Add affRo algorithm as an external library

Reviewed-on: #465

.gitignore

@@ -27,3 +27,4 @@ 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

@@ -80,7 +80,15 @@ class WritePredefinedProjectPropertiesTest {
 		mojo.outputFile = testFolder;
 
 		// execute
-		Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
+		try {
+			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/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.slf4j.LoggerFactory;
+import org.apache.commons.logging.Log;
+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 (IOException e) {
+		} catch (Exception 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 +1,363 @@
+
+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
+	 */
+	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

@@ -12,9 +12,7 @@ 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;
 

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 {
@@ -1003,41 +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/MergeUtils.java

@@ -30,7 +30,6 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
-
 	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
 		return mergeGroup(s, oafEntityIterator, true);
 	}
@@ -89,7 +88,7 @@ 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);
 			}
 
@@ -433,10 +432,7 @@ 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<>();
-			di.addAll(r.getDataInfo());
-			di.addAll(l.getDataInfo());
-			r.setDataInfo(di);
+			r.getDataInfo().addAll(l.getDataInfo());
 			return r;
 		}));
 
@@ -468,6 +464,10 @@ 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;
 	}
 

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

@@ -154,5 +154,13 @@
   "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

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

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

@@ -65,7 +65,11 @@ object ScholixUtils extends Serializable {
   }
 
   def generateScholixResourceFromResult(r: Result): ScholixResource = {
-    generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
+    val sum = ScholixUtils.resultToSummary(r)
+    if (sum != null)
+      generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
+    else
+      null
   }
 
   val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
@@ -153,6 +157,14 @@ 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 =>
@@ -377,10 +389,7 @@ object ScholixUtils extends Serializable {
     if (persistentIdentifiers.isEmpty)
       return null
     s.setLocalIdentifier(persistentIdentifiers.asJava)
-    if (r.isInstanceOf[Publication])
-      s.setTypology(Typology.publication)
-    else
-      s.setTypology(Typology.dataset)
+//    s.setTypology(r.getResulttype.getClassid)
 
     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-pace-core/pom.xml

@@ -24,7 +24,7 @@
 				<executions>
 					<execution>
 						<id>scala-compile-first</id>
-						<phase>initialize</phase>
+						<phase>process-resources</phase>
 						<goals>
 							<goal>add-source</goal>
 							<goal>compile</goal>
@@ -59,14 +59,6 @@
 			<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>
@@ -91,10 +83,6 @@
 			<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>
@@ -113,4 +101,90 @@
 		</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/LegalnameClustering.java

@@ -2,31 +2,41 @@
 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("keywordsclustering")
-public class KeywordsClustering extends AbstractClusteringFunction {
+@ClusteringClass("legalnameclustering")
+public class LegalnameClustering extends AbstractClusteringFunction {
 
-	public KeywordsClustering(Map<String, Object> params) {
+	private static final Pattern CITY_CODE_PATTERN = Pattern.compile("city::\\d+");
+	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 : keywordsToCodes(keywords, conf.translationMap())) {
-			for (String city : citiesToCodes(cities)) {
+		for (String keyword : getRegexList(s, KEYWORD_CODE_PATTERN)) {
+			for (String city : getRegexList(s, CITY_CODE_PATTERN)) {
 				combinations.add(keyword + "-" + city);
 				if (combinations.size() >= paramOrDefault("max", 2)) {
 					return combinations;
@@ -42,9 +52,6 @@ public class KeywordsClustering 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

@@ -27,6 +27,14 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 	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");
@@ -74,6 +82,64 @@ 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
@@ -208,6 +274,30 @@ 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 + " ";
@@ -237,6 +327,10 @@ 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();
 	}

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

@@ -47,9 +47,21 @@ 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;
 	}
@@ -126,6 +138,14 @@ 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/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
+import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
 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))(RowEncoder(schema))
+    df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
   }
 
   def rowFromJson(json: String): Row = {
@@ -123,9 +123,19 @@ 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)
@@ -146,5 +156,17 @@ 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

@@ -1,48 +0,0 @@
-
-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

@@ -0,0 +1,51 @@
+
+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

@@ -2,6 +2,7 @@
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
+import java.util.Set;
 
 import com.wcohen.ss.AbstractStringDistance;
 
