private String conceptrecid;
+	private String created;
+
+	private List<File> files;
+	private String id;
+	private Links links;
+	private Metadata metadata;
+	private String modified;
+	private String owner;
+	private String record_id;
+	private String state;
+	private boolean submitted;
+	private String title;
+
+	public String getConceptrecid() {
+		return conceptrecid;
+	}
+
+	public void setConceptrecid(String conceptrecid) {
+		this.conceptrecid = conceptrecid;
+	}
+
+	public String getCreated() {
+		return created;
+	}
+
+	public void setCreated(String created) {
+		this.created = created;
+	}
+
+	public List<File> getFiles() {
+		return files;
+	}
+
+	public void setFiles(List<File> files) {
+		this.files = files;
+	}
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public Links getLinks() {
+		return links;
+	}
+
+	public void setLinks(Links links) {
+		this.links = links;
+	}
+
+	public Metadata getMetadata() {
+		return metadata;
+	}
+
+	public void setMetadata(Metadata metadata) {
+		this.metadata = metadata;
+	}
+
+	public String getModified() {
+		return modified;
+	}
+
+	public void setModified(String modified) {
+		this.modified = modified;
+	}
+
+	public String getOwner() {
+		return owner;
+	}
+
+	public void setOwner(String owner) {
+		this.owner = owner;
+	}
+
+	public String getRecord_id() {
+		return record_id;
+	}
+
+	public void setRecord_id(String record_id) {
+		this.record_id = record_id;
+	}
+
+	public String getState() {
+		return state;
+	}
+
+	public void setState(String state) {
+		this.state = state;
+	}
+
+	public boolean isSubmitted() {
+		return submitted;
+	}
+
+	public void setSubmitted(boolean submitted) {
+		this.submitted = submitted;
+	}
+
+	public String getTitle() {
+		return title;
+	}
+
+	public void setTitle(String title) {
+		this.title = title;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java

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

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

@@ -12,7 +12,9 @@ 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;
 
@@ -212,11 +214,11 @@ public class HttpConnector2 {
 					.format(
 						"Unexpected status code: %s errors: %s", urlConn.getResponseCode(),
 						MAPPER.writeValueAsString(report)));
-		} catch (MalformedURLException e) {
+		} catch (MalformedURLException | UnknownHostException e) {
 			log.error(e.getMessage(), e);
 			report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e.getMessage(), e);
-		} catch (SocketTimeoutException | SocketException | UnknownHostException e) {
+		} catch (SocketTimeoutException | SocketException e) {
 			log.error(e.getMessage(), e);
 			report.put(e.getClass().getName(), e.getMessage());
 			backoffAndSleep(getClientParams().getRetryDelay() * retryNumber * 1000);

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

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

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

@@ -1,70 +0,0 @@
-/*
- * Copyright (c) 2024.
- * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
- * SPDX-License-Identifier: AGPL-3.0-or-later
- */
-
-package eu.dnetlib.dhp.schema.oaf;
-
-import org.apache.commons.lang3.builder.EqualsBuilder;
-import org.apache.commons.lang3.builder.HashCodeBuilder;
-
-public class HashableStructuredProperty extends StructuredProperty {
-
-	private static final long serialVersionUID = 8371670185221126045L;
-
-	public static HashableStructuredProperty newInstance(String value, Qualifier qualifier, DataInfo dataInfo) {
-		if (value == null) {
-			return null;
-		}
-		final HashableStructuredProperty sp = new HashableStructuredProperty();
-		sp.setValue(value);
-		sp.setQualifier(qualifier);
-		sp.setDataInfo(dataInfo);
-		return sp;
-	}
-
-	public static HashableStructuredProperty newInstance(StructuredProperty sp) {
-		HashableStructuredProperty hsp = new HashableStructuredProperty();
-		hsp.setQualifier(sp.getQualifier());
-		hsp.setValue(sp.getValue());
-		hsp.setQualifier(sp.getQualifier());
-		return hsp;
-	}
-
-	public static StructuredProperty toStructuredProperty(HashableStructuredProperty hsp) {
-		StructuredProperty sp = new StructuredProperty();
-		sp.setQualifier(hsp.getQualifier());
-		sp.setValue(hsp.getValue());
-		sp.setQualifier(hsp.getQualifier());
-		return sp;
-	}
-
-	@Override
-	public int hashCode() {
-		return new HashCodeBuilder(11, 91)
-			.append(getQualifier().getClassid())
-			.append(getQualifier().getSchemeid())
-			.append(getValue())
-			.hashCode();
-	}
-
-	@Override
-	public boolean equals(Object obj) {
-		if (obj == null) {
-			return false;
-		}
-		if (obj == this) {
-			return true;
-		}
-		if (obj.getClass() != getClass()) {
-			return false;
-		}
-		final HashableStructuredProperty rhs = (HashableStructuredProperty) obj;
-		return new EqualsBuilder()
-			.append(getQualifier().getClassid(), rhs.getQualifier().getClassid())
-			.append(getQualifier().getSchemeid(), rhs.getQualifier().getSchemeid())
-			.append(getValue(), rhs.getValue())
-			.isEquals();
-	}
-}

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

@@ -43,4 +43,34 @@ public class CleaningFunctions {
 		return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
 	}
 
+	/**
+	 * Utility method that normalises PID values on a per-type basis.
+	 * @param pid the PID whose value will be normalised.
+	 * @return the PID containing the normalised value.
+	 */
+	public static StructuredProperty normalizePidValue(StructuredProperty pid) {
+		pid
+			.setValue(
+				normalizePidValue(
+					pid.getQualifier().getClassid(),
+					pid.getValue()));
+
+		return pid;
+	}
+
+	public static String normalizePidValue(String pidType, String pidValue) {
+		String value = Optional
+			.ofNullable(pidValue)
+			.map(String::trim)
+			.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
+
+		switch (pidType) {
+
+			// TODO add cleaning for more PID types as needed
+			case "doi":
+				return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
+		}
+		return value;
+	}
+
 }

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

@@ -6,11 +6,18 @@ import org.apache.commons.lang3.StringUtils;
 public class DoiCleaningRule {
 
 	public static String clean(final String doi) {
-		if (doi == null)
+		return doi
-			return null;
+			.toLowerCase()
-		final String replaced = doi
+			.replaceAll("\\s", "")
-			.replaceAll("\\n|\\r|\\t|\\s", "")
 			.replaceAll("^doi:", "")
+			.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
+	}
+
+	public static String normalizeDoi(final String input) {
+		if (input == null)
+			return null;
+		final String replaced = input
+			.replaceAll("\\n|\\r|\\t|\\s", "")
 			.toLowerCase()
 			.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
 		if (StringUtils.isEmpty(replaced))
@@ -25,6 +32,7 @@ public class DoiCleaningRule {
 			return null;
 
 		return ret;
+
 	}
 
 }

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

@@ -119,7 +119,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 							.getContext()
 							.stream()
 							.filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId))
-							.collect(Collectors.toCollection(ArrayList::new)));
+							.collect(Collectors.toList()));
 			}
 			return (T) res;
 		} else {
@@ -563,24 +563,12 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						Optional
 							.ofNullable(i.getPid())
 							.ifPresent(pid -> {
-								final Set<HashableStructuredProperty> pids = pid
+								final Set<StructuredProperty> pids = Sets.newHashSet(pid);
-									.stream()
-									.map(HashableStructuredProperty::newInstance)
-									.collect(Collectors.toCollection(HashSet::new));
 								Optional
 									.ofNullable(i.getAlternateIdentifier())
 									.ifPresent(altId -> {
-										final Set<HashableStructuredProperty> altIds = altId
+										final Set<StructuredProperty> altIds = Sets.newHashSet(altId);
-											.stream()
+										i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids)));
-											.map(HashableStructuredProperty::newInstance)
-											.collect(Collectors.toCollection(HashSet::new));
-										i
-											.setAlternateIdentifier(
-												Sets
-													.difference(altIds, pids)
-													.stream()
-													.map(HashableStructuredProperty::toStructuredProperty)
-													.collect(Collectors.toList()));
 									});
 							});
 
@@ -1015,41 +1003,4 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 			.orElse(null);
 	}
 
-	/**
-	 * Implements bad and ugly things that we should get rid of ASAP.
-	 *
-	 * @param value
-	 * @return
-	 * @param <T>
-	 */
-	public static <T extends Oaf> T dedicatedUglyHacks(T value) {
-		if (value instanceof OafEntity) {
-			if (value instanceof Result) {
-				final Result r = (Result) value;
-
-				// Fix for AMS Acta
-				Optional
-					.ofNullable(r.getInstance())
-					.map(
-						instance -> instance
-							.stream()
-							.filter(
-								i -> Optional
-									.ofNullable(i.getHostedby())
-									.map(KeyValue::getKey)
-									.map(dsId -> dsId.equals("10|re3data_____::4cc76bed7ce2fb95fd8e7a2dfde16016"))
-									.orElse(false)))
-					.ifPresent(instance -> instance.forEach(i -> {
-						if (Optional
-							.ofNullable(i.getPid())
-							.map(pid -> pid.stream().noneMatch(p -> p.getValue().startsWith("10.6092/unibo/amsacta")))
-							.orElse(false)) {
-							i.setHostedby(UNKNOWN_REPOSITORY);
-						}
-					}));
-			}
-		}
-		return value;
-	}
-
 }

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

@@ -175,7 +175,7 @@ public class IdentifierFactory implements Serializable {
 			return entity
 				.getPid()
 				.stream()
-				.map(PidCleaner::normalizePidValue)
+				.map(CleaningFunctions::normalizePidValue)
 				.filter(CleaningFunctions::pidFilter)
 				.collect(
 					Collectors
@@ -207,7 +207,7 @@ public class IdentifierFactory implements Serializable {
 					// filter away PIDs provided by a DS that is not considered an authority for the
 					// given PID Type
 					.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
-					.map(PidCleaner::normalizePidValue)
+					.map(CleaningFunctions::normalizePidValue)
 					.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
 					.filter(CleaningFunctions::pidFilter))
 			.orElse(Stream.empty());

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

@@ -1,106 +0,0 @@
-
-package eu.dnetlib.dhp.schema.oaf.utils;
-
-import java.util.*;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
-public class MergeEntitiesComparator implements Comparator<Oaf> {
-	static final List<String> PID_AUTHORITIES = Arrays
-		.asList(
-			ModelConstants.ARXIV_ID,
-			ModelConstants.PUBMED_CENTRAL_ID,
-			ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
-			ModelConstants.DATACITE_ID,
-			ModelConstants.CROSSREF_ID);
-
-	static final List<String> RESULT_TYPES = Arrays
-		.asList(
-			ModelConstants.ORP_RESULTTYPE_CLASSID,
-			ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
-			ModelConstants.DATASET_RESULTTYPE_CLASSID,
-			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
-
-	public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
-
-	@Override
-	public int compare(Oaf left, Oaf right) {
-		if (left == null && right == null)
-			return 0;
-		if (left == null)
-			return -1;
-		if (right == null)
-			return 1;
-
-		int res = 0;
-
-		// pid authority
-		int cfp1 = Optional
-			.ofNullable(left.getCollectedfrom())
-			.map(
-				cf -> cf
-					.stream()
-					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
-					.max(Integer::compare)
-					.orElse(-1))
-			.orElse(-1);
-		int cfp2 = Optional
-			.ofNullable(right.getCollectedfrom())
-			.map(
-				cf -> cf
-					.stream()
-					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
-					.max(Integer::compare)
-					.orElse(-1))
-			.orElse(-1);
-
-		if (cfp1 >= 0 && cfp1 > cfp2) {
-			return 1;
-		} else if (cfp2 >= 0 && cfp2 > cfp1) {
-			return -1;
-		}
-
-		// trust
-		if (left.getDataInfo() != null && right.getDataInfo() != null) {
-			res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
-		}
-
-		// result type
-		if (res == 0) {
-			if (left instanceof Result && right instanceof Result) {
-				Result r1 = (Result) left;
-				Result r2 = (Result) right;
-
-				if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
-					if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
-						return -1;
-					}
-				} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
-					return 1;
-				}
-
-				int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
-				int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
-
-				if (rt1 >= 0 && rt1 > rt2) {
-					return 1;
-				} else if (rt2 >= 0 && rt2 > rt1) {
-					return -1;
-				}
-			}
-		}
-
-		// id
-		if (res == 0) {
-			if (left instanceof OafEntity && right instanceof OafEntity) {
-				res = ((OafEntity) right).getId().compareTo(((OafEntity) left).getId());
-			}
-		}
-
-		return res;
-	}
-
-}

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

@@ -31,37 +31,39 @@ import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
 
-	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
-		return mergeGroup(s, oafEntityIterator, true);
-	}
-
 	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator) {
-		return mergeGroup(s, oafEntityIterator, false);
+		TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
+			int res = 0;
+
+			if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
+				res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
 			}
 
-	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
+			if (res == 0) {
-		boolean checkDelegateAuthority) {
+				if (o1 instanceof Result && o2 instanceof Result) {
+					return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
+				}
+			}
 
-		ArrayList<T> sortedEntities = new ArrayList<>();
+			return res;
-		oafEntityIterator.forEachRemaining(sortedEntities::add);
+		});
-		sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
 
-		Iterator<T> it = sortedEntities.iterator();
+		while (oafEntityIterator.hasNext()) {
-		T merged = it.next();
+			sortedEntities.add(oafEntityIterator.next());
+		}
 
+		T merged = sortedEntities.descendingIterator().next();
+
+		Iterator<T> it = sortedEntities.descendingIterator();
 		while (it.hasNext()) {
-			merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
+			merged = checkedMerge(merged, it.next());
 		}
 
 		return merged;
 	}
 
-	public static <T extends Oaf> T checkedMerge(final T left, final T right, boolean checkDelegateAuthority) {
+	public static <T extends Oaf> T checkedMerge(final T left, final T right) {
-		return (T) merge(left, right, checkDelegateAuthority);
+		return (T) merge(left, right, false);
-	}
-
-	public static <T extends Result, E extends Result> Result mergeResult(final T left, final E right) {
-		return (Result) merge(left, right, false);
 	}
 
 	public static Oaf merge(final Oaf left, final Oaf right) {
@@ -89,7 +91,7 @@ public class MergeUtils {
 	private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
 
 		if (sameClass(left, right, Result.class)) {
-			if (checkDelegatedAuthority) {
+			if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
 				return mergeResultsOfDifferentTypes((Result) left, (Result) right);
 			}
 