@@ -12,8 +13,11 @@ 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) {
@@ -26,6 +30,7 @@ public class CountryMatch extends AbstractStringComparator {
 
 	@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
 		}
@@ -45,4 +50,5 @@ public class CountryMatch extends AbstractStringComparator {
 	protected double normalize(final double d) {
 		return d;
 	}
+
 }

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

@@ -0,0 +1,59 @@
+
+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

@@ -1,74 +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("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

@@ -1,50 +0,0 @@
-
-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/tree/support/TreeNodeDef.java

@@ -48,7 +48,7 @@ public class TreeNodeDef implements Serializable {
 	// function for the evaluation of the node
 	public TreeNodeStats evaluate(Row doc1, Row doc2, Config conf) {
 
-		TreeNodeStats stats = new TreeNodeStats();
+		TreeNodeStats stats = new TreeNodeStats(ignoreUndefined);
 
 		// for each field in the node, it computes the
 		for (FieldConf fieldConf : fields) {

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

@@ -9,8 +9,11 @@ public class TreeNodeStats implements Serializable {
 
 	private Map<String, FieldStats> results; // this is an accumulator for the results of the node
 
-	public TreeNodeStats() {
+	private final boolean ignoreUndefined;
+
+	public TreeNodeStats(boolean ignoreUndefined) {
 		this.results = new HashMap<>();
+		this.ignoreUndefined = ignoreUndefined;
 	}
 
 	public Map<String, FieldStats> getResults() {
@@ -22,7 +25,10 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		return this.results.size();
+		if (ignoreUndefined)
+			return this.results.size();
+		else
+			return this.results.size() - undefinedCount(); // do not count undefined
 	}
 
 	public int undefinedCount() {
@@ -78,11 +84,22 @@ public class TreeNodeStats implements Serializable {
 		double min = 100.0; // random high value
 		for (FieldStats fs : this.results.values()) {
 			if (fs.getResult() < min) {
-				if (fs.getResult() >= 0.0 || (fs.getResult() == -1 && fs.isCountIfUndefined()))
+				if (fs.getResult() == -1) {
+					if (fs.isCountIfUndefined()) {
+						min = 0.0;
+					} else {
+						min = -1;
+					}
+				} else {
 					min = fs.getResult();
+				}
 			}
 		}
-		return min;
+		if (ignoreUndefined) {
+			return min == -1.0 ? 0.0 : min;
+		} else {
+			return min;
+		}
 	}
 
 	// if at least one is true, return 1.0
@@ -91,7 +108,11 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		return 0.0;
+		if (!ignoreUndefined && undefinedCount() > 0) {
+			return -1.0;
+		} else {
+			return 0.0;
+		}
 	}
 
 	// if at least one is false, return 0.0
@@ -100,7 +121,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return 0.0;
+					return ignoreUndefined ? 0.0 : -1.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;

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

@@ -44,12 +44,10 @@ public class TreeProcessor {
 			TreeNodeStats stats = currentNode.evaluate(doc1, doc2, config);
 			treeStats.addNodeStats(nextNodeName, stats);
 
-			// if ignoreUndefined=false the miss is considered as undefined
-			if (!currentNode.isIgnoreUndefined() && stats.undefinedCount() > 0) {
+			double finalScore = stats.getFinalScore(currentNode.getAggregation());
+			if (finalScore == -1.0)
 				nextNodeName = currentNode.getUndefined();
-			}
-			// if ignoreUndefined=true the miss is ignored and the score computed anyway
-			else if (stats.getFinalScore(currentNode.getAggregation()) >= currentNode.getThreshold()) {
+			else if (finalScore >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
 			} else {
 				nextNodeName = currentNode.getNegative();

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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,12 @@
+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

@@ -8,6 +8,7 @@ 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;
@@ -177,41 +178,16 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void testKeywordsClustering() {
+	public void legalnameClustering() {
 
-		final ClusteringFunction cf = new KeywordsClustering(params);
-		final String s = "Polytechnic University of Turin";
+		final ClusteringFunction cf = new LegalnameClustering(params);
+		String s = "key::1 key::2 city::1";
 		System.out.println(s);
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 
-		final String s1 = "POLITECNICO DI TORINO";
-		System.out.println(s1);
-		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)));
-
+		s = "key::1 key::2 city::1 city::2";
+		System.out.println(s);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 	}
 
 	@Test

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

@@ -54,4 +54,47 @@ 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

@@ -35,6 +35,7 @@ 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
@@ -44,52 +45,23 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void cityMatchTest() {
-		final CityMatch cityMatch = new CityMatch(params);
+	public void codeMatchTest() {
+		CodeMatch codeMatch = new CodeMatch(params);
 
-		// both names with no cities
-		assertEquals(1.0, cityMatch.distance("Università", "Centro di ricerca", conf));
+		// both names with no codes
+		assertEquals(1.0, codeMatch.distance("testing1", "testing2", conf));
 
-		// one of the two names with no cities
-		assertEquals(-1.0, cityMatch.distance("Università di Bologna", "Centro di ricerca", conf));
+		// one of the two names with no codes
+		assertEquals(-1.0, codeMatch.distance("testing1 key::1", "testing", conf));
 
-		// both names with cities (same)
-		assertEquals(1.0, cityMatch.distance("Universita di Bologna", "Biblioteca di Bologna", conf));
+		// both names with codes (same)
+		assertEquals(1.0, codeMatch.distance("testing1 key::1", "testing2 key::1", conf));
 
-		// both names with cities (different)
-		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 (different)
+		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
 
-		// particular cases
-		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));
+		// both names with codes (1 same, 1 different)
+		assertEquals(0.5, codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
 
 	}
 
@@ -155,15 +127,15 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void jaroWinklerNormalizedNameTest() {
+	public void jaroWinklerLegalnameTest() {
 
-		final JaroWinklerNormalizedName jaroWinklerNormalizedName = new JaroWinklerNormalizedName(params);
+		final JaroWinklerLegalname jaroWinklerLegalname = new JaroWinklerLegalname(params);
 
-		double result = jaroWinklerNormalizedName
-			.distance("AT&T (United States)", "United States Military Academy", conf);
+		double result = jaroWinklerLegalname
+			.distance("AT&T (United States)", "United States key::2 key::1", conf);
 		System.out.println("result = " + result);
 
-		result = jaroWinklerNormalizedName.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
+		result = jaroWinklerLegalname.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
 		System.out.println("result = " + result);
 
 	}
@@ -344,13 +316,13 @@ public class ComparatorTest extends AbstractPaceTest {
 		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CHILE", "UNKNOWN", conf);
+		result = countryMatch.distance("CL", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CHILE", "ITALY", conf);
+		result = countryMatch.distance("CL", "IT", conf);
 		assertEquals(0.0, result);
 
-		result = countryMatch.distance("CHILE", "CHILE", conf);
+		result = countryMatch.distance("CL", "CL", conf);
 		assertEquals(1.0, result);
 
 	}

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

@@ -11,6 +11,7 @@ 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/pom.xml

@@ -0,0 +1,169 @@
+<?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

@@ -51,48 +51,5 @@
             <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

@@ -4,7 +4,6 @@ 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;
@@ -22,7 +21,6 @@ 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;
@@ -65,7 +63,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ActionManagerException | ISLookUpException e) {
+		} catch (ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -89,31 +87,18 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ActionManagerException {
+		throws ISLookUpException {
 		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);
-		}
+
+		final List<String> value = isLookup.quickSearchProfile(q);
+		return Iterables.getOnlyElement(value);
 	}
 }

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/pom.xml

@@ -6,7 +6,18 @@
         <artifactId>dhp-workflows</artifactId>
         <version>1.2.5-SNAPSHOT</version>
     </parent>
+
     <artifactId>dhp-aggregation</artifactId>
+
+    <properties>
+        <affro.release.version>1.0.0</affro.release.version>
+    </properties>
+
+    <scm>
+        <url>https://code-repo.d4science.org/mkallipo/affRo</url>
+        <connection>scm:git:https://code-repo.d4science.org/mkallipo/affRo.git</connection>
+    </scm>
+
     <build>
         <plugins>
             <plugin>
@@ -43,6 +54,28 @@
                     <scalaVersion>${scala.version}</scalaVersion>
                 </configuration>
             </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-scm-plugin</artifactId>
+                <version>1.8.1</version>
+                <configuration>
+                    <connectionType>connection</connectionType>
+                    <scmVersionType>tag</scmVersionType><!-- 'branch' can also be provided here -->
+                    <scmVersion>${affro.release.version}</scmVersion><!-- in case of scmVersionType == 'branch', this field points to the branch name -->
+                    <checkoutDirectory>${project.build.directory}/${oozie.package.file.name}/${oozieAppDir}/affRo</checkoutDirectory>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>checkout-affro</id>
+                        <phase>prepare-package</phase>
+                        <goals>
+                            <goal>checkout</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
         </plugins>
 