@@ -106,7 +108,7 @@ public class MergeUtils {
 				return mergeSoftware((Software) left, (Software) right);
 			}
 
-			return mergeResultFields((Result) left, (Result) right);
+			return mergeResult((Result) left, (Result) right);
 		} else if (sameClass(left, right, Datasource.class)) {
 			// TODO
 			final int trust = compareTrust(left, right);
@@ -129,7 +131,7 @@ public class MergeUtils {
 	 * 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 MergeEntitiesComparator}
+	 * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
 	 * and proceeds with the canonical property merging.
 	 *
 	 * @param left
@@ -147,12 +149,11 @@ public class MergeUtils {
 		if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
 			return right;
 		}
-
 		// TODO: raise trust to have preferred fields from one or the other??
-		if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
+		if (new ResultTypeComparator().compare(left, right) < 0) {
-			return mergeResultFields(left, right);
+			return mergeResult(left, right);
 		} else {
-			return mergeResultFields(right, left);
+			return mergeResult(right, left);
 		}
 	}
 
@@ -212,9 +213,9 @@ public class MergeUtils {
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
 		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
-		if (left == null || left.isEmpty()) {
+		if (left == null) {
-			return right != null ? right : new ArrayList<>();
+			return right;
-		} else if (right == null || right.isEmpty()) {
+		} else if (right == null) {
 			return left;
 		}
 
@@ -262,12 +263,6 @@ public class MergeUtils {
 
 	// TODO review
 	private static List<KeyValue> mergeByKey(List<KeyValue> left, List<KeyValue> right, int trust) {
-		if (left == null) {
-			return right;
-		} else if (right == null) {
-			return left;
-		}
-
 		if (trust < 0) {
 			List<KeyValue> s = left;
 			left = right;
@@ -329,7 +324,7 @@ public class MergeUtils {
 		final T merged = mergeOafFields(original, enrich, trust);
 
 		merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId()));
-		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
+		merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
 			.setDateoftransformation(
@@ -373,7 +368,7 @@ public class MergeUtils {
 		return merge;
 	}
 
-	private static <T extends Result> T mergeResultFields(T original, T enrich) {
+	public static <T extends Result> T mergeResult(T original, T enrich) {
 		final int trust = compareTrust(original, enrich);
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
@@ -392,7 +387,7 @@ public class MergeUtils {
 		}
 
 		// should be an instance attribute, get the first non-null value
-		merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
+		merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
 
 		// distinct countries, do not manage datainfo
 		merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@@ -433,10 +428,7 @@ public class MergeUtils {
 
 		// merge datainfo for same context id
 		merge.setContext(mergeLists(merge.getContext(), enrich.getContext(), trust, Context::getId, (r, l) -> {
-			ArrayList<DataInfo> di = new ArrayList<>();
+			r.getDataInfo().addAll(l.getDataInfo());
-			di.addAll(r.getDataInfo());
-			di.addAll(l.getDataInfo());
-			r.setDataInfo(di);
 			return r;
 		}));
 
@@ -468,10 +460,6 @@ public class MergeUtils {
 		merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal()));
 		merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded()));
 
-		if (StringUtils.isBlank(merge.getTransformativeAgreement())) {
-			merge.setTransformativeAgreement(enrich.getTransformativeAgreement());
-		}
-
 		return merge;
 	}
 
@@ -569,13 +557,6 @@ public class MergeUtils {
 		return m != null ? m : e;
 	}
 
-	private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
-		if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
-			return e;
-		}
-		return m;
-	}
-
 	private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
 		List<List<Author>> authors = new ArrayList<>();
 		if (author != null) {
@@ -588,10 +569,6 @@ public class MergeUtils {
 	}
 
 	private static String instanceKeyExtractor(Instance i) {
-		// three levels of concatenating:
-		// 1. ::
-		// 2. @@
-		// 3. ||
 		return String
 			.join(
 				"::",
@@ -599,10 +576,10 @@ public class MergeUtils {
 				kvKeyExtractor(i.getCollectedfrom()),
 				qualifierKeyExtractor(i.getAccessright()),
 				qualifierKeyExtractor(i.getInstancetype()),
-				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
 				Optional
 					.ofNullable(i.getPid())
-					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
 					.orElse(null));
 	}
 
@@ -663,13 +640,6 @@ public class MergeUtils {
 			return d1;
 		}
 
-		if (StringUtils.contains(d1.getValue(), "null")) {
-			return d2;
-		}
-		if (StringUtils.contains(d2.getValue(), "null")) {
-			return d1;
-		}
-
 		return Stream
 			.of(d1, d2)
 			.min(
@@ -718,13 +688,13 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
+			.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
 			.orElse(null);
 	}
 
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		final T merge = mergeResultFields(original, enrich);
+		final T merge = mergeResult(original, enrich);
 
 		merge.setContactperson(unionDistinctLists(merge.getContactperson(), enrich.getContactperson(), trust));
 		merge.setContactgroup(unionDistinctLists(merge.getContactgroup(), enrich.getContactgroup(), trust));
@@ -735,7 +705,7 @@ public class MergeUtils {
 
 	private static <T extends Software> T mergeSoftware(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		final T merge = mergeResultFields(original, enrich);
+		final T merge = mergeResult(original, enrich);
 
 		merge.setDocumentationUrl(unionDistinctLists(merge.getDocumentationUrl(), enrich.getDocumentationUrl(), trust));
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
@@ -749,7 +719,7 @@ public class MergeUtils {
 
 	private static <T extends Dataset> T mergeDataset(T original, T enrich) {
 		int trust = compareTrust(original, enrich);
-		T merge = mergeResultFields(original, enrich);
+		T merge = mergeResult(original, enrich);
 
 		merge.setStoragedate(chooseReference(merge.getStoragedate(), enrich.getStoragedate(), trust));
 		merge.setDevice(chooseReference(merge.getDevice(), enrich.getDevice(), trust));
@@ -768,7 +738,7 @@ public class MergeUtils {
 
 	public static <T extends Publication> T mergePublication(T original, T enrich) {
 		final int trust = compareTrust(original, enrich);
-		T merged = mergeResultFields(original, enrich);
+		T merged = mergeResult(original, enrich);
 
 		merged.setJournal(chooseReference(merged.getJournal(), enrich.getJournal(), trust));
 
@@ -886,11 +856,9 @@ public class MergeUtils {
 		if (toEnrichInstances == null) {
 			return enrichmentResult;
 		}
-
+		if (enrichmentInstances == null) {
-		if (enrichmentInstances == null || enrichmentInstances.isEmpty()) {
+			return enrichmentResult;
-			return toEnrichInstances;
 		}
-
 		Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
 
 		toEnrichInstances.forEach(i -> {
@@ -975,7 +943,7 @@ public class MergeUtils {
 	private static String extractKeyFromPid(final StructuredProperty pid) {
 		if (pid == null)
 			return null;
-		final StructuredProperty normalizedPid = PidCleaner.normalizePidValue(pid);
+		final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
 
 		return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
 	}

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

@@ -18,8 +18,8 @@ public class PidValueComparator implements Comparator<StructuredProperty> {
 		if (right == null)
 			return -1;
 
-		StructuredProperty l = PidCleaner.normalizePidValue(left);
+		StructuredProperty l = CleaningFunctions.normalizePidValue(left);
-		StructuredProperty r = PidCleaner.normalizePidValue(right);
+		StructuredProperty r = CleaningFunctions.normalizePidValue(right);
 
 		return Optional
 			.ofNullable(l.getValue())

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

@@ -0,0 +1,78 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
+
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class ResultTypeComparator implements Comparator<Result> {
+
+	public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
+
+	@Override
+	public int compare(Result left, Result right) {
+
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return 1;
+		if (right == null)
+			return -1;
+
+		HashSet<String> lCf = getCollectedFromIds(left);
+		HashSet<String> rCf = getCollectedFromIds(right);
+
+		if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
+			return -1;
+		}
+		if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
+			return 1;
+		}
+
+		String lClass = left.getResulttype().getClassid();
+		String rClass = right.getResulttype().getClassid();
+
+		if (!lClass.equals(rClass)) {
+			if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
+				return -1;
+			if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
+				return 1;
+
+			if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
+				return -1;
+			if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
+				return 1;
+
+			if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
+				return -1;
+			if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
+				return 1;
+
+			if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
+				return -1;
+			if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
+				return 1;
+		}
+
+		// Else (but unlikely), lexicographical ordering will do.
+		return lClass.compareTo(rClass);
+	}
+
+	protected HashSet<String> getCollectedFromIds(Result left) {
+		return Optional
+			.ofNullable(left.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.toCollection(HashSet::new)))
+			.orElse(new HashSet<>());
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java

@@ -28,7 +28,6 @@ import com.jayway.jsonpath.JsonPath;
 
 import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 import net.minidev.json.JSONArray;
 import scala.collection.JavaConverters;
 import scala.collection.Seq;
@@ -105,7 +104,7 @@ public class DHPUtils {
 
 	public static String generateUnresolvedIdentifier(final String pid, final String pidType) {
 
-		final String cleanedPid = PidCleaner.normalizePidValue(pidType, pid);
+		final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid);
 
 		return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim());
 	}

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

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

dhp-common/src/main/resources/eu/dnetlib/scholexplorer/relation/relations.json

@@ -154,13 +154,5 @@
   "unknown":{
     "original":"Unknown",
     "inverse":"Unknown"
-  },
-  "isamongtopnsimilardocuments": {
-    "original": "IsAmongTopNSimilarDocuments",
-    "inverse": "HasAmongTopNSimilarDocuments"
-  },
-  "hasamongtopnsimilardocuments": {
-    "original": "HasAmongTopNSimilarDocuments",
-    "inverse": "IsAmongTopNSimilarDocuments"
   }
 }

dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala

@@ -65,13 +65,12 @@ abstract class AbstractScalaApplication(
     val conf: SparkConf = new SparkConf()
     val master = parser.get("master")
     log.info(s"Creating Spark session: Master: $master")
-    val b = SparkSession
+    SparkSession
       .builder()
       .config(conf)
       .appName(getClass.getSimpleName)
-    if (master != null)
+      .master(master)
-      b.master(master)
+      .getOrCreate()
-    b.getOrCreate()
   }
 
   def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {

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

@@ -65,11 +65,7 @@ object ScholixUtils extends Serializable {
   }
 
   def generateScholixResourceFromResult(r: Result): ScholixResource = {
-    val sum = ScholixUtils.resultToSummary(r)
-    if (sum != null)
     generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
-    else
-      null
   }
 
   val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
@@ -157,14 +153,6 @@ object ScholixUtils extends Serializable {
 
   }
 
-  def invRel(rel: String): String = {
-    val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
-    if (semanticRelation != null)
-      semanticRelation.inverse
-    else
-      null
-  }
-
   def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
     if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
       val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map { d =>
@@ -389,7 +377,10 @@ object ScholixUtils extends Serializable {
     if (persistentIdentifiers.isEmpty)
       return null
     s.setLocalIdentifier(persistentIdentifiers.asJava)
-//    s.setTypology(r.getResulttype.getClassid)
+    if (r.isInstanceOf[Publication])
+      s.setTypology(Typology.publication)
+    else
+      s.setTypology(Typology.dataset)
 
     s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
 

dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java

@@ -0,0 +1,109 @@
+
+package eu.dnetlib.dhp.common.api;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+
+@Disabled
+class ZenodoAPIClientTest {
+
+	private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
+	private final String ACCESS_TOKEN = "";
+
+	private final String CONCEPT_REC_ID = "657113";
+
+	private final String depositionId = "674915";
+
+	@Test
+	void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
+		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
+			ACCESS_TOKEN);
+		Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId));
+
+		File file = new File(getClass()
+			.getResource("/eu/dnetlib/dhp/common/api/COVID-19.json.gz")
+			.getPath());
+
+		InputStream is = new FileInputStream(file);
+
+		Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
+
+		String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
+
+		Assertions.assertEquals(200, client.sendMretadata(metadata));
+
+		Assertions.assertEquals(202, client.publish());
+
+	}
+
+	@Test
+	void testNewDeposition() throws IOException {
+
+		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
+			ACCESS_TOKEN);
+		Assertions.assertEquals(201, client.newDeposition());
+
+		File file = new File(getClass()
+			.getResource("/eu/dnetlib/dhp/common/api/COVID-19.json.gz")
+			.getPath());
+
+		InputStream is = new FileInputStream(file);
+
+		Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
+
+		String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
+
+		Assertions.assertEquals(200, client.sendMretadata(metadata));
+
+		Assertions.assertEquals(202, client.publish());
+
+	}
+
+	@Test
+	void testNewVersionNewName() throws IOException, MissingConceptDoiException {
+
+		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
+			ACCESS_TOKEN);
+
+		Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID));
+
+		File file = new File(getClass()
+			.getResource("/eu/dnetlib/dhp/common/api/newVersion")
+			.getPath());
+
+		InputStream is = new FileInputStream(file);
+
+		Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
+
+		Assertions.assertEquals(202, client.publish());
+
+	}
+
+	@Test
+	void testNewVersionOldName() throws IOException, MissingConceptDoiException {
+
+		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
+			ACCESS_TOKEN);
+
+		Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID));
+
+		File file = new File(getClass()
+			.getResource("/eu/dnetlib/dhp/common/api/newVersion2")
+			.getPath());
+
+		InputStream is = new FileInputStream(file);
+
+		Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
+
+		Assertions.assertEquals(202, client.publish());
+
+	}
+
+}

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

@@ -29,7 +29,7 @@ class IdentifierFactoryTest {
 			"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
 
 		verifyIdentifier(
-			"publication_doi3.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true);
+			"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
 
 		verifyIdentifier(
 			"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
@@ -41,7 +41,7 @@ class IdentifierFactoryTest {
 			"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
 
 		verifyIdentifier(
-			"publication_pmc2.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true);
+			"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
 
 		verifyIdentifier(
 			"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);

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

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

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

@@ -177,7 +177,7 @@ class OafMapperUtilsTest {
 		assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
 		assertEquals(
-			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
+			ModelConstants.DATASET_RESULTTYPE_CLASSID,
 			((Result) MergeUtils
 				.merge(p2, d1))
 					.getResulttype()

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json

@@ -29,7 +29,7 @@
         },
         {
           "qualifier": {"classid": "pmc"},
-          "value": "PMC21459329"
+          "value": "21459329"
         }
       ]
     }

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json

@@ -13,7 +13,7 @@
         },
         {
           "qualifier":{"classid":"pmc"},
-          "value":"PMC21459329"
+          "value":"21459329"
         }
       ]
     }

dhp-pace-core/pom.xml

@@ -24,7 +24,7 @@
 				<executions>
 					<execution>
 						<id>scala-compile-first</id>
-						<phase>process-resources</phase>
+						<phase>initialize</phase>
 						<goals>
 							<goal>add-source</goal>
 							<goal>compile</goal>
@@ -49,16 +49,18 @@
 	</build>
 
 	<dependencies>
-		<dependency>
-			<groupId>eu.dnetlib.dhp</groupId>
-			<artifactId>dhp-common</artifactId>
-			<version>${project.version}</version>
-		</dependency>
-
 		<dependency>
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
@@ -83,6 +85,10 @@
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-math3</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>
 			<artifactId>json-path</artifactId>
@@ -101,90 +107,4 @@
 		</dependency>
 	</dependencies>
 
-	<profiles>
-		<profile>
-			<id>spark-24</id>
-			<activation>
-				<activeByDefault>true</activeByDefault>
-			</activation>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-2</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-
-		<profile>
-			<id>spark-34</id>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-2</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-
-		<profile>
-			<id>spark-35</id>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-35</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-	</profiles>
-
 </project>

dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java

@@ -2,41 +2,31 @@
 package eu.dnetlib.pace.clustering;
 
 import java.util.*;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.pace.config.Config;
 
-@ClusteringClass("legalnameclustering")
+@ClusteringClass("keywordsclustering")
-public class LegalnameClustering extends AbstractClusteringFunction {
+public class KeywordsClustering extends AbstractClusteringFunction {
 
-	private static final Pattern CITY_CODE_PATTERN = Pattern.compile("city::\\d+");
+	public KeywordsClustering(Map<String, Object> params) {
-	private static final Pattern KEYWORD_CODE_PATTERN = Pattern.compile("key::\\d+");
-
-	public LegalnameClustering(Map<String, Object> params) {
 		super(params);
 	}
 
-	public Set<String> getRegexList(String input, Pattern codeRegex) {
-		Matcher matcher = codeRegex.matcher(input);
-		Set<String> cities = new HashSet<>();
-		while (matcher.find()) {
-			cities.add(matcher.group());
-		}
-		return cities;
-	}
-
 	@Override
 	protected Collection<String> doApply(final Config conf, String s) {
 
+		// takes city codes and keywords codes without duplicates
+		Set<String> keywords = getKeywords(s, conf.translationMap(), paramOrDefault("windowSize", 4));
+		Set<String> cities = getCities(s, paramOrDefault("windowSize", 4));
+
 		// list of combination to return as result
 		final Collection<String> combinations = new LinkedHashSet<String>();
 
-		for (String keyword : getRegexList(s, KEYWORD_CODE_PATTERN)) {
+		for (String keyword : keywordsToCodes(keywords, conf.translationMap())) {
-			for (String city : getRegexList(s, CITY_CODE_PATTERN)) {
+			for (String city : citiesToCodes(cities)) {
 				combinations.add(keyword + "-" + city);
 				if (combinations.size() >= paramOrDefault("max", 2)) {
 					return combinations;
@@ -52,6 +42,9 @@ public class LegalnameClustering extends AbstractClusteringFunction {
 		return fields
 			.stream()
 			.filter(f -> !f.isEmpty())
+			.map(KeywordsClustering::cleanup)
+			.map(KeywordsClustering::normalize)
+			.map(s -> filterAllStopWords(s))
 			.map(s -> doApply(conf, s))
 			.map(c -> filterBlacklisted(c, ngramBlacklist))
 			.flatMap(c -> c.stream())

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

@@ -4,6 +4,7 @@ package eu.dnetlib.pace.common;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
+import java.text.Normalizer;
 import java.util.*;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -13,28 +14,24 @@ import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 
 import com.google.common.base.Joiner;
+import com.google.common.base.Splitter;
+import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 import com.ibm.icu.text.Transliterator;
 
+import eu.dnetlib.pace.clustering.NGramUtils;
+
 /**
  * Set of common functions for the framework
  *
  * @author claudio
  */
-public class AbstractPaceFunctions extends PaceCommonUtils {
+public class AbstractPaceFunctions {
 
 	// city map to be used when translating the city names into codes
 	private static Map<String, String> cityMap = AbstractPaceFunctions
 		.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
 
-	// keywords map to be used when translating the keyword names into codes
-	private static Map<String, String> keywordMap = AbstractPaceFunctions
-		.loadMapFromClasspath("/eu/dnetlib/pace/config/translation_map.csv");
-
-	// country map to be used when inferring the country from the city name
-	private static Map<String, String> countryMap = AbstractPaceFunctions
-		.loadCountryMapFromClasspath("/eu/dnetlib/pace/config/country_map.csv");
-
 	// list of stopwords in different languages
 	protected static Set<String> stopwords_gr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_gr.txt");
 	protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
@@ -44,6 +41,9 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 	protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
 	protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
 
+	// transliterator
+	protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
 	// blacklist of ngrams: to avoid generic keys
 	protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
 
@@ -51,6 +51,8 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 	public static final Pattern HTML_REGEX = Pattern.compile("<[^>]*>");
 
 	private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
+	private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
+	private static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
 
 	// doi prefix for normalization
 	public static final Pattern DOI_PREFIX = Pattern.compile("(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)");
@@ -82,64 +84,6 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return s12;
 	}
 
-	public static String countryInference(final String original, String inferFrom) {
-		if (!original.equalsIgnoreCase("unknown"))
-			return original;
-
-		inferFrom = cleanup(inferFrom);
-		inferFrom = normalize(inferFrom);
-		inferFrom = filterAllStopWords(inferFrom);
-		Set<String> cities = getCities(inferFrom, 4);
-		return citiesToCountry(cities).stream().findFirst().orElse("UNKNOWN");
-	}
-
-	public static String cityInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> cities = getCities(original, 4);
-
-		for (String city : cities) {
-			original = original.replaceAll(city, cityMap.get(city));
-		}
-
-		return original;
-	}
-
-	public static String keywordInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> keywords = getKeywords(original, keywordMap, 4);
-
-		for (String keyword : keywords) {
-			original = original.replaceAll(keyword, keywordMap.get(keyword));
-		}
-
-		return original;
-	}
-
-	public static String cityKeywordInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> keywords = getKeywords(original, keywordMap, 4);
-		Set<String> cities = getCities(original, 4);
-
-		for (String keyword : keywords) {
-			original = original.replaceAll(keyword, keywordMap.get(keyword));
-		}
-
-		for (String city : cities) {
-			original = original.replaceAll(city, cityMap.get(city));
-		}
-
-		return original;
-	}
-
 	protected static String fixXML(final String a) {
 
 		return a
@@ -185,6 +129,25 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return numberPattern.matcher(strNum).matches();
 	}
 
+	protected static String fixAliases(final String s) {
+		final StringBuilder sb = new StringBuilder();
+
+		s.chars().forEach(ch -> {
+			final int i = StringUtils.indexOf(aliases_from, ch);
+			sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
+		});
+
+		return sb.toString();
+	}
+
+	protected static String transliterate(final String s) {
+		try {
+			return transliterator.transliterate(s);
+		} catch (Exception e) {
+			return s;
+		}
+	}
+
 	protected static String removeSymbols(final String s) {
 		final StringBuilder sb = new StringBuilder();
 
@@ -199,6 +162,23 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return s != null;
 	}
 
+	public static String normalize(final String s) {
+		return fixAliases(transliterate(nfd(unicodeNormalization(s))))
+			.toLowerCase()
+			// do not compact the regexes in a single expression, would cause StackOverflowError in case of large input
+			// strings
+			.replaceAll("[^ \\w]+", "")
+			.replaceAll("(\\p{InCombiningDiacriticalMarks})+", "")
+			.replaceAll("(\\p{Punct})+", " ")
+			.replaceAll("(\\d)+", " ")
+			.replaceAll("(\\n)+", " ")
+			.trim();
+	}
+
+	public static String nfd(final String s) {
+		return Normalizer.normalize(s, Normalizer.Form.NFD);
+	}
+
 	public static String utf8(final String s) {
 		byte[] bytes = s.getBytes(StandardCharsets.UTF_8);
 		return new String(bytes, StandardCharsets.UTF_8);
@@ -253,6 +233,22 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return newset;
 	}
 
+	public static Set<String> loadFromClasspath(final String classpath) {
+
+		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+		final Set<String> h = Sets.newHashSet();
+		try {
+			for (final String s : IOUtils
+				.readLines(NGramUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
+				h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
+			}
+		} catch (final Throwable e) {
+			return Sets.newHashSet();
+		}
+		return h;
+	}
+
 	public static Map<String, String> loadMapFromClasspath(final String classpath) {
 
 		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
@@ -274,30 +270,6 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return m;
 	}
 
-	public static Map<String, String> loadCountryMapFromClasspath(final String classpath) {
-
-		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
-		final Map<String, String> m = new HashMap<>();
-		try {
-			for (final String s : IOUtils
-				.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
-				// string is like this: country_code;city1;city2;city3
-				String[] line = s.split(";");
-				String value = line[0];
-				for (int i = 1; i < line.length; i++) {
-					String city = fixAliases(transliterator.transliterate(line[i].toLowerCase()));
-					String code = cityMap.get(city);
-					m.put(code, value);
-				}
-			}
-		} catch (final Throwable e) {
-			return new HashMap<>();
-		}
-		return m;
-
-	}
-
 	public static String removeKeywords(String s, Set<String> keywords) {
 
 		s = " " + s + " ";
@@ -327,14 +299,14 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return toCodes(keywords, cityMap);
 	}
 
-	public static Set<String> citiesToCountry(Set<String> cities) {
-		return toCodes(toCodes(cities, cityMap), countryMap);
-	}
-
 	protected static String firstLC(final String s) {
 		return StringUtils.substring(s, 0, 1).toLowerCase();
 	}
 
+	protected static Iterable<String> tokens(final String s, final int maxTokens) {
+		return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
+	}
+
 	public static String normalizePid(String pid) {
 		return DOI_PREFIX.matcher(pid.toLowerCase()).replaceAll("");
 	}

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java

@@ -47,21 +47,9 @@ public class FieldDef implements Serializable {
 
 	private String clean;
 
-	private String infer;
-
-	private String inferenceFrom;
-
 	public FieldDef() {
 	}
 
-	public String getInferenceFrom() {
-		return inferenceFrom;
-	}
-
-	public void setInferenceFrom(final String inferenceFrom) {
-		this.inferenceFrom = inferenceFrom;
-	}
-
 	public String getName() {
 		return name;
 	}
@@ -138,14 +126,6 @@ public class FieldDef implements Serializable {
 		this.clean = clean;
 	}
 
-	public String getInfer() {
-		return infer;
-	}
-
-	public void setInfer(String infer) {
-		this.infer = infer;
-	}
-
 	@Override
 	public String toString() {
 		try {

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

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

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.model
 import com.jayway.jsonpath.{Configuration, JsonPath}
 import eu.dnetlib.pace.common.AbstractPaceFunctions
 import eu.dnetlib.pace.config.{DedupConfig, Type}
-import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
+import eu.dnetlib.pace.util.MapDocumentUtil
 import org.apache.commons.lang3.StringUtils
 import org.apache.spark.sql.catalyst.encoders.RowEncoder
 import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
@@ -52,7 +52,7 @@ case class SparkModel(conf: DedupConfig) {
   val orderingFieldPosition: Int = schema.fieldIndex(orderingFieldName)
 
   val parseJsonDataset: (Dataset[String] => Dataset[Row]) = df => {
-    df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
+    df.map(r => rowFromJson(r))(RowEncoder(schema))
   }
 
   def rowFromJson(json: String): Row = {
@@ -123,19 +123,9 @@ case class SparkModel(conf: DedupConfig) {
               case _ => res(index)
             }
           }
-
-          if (StringUtils.isNotBlank(fdef.getInfer)) {
-            val inferFrom : String = if (StringUtils.isNotBlank(fdef.getInferenceFrom)) fdef.getInferenceFrom else fdef.getPath
-            res(index) = res(index) match {
-              case x: Seq[String] => x.map(inference(_, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer))
-              case _ => inference(res(index).toString, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer)
-            }
-          }
-
         }
 
         res
-
     }
 
     new GenericRowWithSchema(values, schema)
@@ -156,17 +146,5 @@ case class SparkModel(conf: DedupConfig) {
     res
   }
 
-  def inference(value: String, inferfrom: String, infertype: String) : String = {
-    val res = infertype match {
-      case "country" => AbstractPaceFunctions.countryInference(value, inferfrom)
-      case "city" => AbstractPaceFunctions.cityInference(value)
-      case "keyword" => AbstractPaceFunctions.keywordInference(value)
-      case "city_keyword" => AbstractPaceFunctions.cityKeywordInference(value)
-      case _ => value
-    }
-
-    res
-  }
-
 }
 

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

@@ -0,0 +1,48 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("cityMatch")
+public class CityMatch extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	public CityMatch(Map<String, String> params) {
+		super(params);
+		this.params = params;
+	}
+
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+
+		String ca = cleanup(a);
+		String cb = cleanup(b);
+
+		ca = normalize(ca);
+		cb = normalize(cb);
+
+		ca = filterAllStopWords(ca);
+		cb = filterAllStopWords(cb);
+
+		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
+		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
+
+		Set<String> codes1 = citiesToCodes(cities1);
+		Set<String> codes2 = citiesToCodes(cities2);
+
+		// if no cities are detected, the comparator gives 1.0
+		if (codes1.isEmpty() && codes2.isEmpty())
+			return 1.0;
+		else {
+			if (codes1.isEmpty() ^ codes2.isEmpty())
+				return -1; // undefined if one of the two has no cities
+			return commonElementsPercentage(codes1, codes2);
+		}
+	}
+}