     </build>

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

@@ -44,8 +44,6 @@ public class PrepareAffiliationRelations implements Serializable {
 	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
 	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
 	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
-	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
-	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -76,9 +74,6 @@ public class PrepareAffiliationRelations implements Serializable {
 		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);
 
@@ -89,68 +84,43 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
-				createActionSet(
-					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
-					publisherInputPath, outputPath);
+
+				List<KeyValue> collectedFromCrossref = OafMapperUtils
+					.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
+				JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
+					spark, crossrefInputPath, collectedFromCrossref);
+
+				List<KeyValue> collectedFromPubmed = OafMapperUtils
+					.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
+				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
+					spark, pubmedInputPath, collectedFromPubmed);
+
+				List<KeyValue> collectedFromOpenAPC = OafMapperUtils
+					.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
+				JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
+					spark, openapcInputPath, collectedFromOpenAPC);
+
+				List<KeyValue> collectedFromDatacite = OafMapperUtils
+					.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
+				JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
+					spark, dataciteInputPath, collectedFromDatacite);
+
+				List<KeyValue> collectedFromWebCrawl = OafMapperUtils
+					.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
+				JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
+					spark, webcrawlInputPath, collectedFromWebCrawl);
+
+				crossrefRelations
+					.union(pubmedRelations)
+					.union(openAPCRelations)
+					.union(dataciteRelations)
+					.union(webCrawlRelations)
+					.saveAsHadoopFile(
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+
 			});
 	}
 
-	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
-		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
-		String outputPath) {
-		List<KeyValue> collectedFromCrossref = OafMapperUtils
-			.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
-		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
-			spark, crossrefInputPath, collectedFromCrossref);
-
-		List<KeyValue> collectedFromPubmed = OafMapperUtils
-			.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
-		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedFromPubmed);
-
-		List<KeyValue> collectedFromOpenAPC = OafMapperUtils
-			.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
-		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
-			spark, openapcInputPath, collectedFromOpenAPC);
-
-		List<KeyValue> collectedFromDatacite = OafMapperUtils
-			.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
-		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-			spark, dataciteInputPath, collectedFromDatacite);
-
-		List<KeyValue> collectedFromWebCrawl = OafMapperUtils
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
-		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-			spark, webcrawlInputPath, collectedFromWebCrawl);
-
-		List<KeyValue> collectedfromPublisher = OafMapperUtils
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
-		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
-			spark, publisherlInputPath, collectedfromPublisher);
-
-		crossrefRelations
-			.union(pubmedRelations)
-			.union(openAPCRelations)
-			.union(dataciteRelations)
-			.union(webCrawlRelations)
-			.union(publisherRelations)
-			.saveAsHadoopFile(
-				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
-	}
-
-	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,
 		String inputPath,
 		List<KeyValue> collectedfrom) {
@@ -162,10 +132,6 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
-		return getTextTextJavaPairRDD(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")))

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

@@ -10,6 +10,7 @@ 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;
@@ -83,7 +84,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				resultsRDD
 					.union(projectsRDD)
 					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 			});
 	}
 

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

@@ -6,26 +6,23 @@ 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.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.*;
+import org.jetbrains.annotations.NotNull;
 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.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 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 {
@@ -52,42 +49,91 @@ 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 -> {
-				doPrepare(
-					spark,
-					sourcePath,
+				if (distributeDOI)
+					doPrepare(
+						spark,
+						sourcePath,
+
+						outputPath);
+				else
+					doPrepareoaid(spark, sourcePath, outputPath);
 