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

@@ -1,51 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("codeMatch")
-public class CodeMatch extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	private Pattern CODE_REGEX;
-
-	public CodeMatch(Map<String, String> params) {
-		super(params);
-		this.params = params;
-		this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]::\\d+"));
-	}
-
-	public Set<String> getRegexList(String input) {
-		Matcher matcher = this.CODE_REGEX.matcher(input);
-		Set<String> cities = new HashSet<>();
-		while (matcher.find()) {
-			cities.add(matcher.group());
-		}
-		return cities;
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		Set<String> codes1 = getRegexList(a);
-		Set<String> codes2 = getRegexList(b);
-
-		// if no codes are detected, the comparator gives 1.0
-		if (codes1.isEmpty() && codes2.isEmpty())
-			return 1.0;
-		else {
-			if (codes1.isEmpty() ^ codes2.isEmpty())
-				return -1; // undefined if one of the two has no codes
-			return commonElementsPercentage(codes1, codes2);
-		}
-	}
-}

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

@@ -1,54 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import com.wcohen.ss.AbstractStringDistance;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("countryMatch")
-public class CountryMatch extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	public CountryMatch(Map<String, String> params) {
-		super(params, new com.wcohen.ss.JaroWinkler());
-		this.params = params;
-	}
-
-	public CountryMatch(final double weight) {
-		super(weight, new com.wcohen.ss.JaroWinkler());
-	}
-
-	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
-		super(weight, ssalgo);
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		if (a.isEmpty() || b.isEmpty()) {
-			return -1.0; // return -1 if a field is missing
-		}
-		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
-			return -1.0; // return -1 if a country is UNKNOWN
-		}
-
-		return a.equals(b) ? 1.0 : 0;
-	}
-
-	@Override
-	public double getWeight() {
-		return super.weight;
-	}
-
-	@Override
-	protected double normalize(final double d) {
-		return d;
-	}
-
-}

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

@@ -1,59 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import com.wcohen.ss.AbstractStringDistance;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("jaroWinklerLegalname")
-public class JaroWinklerLegalname extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	private final String CITY_CODE_REGEX = "city::\\d+";
-	private final String KEYWORD_CODE_REGEX = "key::\\d+";
-
-	public JaroWinklerLegalname(Map<String, String> params) {
-		super(params, new com.wcohen.ss.JaroWinkler());
-		this.params = params;
-	}
-
-	public JaroWinklerLegalname(double weight) {
-		super(weight, new com.wcohen.ss.JaroWinkler());
-	}
-
-	protected JaroWinklerLegalname(double weight, AbstractStringDistance ssalgo) {
-		super(weight, ssalgo);
-	}
-
-	@Override
-	public double distance(String a, String b, final Config conf) {
-
-		String ca = a.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
-		String cb = b.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
-
-		ca = ca.replaceAll("[ ]{2,}", " ");
-		cb = cb.replaceAll("[ ]{2,}", " ");
-
-		if (ca.isEmpty() && cb.isEmpty())
-			return 1.0;
-		else
-			return normalize(ssalgo.score(ca, cb));
-	}
-
-	@Override
-	public double getWeight() {
-		return super.weight;
-	}
-
-	@Override
-	protected double normalize(double d) {
-		return d;
-	}
-
-}

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

@@ -0,0 +1,74 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("jaroWinklerNormalizedName")
+public class JaroWinklerNormalizedName extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	public JaroWinklerNormalizedName(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
+	}
+
+	public JaroWinklerNormalizedName(double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
+
+	protected JaroWinklerNormalizedName(double weight, AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
+
+	@Override
+	public double distance(String a, String b, final Config conf) {
+		String ca = cleanup(a);
+		String cb = cleanup(b);
+
+		ca = normalize(ca);
+		cb = normalize(cb);
+
+		ca = filterAllStopWords(ca);
+		cb = filterAllStopWords(cb);
+
+		Set<String> keywords1 = getKeywords(
+			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
+		Set<String> keywords2 = getKeywords(
+			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
+
+		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
+		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
+
+		ca = removeKeywords(ca, keywords1);
+		ca = removeKeywords(ca, cities1);
+		cb = removeKeywords(cb, keywords2);
+		cb = removeKeywords(cb, cities2);
+
+		ca = ca.replaceAll("[ ]{2,}", " ");
+		cb = cb.replaceAll("[ ]{2,}", " ");
+
+		if (ca.isEmpty() && cb.isEmpty())
+			return 1.0;
+		else
+			return normalize(ssalgo.score(ca, cb));
+	}
+
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
+
+	@Override
+	protected double normalize(double d) {
+		return d;
+	}
+
+}

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

@@ -0,0 +1,50 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("keywordMatch")
+public class KeywordMatch extends AbstractStringComparator {
+
+	Map<String, String> params;
+
+	public KeywordMatch(Map<String, String> params) {
+		super(params);
+		this.params = params;
+	}
+
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+
+		String ca = cleanup(a);
+		String cb = cleanup(b);
+
+		ca = normalize(ca);
+		cb = normalize(cb);
+
+		ca = filterAllStopWords(ca);
+		cb = filterAllStopWords(cb);
+
+		Set<String> keywords1 = getKeywords(
+			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
+		Set<String> keywords2 = getKeywords(
+			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
+
+		Set<String> codes1 = toCodes(keywords1, conf.translationMap());
+		Set<String> codes2 = toCodes(keywords2, conf.translationMap());
+
+		// if no cities are detected, the comparator gives 1.0
+		if (codes1.isEmpty() && codes2.isEmpty())
+			return 1.0;
+		else {
+			if (codes1.isEmpty() ^ codes2.isEmpty())
+				return -1.0; // undefined if one of the two has no keywords
+			return commonElementsPercentage(codes1, codes2);
+		}
+	}
+}

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

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

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

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

dhp-pace-core/src/main/spark-2/eu/dnetlib/pace/util/SparkCompatUtils.scala

@@ -1,12 +0,0 @@
-package eu.dnetlib.pace.util
-
-import org.apache.spark.sql.Row
-import org.apache.spark.sql.catalyst.encoders.{ExpressionEncoder, RowEncoder}
-import org.apache.spark.sql.types.StructType
-
-object SparkCompatUtils {
-
-  def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
-    RowEncoder(schema)
-  }
-}

dhp-pace-core/src/main/spark-35/eu/dnetlib/pace/util/SparkCompatUtils.scala

@@ -1,12 +0,0 @@
-package eu.dnetlib.pace.util
-
-import org.apache.spark.sql.Row
-import org.apache.spark.sql.catalyst.encoders.ExpressionEncoder
-import org.apache.spark.sql.types.StructType
-
-object SparkCompatUtils {
-
-  def encoderFor(schema: StructType): ExpressionEncoder[Row] = {
-    ExpressionEncoder(schema)
-  }
-}

dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java

@@ -8,7 +8,6 @@ import org.junit.jupiter.api.Test;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.mongodb.connection.Cluster;
 
 import eu.dnetlib.pace.AbstractPaceTest;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
@@ -178,16 +177,41 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void legalnameClustering() {
+	public void testKeywordsClustering() {
 
-		final ClusteringFunction cf = new LegalnameClustering(params);
+		final ClusteringFunction cf = new KeywordsClustering(params);
-		String s = "key::1 key::2 city::1";
+		final String s = "Polytechnic University of Turin";
 		System.out.println(s);
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 
-		s = "key::1 key::2 city::1 city::2";
+		final String s1 = "POLITECNICO DI TORINO";
-		System.out.println(s);
+		System.out.println(s1);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
+		System.out.println(cf.apply(conf, Lists.newArrayList(s1)));
+
+		final String s2 = "Universita farmaceutica culturale di milano bergamo";
+		System.out.println("s2 = " + s2);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s2)));
+
+		final String s3 = "universita universita milano milano";
+		System.out.println("s3 = " + s3);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s3)));
+
+		final String s4 = "Politechniki Warszawskiej (Warsaw University of Technology)";
+		System.out.println("s4 = " + s4);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s4)));
+
+		final String s5 = "İstanbul Ticarət Universiteti";
+		System.out.println("s5 = " + s5);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s5)));
+
+		final String s6 = "National and Kapodistrian University of Athens";
+		System.out.println("s6 = " + s6);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s6)));
+
+		final String s7 = "Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών";
+		System.out.println("s7 = " + s7);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s7)));
+
 	}
 
 	@Test

dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java

@@ -54,47 +54,4 @@ public class PaceFunctionTest extends AbstractPaceFunctions {
 		System.out.println("Fixed aliases  : " + fixAliases(TEST_STRING));
 	}
 
-	@Test
-	public void countryInferenceTest() {
-		assertEquals("IT", countryInference("UNKNOWN", "Università di Bologna"));
-		assertEquals("UK", countryInference("UK", "Università di Bologna"));
-		assertEquals("IT", countryInference("UNKNOWN", "Universiteé de Naples"));
-		assertEquals("UNKNOWN", countryInference("UNKNOWN", "Università del Lavoro"));
-	}
-
-	@Test
-	public void cityInferenceTest() {
-		assertEquals("universita city::3181928", cityInference("Università di Bologna"));
-		assertEquals("university city::3170647", cityInference("University of Pisa"));
-		assertEquals("universita", cityInference("Università del lavoro"));
-		assertEquals("universita city::3173331 city::3169522", cityInference("Università di Modena e Reggio Emilia"));
-	}
-
-	@Test
-	public void keywordInferenceTest() {
-		assertEquals("key::41 turin", keywordInference("Polytechnic University of Turin"));
-		assertEquals("key::41 torino", keywordInference("POLITECNICO DI TORINO"));
-		assertEquals(
-			"key::1 key::60 key::81 milano bergamo",
-			keywordInference("Universita farmaceutica culturale di milano bergamo"));
-		assertEquals("key::1 key::1 milano milano", keywordInference("universita universita milano milano"));
-		assertEquals(
-			"key::10 kapodistriako panepistemio athenon",
-			keywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
-	}
-
-	@Test
-	public void cityKeywordInferenceTest() {
-		assertEquals("key::41 city::3165524", cityKeywordInference("Polytechnic University of Turin"));
-		assertEquals("key::41 city::3165524", cityKeywordInference("POLITECNICO DI TORINO"));
-		assertEquals(
-			"key::1 key::60 key::81 city::3173435 city::3182164",
-			cityKeywordInference("Universita farmaceutica culturale di milano bergamo"));
-		assertEquals(
-			"key::1 key::1 city::3173435 city::3173435", cityKeywordInference("universita universita milano milano"));
-		assertEquals(
-			"key::10 kapodistriako panepistemio city::264371",
-			cityKeywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
-	}
-
 }

dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java

@@ -35,7 +35,6 @@ public class ComparatorTest extends AbstractPaceTest {
 		params.put("name_th", "0.95");
 		params.put("jpath_value", "$.value");
 		params.put("jpath_classid", "$.qualifier.classid");
-		params.put("codeRegex", "key::\\d+");
 	}
 
 	@Test
@@ -45,23 +44,52 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void codeMatchTest() {
+	public void cityMatchTest() {
-		CodeMatch codeMatch = new CodeMatch(params);
+		final CityMatch cityMatch = new CityMatch(params);
 
-		// both names with no codes
+		// both names with no cities
-		assertEquals(1.0, codeMatch.distance("testing1", "testing2", conf));
+		assertEquals(1.0, cityMatch.distance("Università", "Centro di ricerca", conf));
 
-		// one of the two names with no codes
+		// one of the two names with no cities
-		assertEquals(-1.0, codeMatch.distance("testing1 key::1", "testing", conf));
+		assertEquals(-1.0, cityMatch.distance("Università di Bologna", "Centro di ricerca", conf));
 
-		// both names with codes (same)
+		// both names with cities (same)
-		assertEquals(1.0, codeMatch.distance("testing1 key::1", "testing2 key::1", conf));
+		assertEquals(1.0, cityMatch.distance("Universita di Bologna", "Biblioteca di Bologna", conf));
 
-		// both names with codes (different)
+		// both names with cities (different)
-		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
+		assertEquals(0.0, cityMatch.distance("Universita di Bologna", "Universita di Torino", conf));
+		assertEquals(0.0, cityMatch.distance("Franklin College", "Concordia College", conf));
 
-		// both names with codes (1 same, 1 different)
+		// particular cases
-		assertEquals(0.5, codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
+		assertEquals(1.0, cityMatch.distance("Free University of Bozen-Bolzano", "Università di Bolzano", conf));
+		assertEquals(
+			1.0,
+			cityMatch
+				.distance(
+					"Politechniki Warszawskiej (Warsaw University of Technology)", "Warsaw University of Technology",
+					conf));
+
+		// failing becasuse 'Allen' is a transliterrated greek stopword
+		// assertEquals(-1.0, cityMatch.distance("Allen (United States)", "United States Military Academy", conf));
+		assertEquals(-1.0, cityMatch.distance("Washington (United States)", "United States Military Academy", conf));
+	}
+
+	@Test
+	public void keywordMatchTest() {
+		params.put("threshold", "0.5");
+
+		final KeywordMatch keywordMatch = new KeywordMatch(params);
+
+		assertEquals(
+			0.5, keywordMatch.distance("Biblioteca dell'Universita di Bologna", "Università di Bologna", conf));
+		assertEquals(1.0, keywordMatch.distance("Universita degli studi di Pisa", "Universita di Pisa", conf));
+		assertEquals(1.0, keywordMatch.distance("Polytechnic University of Turin", "POLITECNICO DI TORINO", conf));
+		assertEquals(1.0, keywordMatch.distance("Istanbul Commerce University", "İstanbul Ticarət Universiteti", conf));
+		assertEquals(1.0, keywordMatch.distance("Franklin College", "Concordia College", conf));
+		assertEquals(2.0 / 3.0, keywordMatch.distance("University of Georgia", "Georgia State University", conf));
+		assertEquals(0.5, keywordMatch.distance("University College London", "University of London", conf));
+		assertEquals(0.5, keywordMatch.distance("Washington State University", "University of Washington", conf));
+		assertEquals(-1.0, keywordMatch.distance("Allen (United States)", "United States Military Academy", conf));
 
 	}
 
@@ -127,15 +155,15 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void jaroWinklerLegalnameTest() {
+	public void jaroWinklerNormalizedNameTest() {
 
-		final JaroWinklerLegalname jaroWinklerLegalname = new JaroWinklerLegalname(params);
+		final JaroWinklerNormalizedName jaroWinklerNormalizedName = new JaroWinklerNormalizedName(params);
 