-					outputPath);
 			});
 	}
 
 	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
+		Dataset<Row> sdgDataset = spark
+			.read()
+			.format("csv")
+			.option("sep", DEFAULT_DELIMITER)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(sourcePath);
 
 		sdgDataset
-			.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
-				Result r = new Result();
-				r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
-				SDGDataModel first = it.next();
-				List<Subject> sbjs = new ArrayList<>();
-				sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
-				it
-					.forEachRemaining(
-						s -> sbjs
-							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
-				r.setSubject(sbjs);
-
-				return r;
-			}, Encoders.bean(Result.class))
+			.groupByKey((MapFunction<Row, String>) v -> ((String) v.getAs("doi")).toLowerCase(), Encoders.STRING())
+			.mapGroups(
+				(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);
+		Row 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));
+		it
+			.forEachRemaining(
+				s -> sbjs
+					.add(getSubject(s.getAs("sdg"), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
+		r.setSubject(sbjs);
+
+		return r;
+	}
+
 }

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

@@ -13,9 +13,6 @@ 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;
@@ -24,13 +21,9 @@ 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/personentity/CoAuthorshipIterator.java

@@ -0,0 +1,80 @@
+
+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

@@ -0,0 +1,20 @@
+
+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

@@ -0,0 +1,40 @@
+
+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

@@ -0,0 +1,437 @@
+
+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

@@ -0,0 +1,25 @@
+
+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

@@ -0,0 +1,91 @@
+
+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

@@ -5,11 +5,10 @@ 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.GzipCodec;
+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.FilterFunction;
@@ -113,7 +112,7 @@ 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, GzipCodec.class);
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 
 	}
 
@@ -153,11 +152,40 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			.select("OpenAlexId");
 	}
 
+	private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
+		if (pmcid == null)
+			return new ArrayList<>();
+
+		return createAffiliatioRelationPair(
+			PMCID_PREFIX
+				+ IdentifierFactory
+					.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
+			ror);
+	}
+
+	private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
+		if (pmid == null)
+			return new ArrayList<>();
+
+		return createAffiliatioRelationPair(
+			PMID_PREFIX
+				+ IdentifierFactory
+					.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
+			ror);
+	}
+
 	private static String removeResolver(String pidType, String pid) {
-		if (pidType.equals("DOI")) {
-			return pid.substring(16);
+		switch (pidType) {
+			case "PMID":
+				return pid.substring(33);
+			case "PMC":
+				return "PMC" + pid.substring(43);
+			case "DOI":
+				return pid.substring(16);
 		}
-		throw new IllegalArgumentException("DOI is the only supported PID type");
+
+		throw new RuntimeException();
+
 	}
 
 	private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {

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

@@ -0,0 +1,158 @@
+
+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/orcid/model/Author.java

@@ -20,6 +20,9 @@ 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

@@ -11,4 +11,7 @@ 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

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

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

@@ -0,0 +1,76 @@
+
+package eu.dnetlib.dhp.collection.plugin.researchfi;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.message.BasicNameValuePair;
+import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ResearchFiCollectorPlugin implements CollectorPlugin {
+
+	private static final Logger log = LoggerFactory.getLogger(ResearchFiCollectorPlugin.class);
+
+	@Override
+	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
+		throws CollectorException {
+
+		final String authUrl = api.getParams().get("auth_url");
+		final String clientId = api.getParams().get("auth_client_id");
+		final String clientSecret = api.getParams().get("auth_client_secret");
+
+		final String authToken = authenticate(authUrl, clientId, clientSecret);
+
+		final Iterator<String> iter = new ResearchFiIterator(api.getBaseUrl(), authToken);
+
+		return StreamSupport.stream(Spliterators.spliteratorUnknownSize(iter, Spliterator.ORDERED), false);
+	}
+
+	private String authenticate(final String authUrl, final String clientId, final String clientSecret)
+		throws CollectorException {
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			final HttpPost req = new HttpPost(authUrl);
+			final List<NameValuePair> params = new ArrayList<>();
+			params.add(new BasicNameValuePair("grant_type", "client_credentials"));
+			params.add(new BasicNameValuePair("client_id", clientId));
+			params.add(new BasicNameValuePair("client_secret", clientSecret));
+
+			req.setEntity(new UrlEncodedFormEntity(params, "UTF-8"));
+
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				final String content = IOUtils.toString(response.getEntity().getContent());
+				final JSONObject obj = new JSONObject(content);
+				final String token = obj.getString("access_token");
+				if (StringUtils.isNotBlank(token)) {
+					return token;
+				}
+			}
+		} catch (final Throwable e) {
+			log.warn("Error obtaining access token", e);
+			throw new CollectorException("Error obtaining access token", e);
+		}
+		throw new CollectorException("Access token is missing");
+
+	}
+
+}