-		double result = jaroWinklerLegalname
+		double result = jaroWinklerNormalizedName
-			.distance("AT&T (United States)", "United States key::2 key::1", conf);
+			.distance("AT&T (United States)", "United States Military Academy", conf);
 		System.out.println("result = " + result);
 
-		result = jaroWinklerLegalname.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
+		result = jaroWinklerNormalizedName.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
 		System.out.println("result = " + result);
 
 	}
@@ -308,23 +336,4 @@ public class ComparatorTest extends AbstractPaceTest {
 		System.out.println("compare = " + compare);
 	}
 
-	@Test
-	public void countryMatch() {
-
-		CountryMatch countryMatch = new CountryMatch(params);
-
-		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
-		assertEquals(-1.0, result);
-
-		result = countryMatch.distance("CL", "UNKNOWN", conf);
-		assertEquals(-1.0, result);
-
-		result = countryMatch.distance("CL", "IT", conf);
-		assertEquals(0.0, result);
-
-		result = countryMatch.distance("CL", "CL", conf);
-		assertEquals(1.0, result);
-
-	}
-
 }

dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java

@@ -11,7 +11,6 @@ import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import eu.dnetlib.pace.model.Person;
-import jdk.nashorn.internal.ir.annotations.Ignore;
 
 public class UtilTest {
 

dhp-shade-package/dependency-reduced-pom.xml

@@ -1,113 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <parent>
-    <artifactId>dhp</artifactId>
-    <groupId>eu.dnetlib.dhp</groupId>
-    <version>1.2.5-SNAPSHOT</version>
-  </parent>
-  <modelVersion>4.0.0</modelVersion>
-  <artifactId>dhp-shade-package</artifactId>
-  <description>This module create a jar of all module dependencies</description>
-  <build>
-    <plugins>
-      <plugin>
-        <artifactId>maven-shade-plugin</artifactId>
-        <executions>
-          <execution>
-            <phase>package</phase>
-            <goals>
-              <goal>shade</goal>
-            </goals>
-            <configuration>
-              <transformers>
-                <transformer>
-                  <mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
-                </transformer>
-                <transformer />
-                <transformer>
-                  <resource>META-INF/cxf/bus-extensions.txt</resource>
-                </transformer>
-              </transformers>
-              <filters>
-                <filter>
-                  <artifact>*:*</artifact>
-                  <excludes>
-                    <exclude>META-INF/maven/**</exclude>
-                    <exclude>META-INF/*.SF</exclude>
-                    <exclude>META-INF/*.DSA</exclude>
-                    <exclude>META-INF/*.RSA</exclude>
-                  </excludes>
-                </filter>
-              </filters>
-              <relocations>
-                <relocation>
-                  <pattern>com</pattern>
-                  <shadedPattern>repackaged.com.google.common</shadedPattern>
-                  <includes>
-                    <include>com.google.common.**</include>
-                  </includes>
-                </relocation>
-              </relocations>
-            </configuration>
-          </execution>
-        </executions>
-      </plugin>
-    </plugins>
-  </build>
-  <dependencies>
-    <dependency>
-      <groupId>org.projectlombok</groupId>
-      <artifactId>lombok</artifactId>
-      <version>1.18.28</version>
-      <scope>provided</scope>
-    </dependency>
-    <dependency>
-      <groupId>org.junit.jupiter</groupId>
-      <artifactId>junit-jupiter</artifactId>
-      <version>5.6.1</version>
-      <scope>test</scope>
-      <exclusions>
-        <exclusion>
-          <artifactId>junit-jupiter-api</artifactId>
-          <groupId>org.junit.jupiter</groupId>
-        </exclusion>
-        <exclusion>
-          <artifactId>junit-jupiter-params</artifactId>
-          <groupId>org.junit.jupiter</groupId>
-        </exclusion>
-        <exclusion>
-          <artifactId>junit-jupiter-engine</artifactId>
-          <groupId>org.junit.jupiter</groupId>
-        </exclusion>
-      </exclusions>
-    </dependency>
-    <dependency>
-      <groupId>org.mockito</groupId>
-      <artifactId>mockito-core</artifactId>
-      <version>3.3.3</version>
-      <scope>test</scope>
-      <exclusions>
-        <exclusion>
-          <artifactId>byte-buddy</artifactId>
-          <groupId>net.bytebuddy</groupId>
-        </exclusion>
-        <exclusion>
-          <artifactId>byte-buddy-agent</artifactId>
-          <groupId>net.bytebuddy</groupId>
-        </exclusion>
-      </exclusions>
-    </dependency>
-    <dependency>
-      <groupId>org.mockito</groupId>
-      <artifactId>mockito-junit-jupiter</artifactId>
-      <version>3.3.3</version>
-      <scope>test</scope>
-    </dependency>
-  </dependencies>
-  <distributionManagement>
-    <site>
-      <id>DHPSite</id>
-      <url>${dhp.site.stage.path}/dhp-common</url>
-    </site>
-  </distributionManagement>
-</project>

dhp-shade-package/pom.xml

@@ -1,169 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0"
-         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-    <parent>
-        <groupId>eu.dnetlib.dhp</groupId>
-        <artifactId>dhp</artifactId>
-        <version>1.2.5-SNAPSHOT</version>
-        <relativePath>../pom.xml</relativePath>
-
-    </parent>
-
-    <artifactId>dhp-shade-package</artifactId>
-    <packaging>jar</packaging>
-
-    <distributionManagement>
-        <site>
-            <id>DHPSite</id>
-            <url>${dhp.site.stage.path}/dhp-common</url>
-        </site>
-    </distributionManagement>
-
-    <description>This module create a jar of all module dependencies</description>
-
-
-    <dependencies>
-
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-actionmanager</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-<!--        <dependency>-->
-<!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-aggregation</artifactId>-->
-<!--            <version>${project.version}</version>-->
-<!--        </dependency>-->
-<!--        <dependency>-->
-<!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-blacklist</artifactId>-->
-<!--            <version>${project.version}</version>-->
-<!--        </dependency>-->
-<!--        <dependency>-->
-<!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-broker-events</artifactId>-->
-<!--            <version>${project.version}</version>-->
-<!--        </dependency>-->
-<!--        <dependency>-->
-<!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-dedup-openaire</artifactId>-->
-<!--            <version>${project.version}</version>-->
-<!--        </dependency>-->
-<!--        <dependency>-->
-<!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-enrichment</artifactId>-->
-<!--            <version>${project.version}</version>-->
-<!--        </dependency>-->
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-graph-mapper</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-graph-provision</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-impact-indicators</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-actionsets</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-hist-snaps</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-monitor-irish</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-promote</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-update</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-swh</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-usage-raw-data-update</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-usage-stats-build</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-    </dependencies>
-
-
-    <build>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-shade-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <phase>package</phase>
-                        <goals>
-                            <goal>shade</goal>
-                        </goals>
-                        <configuration>
-                            <transformers>
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
-                                    <mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
-                                </transformer>
-                                <!-- This is needed if you have dependencies that use Service Loader. Most Google Cloud client libraries do. -->
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer"/>
-                                <transformer
-                                        implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
-                                    <resource>META-INF/cxf/bus-extensions.txt</resource>
-                                </transformer>
-                            </transformers>
-                            <filters>
-                                <filter>
-                                    <artifact>*:*</artifact>
-                                    <excludes>
-                                        <exclude>META-INF/maven/**</exclude>
-                                        <exclude>META-INF/*.SF</exclude>
-                                        <exclude>META-INF/*.DSA</exclude>
-                                        <exclude>META-INF/*.RSA</exclude>
-                                    </excludes>
-                                </filter>
-                            </filters>
-                            <relocations>
-                                <relocation>
-                                    <pattern>com</pattern>
-                                    <shadedPattern>repackaged.com.google.common</shadedPattern>
-                                    <includes>
-                                        <include>com.google.common.**</include>
-                                    </includes>
-                                </relocation>
-                            </relocations>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-        </plugins>
-    </build>
-
-</project>

dhp-workflows/dhp-actionmanager/pom.xml

@@ -51,5 +51,48 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-common</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>eu.dnetlib</groupId>
+                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon-dom</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>jgrapht</groupId>
+                    <artifactId>jgrapht</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>net.sf.ehcache</groupId>
+                    <artifactId>ehcache</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.springframework</groupId>
+                    <artifactId>spring-test</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>apache</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
     </dependencies>
 </project>

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -21,6 +22,7 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
+import eu.dnetlib.actionmanager.rmi.ActionManagerException;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -63,7 +65,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ISLookUpException e) {
+		} catch (ActionManagerException | ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -87,18 +89,31 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ISLookUpException {
+		throws ActionManagerException {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
 		log.debug("quering for service property: {}", q);
-
+		try {
 			final List<String> value = isLookup.quickSearchProfile(q);
 			return Iterables.getOnlyElement(value);
+		} catch (ISLookUpException e) {
+			String msg = "Error accessing service profile, using query: " + q;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		} catch (NoSuchElementException e) {
+			String msg = "missing service property: " + propertyName;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		} catch (IllegalArgumentException e) {
+			String msg = "found more than one service property: " + propertyName;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		}
 	}
 }

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

@@ -103,7 +103,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -157,7 +156,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -95,7 +95,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -125,7 +125,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -135,10 +134,21 @@
             <arg>--outputPath</arg><arg>${workingDir}/action_payload_by_type</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>
-        <ok to="PromoteActionPayloadForDatasetTable"/>
+        <ok to="ForkPromote"/>
         <error to="Kill"/>
     </action>
 
+    <fork name="ForkPromote">
+        <path start="PromoteActionPayloadForDatasetTable"/>
+        <path start="PromoteActionPayloadForDatasourceTable"/>
+        <path start="PromoteActionPayloadForOrganizationTable"/>
+        <path start="PromoteActionPayloadForOtherResearchProductTable"/>
+        <path start="PromoteActionPayloadForProjectTable"/>
+        <path start="PromoteActionPayloadForPublicationTable"/>
+        <path start="PromoteActionPayloadForRelationTable"/>
+        <path start="PromoteActionPayloadForSoftwareTable"/>
+    </fork>
+
     <action name="PromoteActionPayloadForDatasetTable">
         <sub-workflow>
             <app-path>${wf:appPath()}/promote_action_payload_for_dataset_table</app-path>
@@ -150,7 +160,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForDatasourceTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -165,7 +175,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForOrganizationTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -180,7 +190,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForOtherResearchProductTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -195,7 +205,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForProjectTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -210,7 +220,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForPublicationTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -225,7 +235,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForRelationTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -240,7 +250,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="PromoteActionPayloadForSoftwareTable"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
@@ -255,9 +265,11 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="End"/>
+        <ok to="JoinPromote"/>
         <error to="Kill"/>
     </action>
 
+    <join name="JoinPromote" to="End"/>
+
     <end name="End"/>
 </workflow-app>

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

@@ -95,7 +95,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -103,7 +103,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -156,12 +155,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=2560
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>

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

@@ -95,7 +95,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

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

@@ -103,12 +103,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15000
+                --conf spark.sql.shuffle.partitions=7000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@@ -157,12 +156,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15000
+                --conf spark.sql.shuffle.partitions=7000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>

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

@@ -95,12 +95,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15000
+                --conf spark.sql.shuffle.partitions=10000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>

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

@@ -103,7 +103,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -156,12 +155,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=4000
+                --conf spark.sql.shuffle.partitions=2560
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

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

@@ -1,210 +0,0 @@
-/*
- * Copyright (c) 2024.
- * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
- * SPDX-License-Identifier: AGPL-3.0-or-later
- */
-
-package eu.dnetlib.dhp.actionmanager.promote;
-
-import static eu.dnetlib.dhp.common.FunctionalInterfaceSupport.*;
-import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
-import static org.apache.spark.sql.functions.*;
-import static org.junit.jupiter.api.Assertions.*;
-
-import java.io.IOException;
-import java.nio.file.DirectoryStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.HashSet;
-import java.util.List;
-import java.util.function.BiFunction;
-import java.util.function.Function;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.sql.*;
-import org.apache.spark.sql.Dataset;
-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.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.collect.Lists;
-
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
-
-public class PromoteResultWithMeasuresTest {
-
-	private static final Logger log = LoggerFactory.getLogger(PromoteResultWithMeasuresTest.class);
-
-	private static SparkSession spark;
-
-	private static Path tempDir;
-
-	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	@BeforeAll
-	public static void beforeAll() throws IOException {
-		tempDir = Files.createTempDirectory(PromoteResultWithMeasuresTest.class.getSimpleName());
-		log.info("using work dir {}", tempDir);
-
-		SparkConf conf = new SparkConf();
-		conf.setMaster("local[*]");
-		conf.setAppName(PromoteResultWithMeasuresTest.class.getSimpleName());
-		conf.set("spark.driver.host", "localhost");
-
-		conf.set("hive.metastore.local", "true");
-		conf.set("spark.ui.enabled", "false");
-
-		conf.set("spark.sql.warehouse.dir", tempDir.toString());
-		conf.set("hive.metastore.warehouse.dir", tempDir.resolve("warehouse").toString());
-
-		spark = SparkSession.builder().config(conf).getOrCreate();
-	}
-
-	@AfterAll
-	public static void afterAll() throws IOException {
-		spark.stop();
-		FileUtils.deleteDirectory(tempDir.toFile());
-	}
-
-	@Test
-	void testPromoteResultWithMeasures_job() throws Exception {
-
-		final String inputGraphTablePath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
-			.getPath();
-
-		final String inputActionPayloadPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
-			.getPath();
-
-		final String actionPayloadsPath = tempDir.resolve("actionPayloads").toString();
-
-		spark
-			.read()
-			.text(inputActionPayloadPath)
-			.withColumn("payload", col("value"))
-			.select("payload")
-			.write()
-			.parquet(actionPayloadsPath);
-
-		final Path outputGraphTablePath = tempDir.resolve("outputGraphTablePath");
-
-		PromoteActionPayloadForGraphTableJob
-			.main(new String[] {
-				"--isSparkSessionManaged", Boolean.FALSE.toString(),
-				"--graphTableClassName", Publication.class.getCanonicalName(),
-				"--inputGraphTablePath", inputGraphTablePath,
-				"--inputActionPayloadPath", actionPayloadsPath,
-				"--actionPayloadClassName", Result.class.getCanonicalName(),
-				"--outputGraphTablePath", outputGraphTablePath.toString(),
-				"--mergeAndGetStrategy", MergeAndGet.Strategy.MERGE_FROM_AND_GET.toString(),
-				"--promoteActionStrategy", PromoteAction.Strategy.ENRICH.toString(),
-				"--shouldGroupById", "true"
-			});
-
-		assertFalse(isDirEmpty(outputGraphTablePath));
-
-		final Encoder<Publication> pubEncoder = Encoders.bean(Publication.class);
-		List<Publication> results = spark
-			.read()
-			.schema(pubEncoder.schema())
-			.json(outputGraphTablePath.toString())
-			.as(pubEncoder)
-			.collectAsList();
-
-		verify(results);
-	}
-
-	@Test
-	void testPromoteResultWithMeasures_internal() throws JsonProcessingException {
-
-		Dataset<Publication> rowDS = spark
-			.read()
-			.schema(Encoders.bean(Publication.class).schema())
-			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
-			.as(Encoders.bean(Publication.class));
-
-		Dataset<Result> actionPayloadDS = spark
-			.read()
-			.schema(Encoders.bean(Result.class).schema())
-			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
-			.as(Encoders.bean(Result.class));
-
-		final MergeAndGet.Strategy mergeFromAndGet = MergeAndGet.Strategy.MERGE_FROM_AND_GET;
-
-		final SerializableSupplier<Function<Publication, String>> rowIdFn = ModelSupport::idFn;
-		final SerializableSupplier<BiFunction<Publication, Result, Publication>> mergeAndGetFn = MergeAndGet
-			.functionFor(mergeFromAndGet);
-		final SerializableSupplier<Publication> zeroFn = () -> Publication.class
-			.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
-		final SerializableSupplier<Function<Publication, Boolean>> isNotZeroFn = PromoteResultWithMeasuresTest::isNotZeroFnUsingIdOrSourceAndTarget;
-
-		Dataset<Publication> joinedResults = PromoteActionPayloadFunctions
-			.joinGraphTableWithActionPayloadAndMerge(
-				rowDS,
-				actionPayloadDS,
-				rowIdFn,
-				ModelSupport::idFn,
-				mergeAndGetFn,
-				PromoteAction.Strategy.ENRICH,
-				Publication.class,
-				Result.class);
-
-		SerializableSupplier<BiFunction<Publication, Publication, Publication>> mergeRowsAndGetFn = MergeAndGet
-			.functionFor(mergeFromAndGet);
-
-		Dataset<Publication> mergedResults = PromoteActionPayloadFunctions
-			.groupGraphTableByIdAndMerge(
-				joinedResults, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, Publication.class);
-
-		verify(mergedResults.collectAsList());
-	}
-
-	private static void verify(List<Publication> results) throws JsonProcessingException {
-		assertNotNull(results);
-		assertEquals(1, results.size());
-
-		Result r = results.get(0);
-
-		log.info(OBJECT_MAPPER.writeValueAsString(r));
-
-		assertNotNull(r.getMeasures());
-		assertFalse(r.getMeasures().isEmpty());
-		assertTrue(
-			r
-				.getMeasures()
-				.stream()
-				.map(Measure::getId)
-				.collect(Collectors.toCollection(HashSet::new))
-				.containsAll(
-					Lists
-						.newArrayList(
-							"downloads", "views", "influence", "popularity", "influence_alt", "popularity_alt",
-							"impulse")));
-	}
-
-	private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSourceAndTarget() {
-		return t -> {
-			if (isSubClass(t, Relation.class)) {
-				final Relation rel = (Relation) t;
-				return StringUtils.isNotBlank(rel.getSource()) && StringUtils.isNotBlank(rel.getTarget());
-			}
-			return StringUtils.isNotBlank(((OafEntity) t).getId());
-		};
-	}
-
-	private static boolean isDirEmpty(final Path directory) throws IOException {
-		try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(directory)) {
-			return !dirStream.iterator().hasNext();
-		}
-	}
-
-}

dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json

@@ -1,3 +0,0 @@
-{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"downloads","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"125","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"views","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"35","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
-{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"influence","unit":[{"key":"score","value":"3.1167566E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity","unit":[{"key":"score","value":"7.335433E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"influence_alt","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity_alt","unit":[{"key":"score","value":"2.96","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"impulse","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
-{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":null,"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":"hybrid","publiclyFunded":false,"transformativeAgreement":null,"isGreen":true,"isInDiamondJournal":false}

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

@@ -42,9 +42,6 @@ public class Constants {
 	public static final String NULL = "NULL";
 	public static final String NA = "N/A";
 
-	public static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
-	public static final String WEB_CRAWL_NAME = "Web Crawl";
-
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	private Constants() {

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

@@ -9,7 +9,7 @@ import java.util.List;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
+import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
@@ -28,7 +28,6 @@ import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.DoiCleaningRule;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
@@ -41,13 +40,9 @@ public class PrepareAffiliationRelations implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 	private static final String ID_PREFIX = "50|doi_________::";
-	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
+	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
-	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
+	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
-	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
+	public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
-	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
-	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
-	public static final String DOI_URL_PREFIX = "https://doi.org/";
-	public static final int DOI_URL_PREFIX_LENGTH = 16;
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -75,12 +70,6 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String dataciteInputPath = parser.get("dataciteInputPath");
 		log.info("dataciteInputPath: {}", dataciteInputPath);
 
-		final String webcrawlInputPath = parser.get("webCrawlInputPath");
-		log.info("webcrawlInputPath: {}", webcrawlInputPath);
-
-		final String publisherInputPath = parser.get("publisherInputPath");
-		log.info("publisherInputPath: {}", publisherInputPath);
-
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -91,72 +80,35 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
-				createActionSet(
-					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
-					publisherInputPath, outputPath);
-			});
-	}
 
-	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
+				List<KeyValue> collectedFromCrossref = OafMapperUtils
-		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
+					.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
-		String outputPath) {
+				JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
-		List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
+					spark, crossrefInputPath, collectedFromCrossref);
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
-
-		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
-			spark, crossrefInputPath, collectedfromOpenAIRE);
 
+				List<KeyValue> collectedFromPubmed = OafMapperUtils
+					.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
 				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedfromOpenAIRE);
+					spark, pubmedInputPath, collectedFromPubmed);
 
-		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
+				List<KeyValue> collectedFromOpenAPC = OafMapperUtils
-			spark, openapcInputPath, collectedfromOpenAIRE);
+					.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
+				JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
+					spark, openapcInputPath, collectedFromOpenAPC);
 
+				List<KeyValue> collectedFromDatacite = OafMapperUtils
+					.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
 				JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-			spark, dataciteInputPath, collectedfromOpenAIRE);
+					spark, dataciteInputPath, collectedFromDatacite);
-
-		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-			spark, webcrawlInputPath, collectedfromOpenAIRE);
-
-		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
-			spark, publisherlInputPath, collectedfromOpenAIRE);
 
 				crossrefRelations
 					.union(pubmedRelations)
 					.union(openAPCRelations)
 					.union(dataciteRelations)
-			.union(webCrawlRelations)
-			.union(publisherRelations)
 					.saveAsHadoopFile(
-				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
-	}
-
-	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark,
-		String inputPath,
-		List<KeyValue> collectedfrom) {
-
-		Dataset<Row> df = spark
-			.read()
-			.schema(
-				"`DOI` STRING, `Organizations` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>")
-			.json(inputPath)
-			.where("DOI is not null");
-
-		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
-
-	}
-
-	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
-		List<KeyValue> collectedfrom) {
-
-		Dataset<Row> df = spark
-			.read()
-			.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-			.json(inputPath)
-			.where("DOI is not null");
-
-		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
 
+			});
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
@@ -167,27 +119,8 @@ public class PrepareAffiliationRelations implements Serializable {
 		Dataset<Row> df = spark
 			.read()
 			.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-			.json(inputPath)
+			.json(inputPath);
-			.where("DOI is not null");
 
-		return getTextTextJavaPairRDD(collectedfrom, df);
-	}
-
-	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelationsNewModel(SparkSession spark,
-		String inputPath,
-		List<KeyValue> collectedfrom) {
-		// load and parse affiliation relations from HDFS
-		Dataset<Row> df = spark
-			.read()
-			.schema(
-				"`DOI` STRING, `Matchings` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>")
-			.json(inputPath)
-			.where("DOI is not null");
-
-		return getTextTextJavaPairRDDNew(collectedfrom, df);
-	}
-
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
 		// unroll nested arrays
 		df = df
 			.withColumn("matching", functions.explode(new Column("Matchings")))
@@ -203,7 +136,7 @@ public class PrepareAffiliationRelations implements Serializable {
 
 				// DOI to OpenAIRE id
 				final String paperId = ID_PREFIX
-					+ IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi"))));
+					+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
 
 				// ROR id to OpenAIRE id
 				final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
@@ -235,69 +168,6 @@ public class PrepareAffiliationRelations implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
-		// unroll nested arrays
-		df = df
-			.withColumn("matching", functions.explode(new Column("Matchings")))
-			.select(
-				new Column("DOI").as("doi"),
-				new Column("matching.PID").as("pidtype"),
-				new Column("matching.Value").as("pidvalue"),
-				new Column("matching.Confidence").as("confidence"),
-				new Column("matching.Status").as("status"))
-			.where("status = 'active'");
-
-		// prepare action sets for affiliation relations
-		return df
-			.toJavaRDD()
-			.flatMap((FlatMapFunction<Row, Relation>) row -> {
-
-				// DOI to OpenAIRE id
-				final String paperId = ID_PREFIX
-					+ IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi"))));
-
-				// Organization to OpenAIRE identifier
-				String affId = null;
-				if (row.getAs("pidtype").equals("ROR"))
-					// ROR id to OpenIARE id
-					affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("pidvalue"));
-				else
-					// getting the OpenOrgs identifier for the organization
-					affId = row.getAs("pidvalue");
-
-				Qualifier qualifier = OafMapperUtils
-					.qualifier(
-						BIP_AFFILIATIONS_CLASSID,
-						BIP_AFFILIATIONS_CLASSNAME,
-						ModelConstants.DNET_PROVENANCE_ACTIONS,
-						ModelConstants.DNET_PROVENANCE_ACTIONS);
-
-				// format data info; setting `confidence` into relation's `trust`
-				DataInfo dataInfo = OafMapperUtils
-					.dataInfo(
-						false,
-						BIP_INFERENCE_PROVENANCE,
-						true,
-						false,
-						qualifier,
-						Double.toString(row.getAs("confidence")));
-
-				// return bi-directional relations
-				return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
-
-			})
-			.map(p -> new AtomicAction(Relation.class, p))
-			.mapToPair(
-				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
-	}
-
-	private static String removePrefix(String doi) {
-		if (doi.startsWith(DOI_URL_PREFIX))
-			return doi.substring(DOI_URL_PREFIX_LENGTH);
-		return doi;
-	}
-
 	private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
 		DataInfo dataInfo) {
 		return Arrays

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

@@ -10,7 +10,6 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
@@ -84,7 +83,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				resultsRDD
 					.union(projectsRDD)
 					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 			});
 	}
 

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

@@ -80,11 +80,9 @@ public class PrepareFOSSparkJob implements Serializable {
 
 		fosDataset
 			.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
-			.mapGroups(
+			.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
-				(MapGroupsFunction<String, FOSDataModel, Result>) (k,
+				return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it);
-					it) -> getResult(
+			}, Encoders.bean(Result.class))
-						ModelSupport.entityIdPrefix.get(Result.class.getSimpleName().toLowerCase()) + "|" + k, it),
-				Encoders.bean(Result.class))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
@@ -115,7 +113,19 @@ public class PrepareFOSSparkJob implements Serializable {
 			.forEach(
 				l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
 		r.setSubject(sbjs);
-
+		r
+			.setDataInfo(
+				OafMapperUtils
+					.dataInfo(
+						false, null, true,
+						false,
+						OafMapperUtils
+							.qualifier(
+								ModelConstants.PROVENANCE_ENRICH,
+								null,
+								ModelConstants.DNET_PROVENANCE_ACTIONS,
+								ModelConstants.DNET_PROVENANCE_ACTIONS),
+						null));
 		return r;
 	}
 

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

@@ -6,23 +6,26 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Optional;
 
 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.MapGroupsFunction;
-import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
-import org.jetbrains.annotations.NotNull;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class PrepareSDGSparkJob implements Serializable {
@@ -49,91 +52,54 @@ public class PrepareSDGSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final Boolean distributeDOI = Optional
-			.ofNullable(parser.get("distributeDoi"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("distribute doi {}", distributeDOI);
-
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				if (distributeDOI)
 				doPrepare(
 					spark,
 					sourcePath,
 
 					outputPath);
-				else
-					doPrepareoaid(spark, sourcePath, outputPath);
-
 			});
 	}
 
 	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<Row> sdgDataset = spark
+		Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
-			.read()
-			.format("csv")
-			.option("sep", DEFAULT_DELIMITER)
-			.option("inferSchema", "true")
-			.option("header", "true")
-			.option("quotes", "\"")
-			.load(sourcePath);
 
 		sdgDataset
-			.groupByKey((MapFunction<Row, String>) v -> ((String) v.getAs("doi")).toLowerCase(), Encoders.STRING())
+			.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
-			.mapGroups(
+			.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
-				(MapGroupsFunction<String, Row, Result>) (k,
-					it) -> getResult(
-						DHPUtils
-							.generateUnresolvedIdentifier(
-								ModelSupport.entityIdPrefix.get(Result.class.getSimpleName().toLowerCase()) + "|" + k,
-								DOI),
-						it),
-				Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "/sdg");
-	}
-
-	private static void doPrepareoaid(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<Row> sdgDataset = spark
-			.read()
-			.format("csv")
-			.option("sep", DEFAULT_DELIMITER)
-			.option("inferSchema", "true")
-			.option("header", "true")
-			.option("quotes", "\"")
-			.load(sourcePath);
-		;
-
-		sdgDataset
-			.groupByKey((MapFunction<Row, String>) r -> "50|" + ((String) r.getAs("oaid")), Encoders.STRING())
-			.mapGroups(
-				(MapGroupsFunction<String, Row, Result>) PrepareSDGSparkJob::getResult, Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "/sdg");
-	}
-
-	private static @NotNull Result getResult(String id, Iterator<Row> it) {
 				Result r = new Result();
-		r.setId(id);
+				r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
-		Row first = it.next();
+				SDGDataModel first = it.next();
 				List<Subject> sbjs = new ArrayList<>();
-		sbjs.add(getSubject(first.getAs("sdg"), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
+				sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
 				it
 					.forEachRemaining(
 						s -> sbjs
-					.add(getSubject(s.getAs("sdg"), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
+							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
 				r.setSubject(sbjs);
-
+				r
+					.setDataInfo(
+						OafMapperUtils
+							.dataInfo(
+								false, null, true,
+								false,
+								OafMapperUtils
+									.qualifier(
+										ModelConstants.PROVENANCE_ENRICH,
+										null,
+										ModelConstants.DNET_PROVENANCE_ACTIONS,
+										ModelConstants.DNET_PROVENANCE_ACTIONS),
+								null));
 				return r;
+			}, Encoders.bean(Result.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath + "/sdg");
 	}
 