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

@@ -0,0 +1,117 @@
+
+package eu.dnetlib.dhp.collection.plugin.researchfi;
+
+import java.util.Iterator;
+import java.util.Queue;
+import java.util.concurrent.PriorityBlockingQueue;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.http.Header;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.json.JSONArray;
+
+import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ResearchFiIterator implements Iterator<String> {
+
+	private static final Log log = LogFactory.getLog(ResearchFiIterator.class);
+
+	private static final int PAGE_SIZE = 100;
+
+	private final String baseUrl;
+	private final String authToken;
+	private int currPage;
+	private int nPages;
+
+	private final Queue<String> queue = new PriorityBlockingQueue<>();
+
+	public ResearchFiIterator(final String baseUrl, final String authToken) {
+		this.baseUrl = baseUrl;
+		this.authToken = authToken;
+		this.currPage = 0;
+		this.nPages = 0;
+	}
+
+	private void verifyStarted() {
+		if (this.currPage == 0) {
+			try {
+				nextCall();
+			} catch (final CollectorException e) {
+				throw new IllegalStateException(e);
+			}
+		}
+	}
+
+	@Override
+	public boolean hasNext() {
+		synchronized (this.queue) {
+			verifyStarted();
+			return !this.queue.isEmpty();
+		}
+	}
+
+	@Override
+	public String next() {
+		synchronized (this.queue) {
+			verifyStarted();
+			final String res = this.queue.poll();
+			while (this.queue.isEmpty() && (this.currPage < this.nPages)) {
+				try {
+					nextCall();
+				} catch (final CollectorException e) {
+					throw new IllegalStateException(e);
+				}
+			}
+			return res;
+		}
+	}
+
+	private void nextCall() throws CollectorException {
+
+		this.currPage += 1;
+
+		final String url;
+		if (!this.baseUrl.contains("?")) {
+			url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+		} else if (!this.baseUrl.contains("PageSize=")) {
+			url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+		} else {
+			url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
+		}
+		log.info("Calling url: " + url);
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+
+			final HttpGet req = new HttpGet(url);
+			req.addHeader("Authorization", "Bearer " + this.authToken);
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				for (final Header header : response.getAllHeaders()) {
+					log.debug("HEADER: " + header.getName() + " = " + header.getValue());
+					if ("x-page-count".equals(header.getName())) {
+						final int totalPages = NumberUtils.toInt(header.getValue());
+						if (this.nPages != totalPages) {
+							this.nPages = NumberUtils.toInt(header.getValue());
+							log.info("Total pages: " + totalPages);
+						}
+					}
+				}
+
+				final String content = IOUtils.toString(response.getEntity().getContent());
+				final JSONArray jsonArray = new JSONArray(content);
+
+				jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString())));
+			}
+		} catch (final Throwable e) {
+			log.warn("Error calling url: " + url, e);
+			throw new CollectorException("Error calling url: " + url, e);
+		}
+	}
+
+}

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

@@ -8,7 +8,10 @@ import java.io.StringWriter;
 import java.nio.charset.Charset;
 import java.nio.charset.CharsetDecoder;
 import java.nio.charset.CodingErrorAction;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
+import java.util.stream.Collectors;
 
 import javax.xml.stream.XMLEventFactory;
 import javax.xml.stream.XMLEventReader;
@@ -19,6 +22,7 @@ import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -58,13 +62,23 @@ public class XMLIterator implements Iterator<String> {
 
 	private String element;
 
+	private List<String> elements;
+
 	private InputStream inputStream;
 
 	public XMLIterator(final String element, final InputStream inputStream) {
 		super();
 		this.element = element;
+		if (element.contains(",")) {
+			elements = Arrays
+				.stream(element.split(","))
+				.filter(StringUtils::isNoneBlank)
+				.map(String::toLowerCase)
+				.collect(Collectors.toList());
+		}
 		this.inputStream = inputStream;
 		this.parser = getParser();
+
 		try {
 			this.current = findElement(parser);
 		} catch (XMLStreamException e) {
@@ -113,7 +127,7 @@ public class XMLIterator implements Iterator<String> {
 				final XMLEvent event = parser.nextEvent();
 
 				// TODO: replace with depth tracking instead of close tag tracking.
-				if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
+				if (event.isEndElement() && isCheckTag(event.asEndElement().getName().getLocalPart())) {
 					writer.add(event);
 					break;
 				}
@@ -142,18 +156,16 @@ public class XMLIterator implements Iterator<String> {
 		XMLEvent peek = parser.peek();
 		if (peek != null && peek.isStartElement()) {
 			String name = peek.asStartElement().getName().getLocalPart();
-			if (element.equals(name)) {
+			if (isCheckTag(name))
 				return peek;
-			}
 		}
 
 		while (parser.hasNext()) {
-			final XMLEvent event = parser.nextEvent();
+			XMLEvent event = parser.nextEvent();
 			if (event != null && event.isStartElement()) {
 				String name = event.asStartElement().getName().getLocalPart();
-				if (element.equals(name)) {
+				if (isCheckTag(name))
 					return event;
-				}
 			}
 		}
 		return null;
@@ -161,12 +173,31 @@ public class XMLIterator implements Iterator<String> {
 
 	private XMLEventReader getParser() {
 		try {
-			return inputFactory.get().createXMLEventReader(sanitize(inputStream));
+			XMLInputFactory xif = inputFactory.get();
+			xif.setProperty(XMLInputFactory.SUPPORT_DTD, false);
+			return xif.createXMLEventReader(sanitize(inputStream));
 		} catch (XMLStreamException e) {
 			throw new RuntimeException(e);
 		}
 	}
 
+	private boolean isCheckTag(final String tagName) {
+		if (elements != null) {
+			final String found = elements
+				.stream()
+				.filter(e -> e.equalsIgnoreCase(tagName))
+				.findFirst()
+				.orElse(null);
+			if (found != null)
+				return true;
+		} else {
+			if (element.equalsIgnoreCase(tagName)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
 	private Reader sanitize(final InputStream in) {
 		final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
 		charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);

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

@@ -0,0 +1,48 @@
+# --- You can override the following properties (if needed) coming from your ~/.dhp/application.properties ---
+# dhp.hadoop.frontend.temp.dir=/home/ilias.kanellos
+# dhp.hadoop.frontend.user.name=ilias.kanellos
+# dhp.hadoop.frontend.host.name=iis-cdh5-test-gw.ocean.icm.edu.pl
+# dhp.hadoop.frontend.port.ssh=22
+# oozieServiceLoc=http://iis-cdh5-test-m3:11000/oozie
+# jobTracker=yarnRM
+# nameNode=hdfs://nameservice1
+# oozie.execution.log.file.location = target/extract-and-run-on-remote-host.log
+# maven.executable=mvn
+
+# Some memory and driver settings for more demanding tasks
+sparkDriverMemory=10G
+sparkExecutorMemory=10G
+sparkExecutorCores=4
+sparkShufflePartitions=7680
+
+# The above is given differently in an example I found online
+oozie.action.sharelib.for.spark=spark2
+oozieActionShareLibForSpark2=spark2
+spark2YarnHistoryServerAddress=http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089
+spark2EventLogDir=/user/spark/spark2ApplicationHistory
+sparkSqlWarehouseDir=/user/hive/warehouse
+#hiveMetastoreUris=thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083
+# This MAY avoid the no library used error
+oozie.use.system.libpath=true
+# Some stuff copied from openaire's jobs
+spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
+spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
+
+# The following is needed as a property of a workflow
+wfAppPath=${oozieTopWfApplicationPath}
+
+sparkExecutorMemory=10G
+sparkDriverMemory=20G
+sparkExecutorCores=4
+sparkShufflePartitions=7680
+
+resultFolder=${nameNode}/${workingDir}/affro-results
+
+
+#
+#crossrefInputPath=/data/bip-affiliations/crossref-data.json
+#pubmedInputPath=/data/bip-affiliations/pubmed-data.json
+#openapcInputPath=/data/bip-affiliations/openapc-data.json
+#dataciteInputPath=/data/bip-affiliations/datacite-data.json
+#
+#outputPath=/tmp/crossref-affiliations-output-v5