 }

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

@@ -13,6 +13,9 @@ 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.JavaPairRDD;
+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;
@@ -21,9 +24,13 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 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.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java

@@ -49,9 +49,6 @@ public class ReadCOCI implements Serializable {
 		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
-		final String backupPath = parser.get("backupPath");
-		log.info("backupPath {}", backupPath);
-
 		SparkConf sconf = new SparkConf();
 
 		Configuration conf = new Configuration();
@@ -71,14 +68,12 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					fileSystem,
 					outputPath,
-					backupPath,
 					delimiter);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
-		String backupPath,
 		String delimiter) throws IOException {
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
 			.listFiles(
@@ -112,8 +107,7 @@ public class ReadCOCI implements Serializable {
 				.mode(SaveMode.Append)
 				.option("compression", "gzip")
 				.json(outputPath);
-
+			fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
-			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
 		}
 
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java

@@ -1,80 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.personentity;
-
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.utils.DHPUtils;
-
-public class CoAuthorshipIterator implements Iterator<Relation> {
-	private int firstIndex;
-	private int secondIndex;
-	private boolean firstRelation;
-	private List<String> authors;
-	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______::";
-	private static final String OPENAIRE_PREFIX = "openaire____";
-	private static final String SEPARATOR = "::";
-	private static final String ORCID_KEY = "10|" + OPENAIRE_PREFIX + SEPARATOR
-		+ DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
-	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
-	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
-
-	@Override
-	public boolean hasNext() {
-		return firstIndex < authors.size() - 1;
-	}
-
-	@Override
-	public Relation next() {
-		Relation rel = null;
-		if (firstRelation) {
-			rel = getRelation(authors.get(firstIndex), authors.get(secondIndex));
-			firstRelation = Boolean.FALSE;
-		} else {
-			rel = getRelation(authors.get(secondIndex), authors.get(firstIndex));
-			firstRelation = Boolean.TRUE;
-			secondIndex += 1;
-			if (secondIndex >= authors.size()) {
-				firstIndex += 1;
-				secondIndex = firstIndex + 1;
-			}
-		}
-
-		return rel;
-	}
-
-	public CoAuthorshipIterator(List<String> authors) {
-		this.authors = authors;
-		this.firstIndex = 0;
-		this.secondIndex = 1;
-		this.firstRelation = Boolean.TRUE;
-
-	}
-
-	private Relation getRelation(String orcid1, String orcid2) {
-		String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
-		String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
-		return OafMapperUtils
-			.getRelation(
-				source, target, ModelConstants.PERSON_PERSON_RELTYPE,
-				ModelConstants.PERSON_PERSON_SUBRELTYPE,
-				ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-				Arrays.asList(OafMapperUtils.keyValue(ORCID_KEY, ModelConstants.ORCID_DS)),
-				OafMapperUtils
-					.dataInfo(
-						false, null, false, false,
-						OafMapperUtils
-							.qualifier(
-								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
-								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-						"0.91"),
-				null);
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java

@@ -1,20 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.personentity;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class Coauthors implements Serializable {
-	private List<String> coauthors;
-
-	public List<String> getCoauthors() {
-		return coauthors;
-	}
-
-	public void setCoauthors(List<String> coauthors) {
-		this.coauthors = coauthors;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java

@@ -1,40 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.personentity;
-
-import java.io.Serializable;
-
-import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import scala.Tuple2;
-
-public class Couples implements Serializable {
-	Person p;
-	Relation r;
-
-	public Couples() {
-
-	}
-
-	public Person getP() {
-		return p;
-	}
-
-	public void setP(Person p) {
-		this.p = p;
-	}
-
-	public Relation getR() {
-		return r;
-	}
-
-	public void setR(Relation r) {
-		this.r = r;
-	}
-
-	public static <Tuples> Couples newInstance(Tuple2<Person, Relation> couple) {
-		Couples c = new Couples();
-		c.p = couple._1();
-		c.r = couple._2();
-		return c;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java

@@ -1,437 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.personentity;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.*;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.*;
-import java.util.stream.Collectors;
-
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.*;
-import org.apache.spark.sql.*;
-import org.jetbrains.annotations.NotNull;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.spark_project.jetty.util.StringUtil;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.collection.orcid.model.Author;
-import eu.dnetlib.dhp.collection.orcid.model.Employment;
-import eu.dnetlib.dhp.collection.orcid.model.Work;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
-import eu.dnetlib.dhp.schema.oaf.utils.PidType;
-import eu.dnetlib.dhp.utils.DHPUtils;
-import scala.Tuple2;
-
-public class ExtractPerson implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-	private static final String OPENAIRE_PREFIX = "openaire____";
-	private static final String SEPARATOR = "::";
-	private static final String orcidKey = "10|" + OPENAIRE_PREFIX + SEPARATOR
-		+ DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
-
-	private static final String DOI_PREFIX = "50|doi_________::";
-
-	private static final String PMID_PREFIX = "50|pmid________::";
-	private static final String ARXIV_PREFIX = "50|arXiv_______::";
-
-	private static final String PMCID_PREFIX = "50|pmcid_______::";
-	private static final String ROR_PREFIX = "20|ror_________::";
-	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
-	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
-	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
-
-	public static void main(final String[] args) throws IOException, ParseException {
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							ExtractPerson.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/personentity/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);
-
-		final String workingDir = parser.get("workingDir");
-		log.info("workingDir {}", workingDir);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				createActionSet(spark, inputPath, outputPath, workingDir);
-			});
-
-	}
-
-	private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
-
-		Dataset<Author> authors = spark
-			.read()
-			.parquet(inputPath + "Authors")
-			.as(Encoders.bean(Author.class));
-
-		Dataset<Work> works = spark
-			.read()
-			.parquet(inputPath + "Works")
-			.as(Encoders.bean(Work.class))
-			.filter(
-				(FilterFunction<Work>) w -> Optional.ofNullable(w.getPids()).isPresent() &&
-					w
-						.getPids()
-						.stream()
-						.anyMatch(
-							p -> p.getSchema().equalsIgnoreCase("doi") ||
-								p.getSchema().equalsIgnoreCase("pmc") ||
-								p.getSchema().equalsIgnoreCase("pmid") ||
-								p.getSchema().equalsIgnoreCase("arxiv")));
-
-		Dataset<Employment> employmentDataset = spark
-			.read()
-			.parquet(inputPath + "Employments")
-			.as(Encoders.bean(Employment.class));
-
-		Dataset<Author> peopleToMap = authors
-			.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
-			.map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
-			.groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
-
-		Dataset<Employment> employment = employmentDataset
-			.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
-			.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
-
-		Dataset<Person> people;
-		peopleToMap.map((MapFunction<Author, Person>) op -> {
-			Person person = new Person();
-			person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
-			person
-				.setBiography(
-					Optional
-						.ofNullable(op.getBiography())
-
-						.orElse(""));
-			KeyValue kv = OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS);
-			kv.setDataInfo(null);
-			person.setCollectedfrom(Arrays.asList(kv));
-			person
-				.setAlternativeNames(
-					Optional
-						.ofNullable(op.getOtherNames())
-
-						.orElse(new ArrayList<>()));
-			person
-				.setFamilyName(
-					Optional
-						.ofNullable(op.getFamilyName())
-
-						.orElse(""));
-			person
-				.setGivenName(
-					Optional
-						.ofNullable(op.getGivenName())
-
-						.orElse(""));
-			person
-				.setPid(
-					Optional
-						.ofNullable(op.getOtherPids())
-						.map(
-							v -> v
-								.stream()
-								.map(
-									p -> OafMapperUtils
-										.structuredProperty(
-											p.getValue(), p.getSchema(), p.getSchema(), ModelConstants.DNET_PID_TYPES,
-											ModelConstants.DNET_PID_TYPES, null))
-								.collect(Collectors.toList()))
-						.orElse(new ArrayList<>()));
-			person
-				.getPid()
-				.add(
-					OafMapperUtils
-						.structuredProperty(
-							op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
-							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
-			person.setDateofcollection(op.getLastModifiedDate());
-			person.setOriginalId(Arrays.asList(op.getOrcid()));
-			return person;
-		}, Encoders.bean(Person.class))
-			.write()
-			.option("compression", "gzip")
-			.mode(SaveMode.Overwrite)
-			.json(workingDir + "/people");
-
-		works
-			.flatMap(
-				(FlatMapFunction<Work, Relation>) ExtractPerson::getAuthorshipRelationIterator,
-				Encoders.bean(Relation.class))
-			.write()
-			.option("compression", "gzip")
-			.mode(SaveMode.Overwrite)
-			.json(workingDir + "/authorship");
-
-		Dataset<Relation> coauthorship = works
-			.flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
-				List<Tuple2<String, String>> lista = new ArrayList<>();
-				w.getPids().stream().forEach(p -> {
-					if (p.getSchema().equalsIgnoreCase("doi") || p.getSchema().equalsIgnoreCase("pmc")
-						|| p.getSchema().equalsIgnoreCase("pmid") || p.getSchema().equalsIgnoreCase("arxiv"))
-						lista.add(new Tuple2<>(p.getValue(), w.getOrcid()));
-				});
-				return lista.iterator();
-			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
-			.groupByKey((MapFunction<Tuple2<String, String>, String>) Tuple2::_1, Encoders.STRING())
-			.mapGroups(
-				(MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) -> extractCoAuthors(it),
-				Encoders.bean(Coauthors.class))
-			.flatMap(
-				(FlatMapFunction<Coauthors, Relation>) c -> new CoAuthorshipIterator(c.getCoauthors()),
-				Encoders.bean(Relation.class))
-			.groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
-			.mapGroups(
-				(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class));
-
-		coauthorship
-			.write()
-			.option("compression", "gzip")
-			.mode(SaveMode.Overwrite)
-			.json(workingDir + "/coauthorship");
-
-		employment
-			.filter((FilterFunction<Employment>) e -> Optional.ofNullable(e.getAffiliationId()).isPresent())
-			.filter((FilterFunction<Employment>) e -> e.getAffiliationId().getSchema().equalsIgnoreCase("ror"))
-			.map(
-				(MapFunction<Employment, Relation>) ExtractPerson::getAffiliationRelation,
-				Encoders.bean(Relation.class))
-			.write()
-			.option("compression", "gzip")
-			.mode(SaveMode.Overwrite)
-			.json(workingDir + "/affiliation");
-
-		people = spark
-			.read()
-			.textFile(workingDir + "/people")
-			.map(
-				(MapFunction<String, Person>) value -> OBJECT_MAPPER
-					.readValue(value, Person.class),
-				Encoders.bean(Person.class));
-
-		people.show(false);
-		people
-			.toJavaRDD()
-			.map(p -> new AtomicAction(p.getClass(), p))
-			.union(
-				getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
-			.union(
-				getRelations(spark, workingDir + "/coauthorship")
-					.toJavaRDD()
-					.map(r -> new AtomicAction(r.getClass(), r)))
-			.union(
-				getRelations(spark, workingDir + "/affiliation")
-					.toJavaRDD()
-					.map(r -> new AtomicAction(r.getClass(), r)))
-			.mapToPair(
-				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(
-				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
-	}
-
-	private static Dataset<Relation> getRelations(SparkSession spark, String path) {
-		return spark
-			.read()
-			.textFile(path)
-			.map(
-				(MapFunction<String, Relation>) value -> OBJECT_MAPPER
-					.readValue(value, Relation.class),
-				Encoders.bean(Relation.class));// spark.read().json(path).as(Encoders.bean(Relation.class));
-	}
-
-	private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
-		Coauthors coauth = new Coauthors();
-		List<String> coauthors = new ArrayList<>();
-		while (it.hasNext())
-			coauthors.add(it.next()._2());
-		coauth.setCoauthors(coauthors);
-
-		return coauth;
-	}
-
-	private static Relation getAffiliationRelation(Employment row) {
-		String source = PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
-		String target = ROR_PREFIX
-			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
-		List<KeyValue> properties = new ArrayList<>();
-
-		Relation relation = OafMapperUtils
-			.getRelation(
-				source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE,
-				ModelConstants.ORG_PERSON_PARTICIPATES,
-				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				OafMapperUtils
-					.dataInfo(
-						false, null, false, false,
-						OafMapperUtils
-							.qualifier(
-								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						"0.91"),
-				null);
-
-		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
-			KeyValue kv = new KeyValue();
-			kv.setKey("startDate");
-			kv.setValue(row.getStartDate());
-			properties.add(kv);
-		}
-		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
-			KeyValue kv = new KeyValue();
-			kv.setKey("endDate");
-			kv.setValue(row.getEndDate());
-			properties.add(kv);
-		}
-
-		if (properties.size() > 0)
-			relation.setProperties(properties);
-		return relation;
-
-	}
-
-	private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
-		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid1);
-		String target = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid2);
-
-		return Arrays
-			.asList(
-				OafMapperUtils
-					.getRelation(
-						source, target, ModelConstants.PERSON_PERSON_RELTYPE,
-						ModelConstants.PERSON_PERSON_SUBRELTYPE,
-						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						OafMapperUtils
-							.dataInfo(
-								false, null, false, false,
-								OafMapperUtils
-									.qualifier(
-										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
-										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-								"0.91"),
-						null),
-				OafMapperUtils
-					.getRelation(
-						target, source, ModelConstants.PERSON_PERSON_RELTYPE,
-						ModelConstants.PERSON_PERSON_SUBRELTYPE,
-						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						OafMapperUtils
-							.dataInfo(
-								false, null, false, false,
-								OafMapperUtils
-									.qualifier(
-										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
-										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-								"0.91"),
-						null));
-
-	}
-
-	private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
-
-		if (Optional.ofNullable(w.getPids()).isPresent())
-			return w
-				.getPids()
-				.stream()
-				.map(pid -> getRelation(w.getOrcid(), pid))
-				.filter(Objects::nonNull)
-				.collect(Collectors.toList())
-				.iterator();
-		List<Relation> ret = new ArrayList<>();
-		return ret.iterator();
-	}
-
-	private static Relation getRelation(String orcid, eu.dnetlib.dhp.collection.orcid.model.Pid pid) {
-		String target;
-		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-		switch (pid.getSchema()) {
-			case "doi":
-				target = DOI_PREFIX
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), pid.getValue()));
-				break;
-			case "pmid":
-				target = PMID_PREFIX
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pid.getValue()));
-				break;
-			case "arxiv":
-				target = ARXIV_PREFIX
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), pid.getValue()));
-				break;
-			case "pmcid":
-				target = PMCID_PREFIX
-					+ IdentifierFactory
-						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), pid.getValue()));
-				break;
-
-			default:
-				return null;
-		}
-
-		return OafMapperUtils
-			.getRelation(
-				source, target, ModelConstants.RESULT_PERSON_RELTYPE,
-				ModelConstants.RESULT_PERSON_SUBRELTYPE,
-				ModelConstants.RESULT_PERSON_HASAUTHORED,
-				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				OafMapperUtils
-					.dataInfo(
-						false, null, false, false,
-						OafMapperUtils
-							.qualifier(
-								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						"0.91"),
-				null);
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java

@@ -1,25 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.personentity;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-
-import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
-
-import eu.dnetlib.dhp.collection.orcid.model.Work;
-
-public class WorkList implements Serializable {
-	private ArrayList<Work> workArrayList;
-
-	public ArrayList<Work> getWorkArrayList() {
-		return workArrayList;
-	}
-
-	public void setWorkArrayList(ArrayList<Work> workArrayList) {
-		this.workArrayList = workArrayList;
-	}
-
-	public WorkList() {
-		workArrayList = new ArrayList<>();
-	}
-}

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

@@ -1,91 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.sdgnodoi;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.Objects;
-import java.util.Optional;
-
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.fs.Hdfs;
-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.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.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.Result;
-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();
-
-	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/fosnodoi/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("sourcePath");
-		log.info("inputPath {}", inputPath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}", outputPath);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				createActionSet(spark, inputPath, outputPath);
-			});
-
-	}
-
-	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
-		spark
-			.read()
-			.textFile(inputPath)
-			.map(
-				(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
-				Encoders.bean(Result.class))
-			.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);
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java

@@ -5,13 +5,13 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
+import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.sql.types.StructType;
@@ -20,7 +20,6 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -44,7 +43,8 @@ public class CreateActionSetFromWebEntries implements Serializable {
 	private static final String PMID_PREFIX = "50|pmid________::";
 
 	private static final String PMCID_PREFIX = "50|pmc_________::";
-
+	private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
+	private static final String WEB_CRAWL_NAME = "Web Crawl";
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(String[] args) throws Exception {
@@ -70,9 +70,6 @@ public class CreateActionSetFromWebEntries implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final String blackListInputPath = parser.get("blackListPath");
-		log.info("blackListInputPath: {}", blackListInputPath);
-
 		SparkConf conf = new SparkConf();
 
 		runWithSparkSession(
@@ -80,29 +77,25 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 
-				createActionSet(spark, inputPath, outputPath, blackListInputPath);
+				createActionSet(spark, inputPath, outputPath );
 
 			});
 	}
 
 	public static void createActionSet(SparkSession spark, String inputPath,
-		String outputPath, String blackListInputPath) {
+		String outputPath) {
 
 		final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
-			.filter("country_code=='IE'")
+			.filter("publication_year <= 2020 or country_code=='IE'")
 			.drop("publication_year");
 
-		final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
+		dataset.flatMap((FlatMapFunction<Row, Relation>) row -> {
-
-		dataset
-			.join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
-			.filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
-			.drop("OpenAlexId")
-			.flatMap((FlatMapFunction<Row, Relation>) row -> {
 			List<Relation> ret = new ArrayList<>();
 			final String ror = ROR_PREFIX
 				+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 			ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
+			ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
+			ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
 
 			return ret
 				.iterator();
@@ -112,7 +105,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 
 	}
 
@@ -136,22 +129,13 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				"institution", functions
 					.explode(
 						functions.col("institutions")))
-
 			.selectExpr(
-				"id", "doi", "institution.ror as ror",
+				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
 				"institution.country_code as country_code", "publication_year")
 			.distinct();
 
 	}
 
-	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
-
-		return spark
-			.read()
-			.json(inputPath)
-			.select("OpenAlexId");
-	}
-
 	private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
 		if (pmcid == null)
 			return new ArrayList<>();
@@ -159,7 +143,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 		return createAffiliatioRelationPair(
 			PMCID_PREFIX
 				+ IdentifierFactory
-					.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
+					.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC" , pmcid))),
 			ror);
 	}
 
@@ -175,7 +159,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 	}
 
 	private static String removeResolver(String pidType, String pid) {
-		switch (pidType) {
+		switch (pidType){
 			case "PMID":
 				return pid.substring(33);
 			case "PMC":
@@ -195,7 +179,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 		return createAffiliatioRelationPair(
 			DOI_PREFIX
 				+ IdentifierFactory
-					.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI", doi))),
+					.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI" ,doi))),
 			ror);
 
 	}
@@ -211,7 +195,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.IS_AUTHOR_INSTITUTION_OF,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,
@@ -230,7 +214,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.HAS_AUTHOR_INSTITUTION,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java

@@ -1,158 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.webcrawl;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.*;
-
-import java.io.File;
-import java.io.Serializable;
-import java.util.Arrays;
-import java.util.Optional;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.io.filefilter.DirectoryFileFilter;
-import org.apache.commons.io.filefilter.FileFileFilter;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
-import org.apache.hadoop.io.compress.GzipCodec;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.*;
-import org.apache.spark.sql.types.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import scala.Tuple2;
-
-public class RemoveRelationFromActionSet
-	implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
-
-	private static final ObjectMapper MAPPER = new ObjectMapper();
-	private static final StructType KV_SCHEMA = StructType$.MODULE$
-		.apply(
-			Arrays
-				.asList(
-					StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
-					StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
-
-	private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
-		.apply(
-			Arrays
-				.asList(
-					StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
-					StructField$.MODULE$
-						.apply(
-							"payload", DataTypes.StringType, false, Metadata.empty())));
-
-	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(String[] args) throws Exception {
-		String jsonConfiguration = IOUtils
-			.toString(
-				CreateActionSetFromWebEntries.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json"));
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		// the actionSet path
-		final String inputPath = parser.get("sourcePath");
-		log.info("inputPath: {}", inputPath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		final String blackListInputPath = parser.get("blackListPath");
-		log.info("blackListInputPath: {}", blackListInputPath);
-
-		SparkConf conf = new SparkConf();
-
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-
-				removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
-
-			});
-	}
-
-	private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath,
-		String blackListInputPath) {
-		// read the blacklist
-		Dataset<String> blackList = readBlackList(spark, blackListInputPath)
-			.map(
-				(MapFunction<Row, String>) r -> IdentifierFactory
-					.idFromPid("50", "doi", ((String) r.getAs("doi")).substring(16), true),
-				Encoders.STRING());
-
-		// read the old actionset and get the relations in the payload
-		JavaPairRDD<Text, Text> seq = JavaSparkContext
-			.fromSparkContext(spark.sparkContext())
-			.sequenceFile(inputPath, Text.class, Text.class);
-
-		JavaRDD<Row> rdd = seq
-			.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
-
-		Dataset<Row> actionSet = spark
-			.createDataFrame(rdd, KV_SCHEMA)
-			.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
-			.select(expr("atomic_action.*"));
-
-		Dataset<Relation> relation = actionSet
-			.map(
-				(MapFunction<Row, Relation>) r -> MAPPER.readValue((String) r.getAs("payload"), Relation.class),
-				Encoders.bean(Relation.class));
-
-		// select only the relation not matching any pid in the blacklist as source for the relation
-		Dataset<Relation> relNoSource = relation
-			.joinWith(blackList, relation.col("source").equalTo(blackList.col("value")), "left")
-			.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
-			.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class));
-
-		// select only the relation not matching any pid in the blacklist as target of the relation
-		relNoSource
-			.joinWith(blackList, relNoSource.col("target").equalTo(blackList.col("value")), "left")
-			.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
-			.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class))
-			.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, BZip2Codec.class);
-		;
-
-	}
-
-	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
-
-		return spark
-			.read()
-			.json(inputPath)
-			.select("doi");
-	}
-
-}

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

@@ -22,11 +22,9 @@ 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.gtr2.Gtr2PublicationsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
-import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
@@ -60,7 +58,7 @@ public class CollectorWorker extends ReportingJob {
 
 	public void collect() throws UnknownCollectorPluginException, CollectorException, IOException {
 
-		final String outputPath = this.mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
+		final String outputPath = mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
 		log.info("outputPath path is {}", outputPath);
 
 		final CollectorPlugin plugin = getCollectorPlugin();
@@ -70,36 +68,36 @@ public class CollectorWorker extends ReportingJob {
 
 		try (SequenceFile.Writer writer = SequenceFile
 			.createWriter(
-				this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
+				fileSystem.getConf(),
-					.keyClass(IntWritable.class),
+				SequenceFile.Writer.file(new Path(outputPath)),
-				SequenceFile.Writer
+				SequenceFile.Writer.keyClass(IntWritable.class),
-					.valueClass(Text.class),
+				SequenceFile.Writer.valueClass(Text.class),
 				SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
 			final IntWritable key = new IntWritable(counter.get());
 			final Text value = new Text();
 			plugin
-				.collect(this.api, this.report)
+				.collect(api, report)
-				.forEach(content -> {
+				.forEach(
+					content -> {
 						key.set(counter.getAndIncrement());
 						value.set(content);
 						try {
 							writer.append(key, value);
-					} catch (final Throwable e) {
+						} catch (Throwable e) {
 							throw new RuntimeException(e);
 						}
 					});
-		} catch (final Throwable e) {
+		} catch (Throwable e) {
-			this.report.put(e.getClass().getName(), e.getMessage());
+			report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
 		} finally {
 			shutdown();
-			this.report.ongoing(counter.longValue(), counter.longValue());
+			report.ongoing(counter.longValue(), counter.longValue());
 		}
 	}
 
-	private void scheduleReport(final AtomicInteger counter) {
+	private void scheduleReport(AtomicInteger counter) {
 		schedule(new ReporterCallback() {
-
 			@Override
 			public Long getCurrent() {
 				return counter.longValue();
@@ -114,37 +112,33 @@ public class CollectorWorker extends ReportingJob {
 
 	private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
 
-		switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
+		switch (CollectorPlugin.NAME.valueOf(api.getProtocol())) {
 			case oai:
-				return new OaiCollectorPlugin(this.clientParams);
+				return new OaiCollectorPlugin(clientParams);
 			case rest_json2xml:
-				return new RestCollectorPlugin(this.clientParams);
+				return new RestCollectorPlugin(clientParams);
 			case file:
-				return new FileCollectorPlugin(this.fileSystem);
+				return new FileCollectorPlugin(fileSystem);
 			case fileGzip:
-				return new FileGZipCollectorPlugin(this.fileSystem);
+				return new FileGZipCollectorPlugin(fileSystem);
 			case baseDump:
 				return new BaseCollectorPlugin(this.fileSystem);
-			case gtr2Publications:
-				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
-			case osfPreprints:
-				return new OsfPreprintsCollectorPlugin(this.clientParams);
 			case other:
 				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
-					.ofNullable(this.api.getParams().get("other_plugin_type"))
+					.ofNullable(api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
 					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
 				switch (plugin) {
 					case mdstore_mongodb_dump:
-						return new MongoDbDumpCollectorPlugin(this.fileSystem);
+						return new MongoDbDumpCollectorPlugin(fileSystem);
 					case mdstore_mongodb:
 						return new MDStoreCollectorPlugin();
 					default:
 						throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
 				}
 			default:
-				throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
+				throw new UnknownCollectorPluginException("protocol is not managed: " + api.getProtocol());
 		}
 	}
 

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

@@ -20,9 +20,6 @@ public class Author extends ORCIDItem {
 
 	private String lastModifiedDate;
 
-	public Author() {
-	}
-
 	public String getBiography() {
 		return biography;
 	}

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

@@ -11,7 +11,4 @@ public class ORCIDItem {
 	public void setOrcid(String orcid) {
 		this.orcid = orcid;
 	}
-
-	public ORCIDItem() {
-	}
 }

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

@@ -32,6 +32,4 @@ public class Work extends ORCIDItem {
 		pids.add(pid);
 	}
 
-	public Work() {
-	}
 }

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

@@ -11,7 +11,7 @@ public interface CollectorPlugin {
 
 	enum NAME {
 
-		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints;
+		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/gtr2/Gtr2PublicationsCollectorPlugin.java

@@ -1,43 +0,0 @@
-
-package eu.dnetlib.dhp.collection.plugin.gtr2;
-
-import java.util.Iterator;
-import java.util.Spliterator;
-import java.util.Spliterators;
-import java.util.stream.Stream;
-import java.util.stream.StreamSupport;
-
-import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
-import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
-import eu.dnetlib.dhp.common.collection.CollectorException;
-import eu.dnetlib.dhp.common.collection.HttpClientParams;
-
-public class Gtr2PublicationsCollectorPlugin implements CollectorPlugin {
-
-	private final HttpClientParams clientParams;
-
-	public Gtr2PublicationsCollectorPlugin(final HttpClientParams clientParams) {
-		this.clientParams = clientParams;
-	}
-
-	@Override
-	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
-
-		final String baseUrl = api.getBaseUrl();
-		final String startPage = api.getParams().get("startPage");
-		final String endPage = api.getParams().get("endPage");
-		final String fromDate = api.getParams().get("fromDate");
-
-		if ((fromDate != null) && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
-			throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
-		}
-
-		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseUrl, fromDate, startPage, endPage,
-			this.clientParams);
-		final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
-
-		return StreamSupport.stream(spliterator, false);
-	}
-
-}