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

@@ -0,0 +1,30 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,100 @@
+<workflow-app name="AffroAffiliations" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+
+    <start to="run-affro"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="run-affro">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Affiliations inference (Affro)</name>
+            <jar>update_records.py</jar>
+
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
+                --conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.yarn.appMasterEnv.PYSPARK_PYTHON=python3
+                --conf spark.executorEnv.PYSPARK_PYTHON=python3
+                --py-files ${wfAppPath}/affRo/affro_cluster.py,${wfAppPath}/affRo/affro_test_example.py,${wfAppPath}/affRo/create_input_cluster.py,${wfAppPath}/affRo/functions_cluster.py,${wfAppPath}/affRo/matching_cluster.py
+                --files ${wfAppPath}/affRo/dictionaries/dix_acad.json,${wfAppPath}/affRo/dictionaries/dix_categ.json,${wfAppPath}/affRo/dictionaries/dix_city.json,${wfAppPath}/affRo/dictionaries/dix_country.json,${wfAppPath}/affRo/dictionaries/dix_mult.json,${wfAppPath}/affRo/txt_files/city_names.txt,${wfAppPath}/affRo/txt_files/remove_list.txt,${wfAppPath}/affRo/txt_files/stop_words.txt,${wfAppPath}/affRo/txt_files/university_terms.txt
+            </spark-opts>
+
+            <arg>${resultFolder}</arg>
+
+            <file>${wfAppPath}/affRo/update_records.py#update_records.py</file>
+        </spark>
+
+        <ok to="End" />
+        <error to="Kill" />
+
+    </action>
+
+    <end name="End"/>
+</workflow-app>

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

@@ -28,19 +28,13 @@
     "paramLongName": "dataciteInputPath",
     "paramDescription": "the path to get the input data from Datacite",
     "paramRequired": true
-  },
-  {
-    "paramName": "wip",
-    "paramLongName": "webCrawlInputPath",
-    "paramDescription": "the path to get the input data from Web Crawl",
-    "paramRequired": true
-  },
-  {
-    "paramName": "pip",
-    "paramLongName": "publisherInputPath",
-    "paramDescription": "the path to get the input data from publishers",
-    "paramRequired": true
-  },
+  },{
+  "paramName": "wip",
+  "paramLongName": "webCrawlInputPath",
+  "paramDescription": "the path to get the input data from Web Crawl",
+  "paramRequired": true
+}
+,
   {
     "paramName": "o",
     "paramLongName": "outputPath",

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

@@ -35,6 +35,5 @@ crossrefInputPath=/data/bip-affiliations/crossref-data.json
 pubmedInputPath=/data/bip-affiliations/pubmed-data.json
 openapcInputPath=/data/bip-affiliations/openapc-data.json
 dataciteInputPath=/data/bip-affiliations/datacite-data.json
-webCrawlInputPath=/data/bip-affiliations/webCrawl/
 
 outputPath=/tmp/crossref-affiliations-output-v5

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

@@ -21,10 +21,6 @@
             <name>webCrawlInputPath</name>
             <description>the path where to find the inferred affiliation relations from webCrawl</description>
         </property>
-        <property>
-            <name>publisherInputPath</name>
-            <description>the path where to find the inferred affiliation relations from publisher websites</description>
-        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -121,7 +117,6 @@
             <arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
             <arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
             <arg>--webCrawlInputPath</arg><arg>${webCrawlInputPath}</arg>
-            <arg>--publisherInputPath</arg><arg>${publisherInputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

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

@@ -0,0 +1,25 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }, {
+  "paramName": "wd",
+  "paramLongName": "workingDir",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
+}
+]

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

@@ -0,0 +1,2 @@
+inputPath=/data/orcid_2023/tables/
+outputPath=/user/miriam.baglioni/peopleAS

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

@@ -0,0 +1,30 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,111 @@
+<workflow-app name="PersonEntity" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+
+        <property>
+            <name>inputPath</name>
+            <description>inputPath</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="deleteoutputpath"/>
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path="${outputPath}"/>
+            <mkdir path="${outputPath}"/>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="atomicactions"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="atomicactions">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the ActionSet for Person entity and relevant relations</name>
+            <class>eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=4
+                --executor-memory=4G
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=5G
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=15000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

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

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

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

@@ -0,0 +1,30 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,125 @@
+
+<workflow-app name="SDG no doi" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sdgPath</name>
+            <description>the input path of the resources to be extended</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="prepareSDG"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="prepareSDG">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the results from FOS</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sdgPath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
+            <arg>--distributeDoi</arg><arg>false</arg>
+        </spark>
+        <ok to="produceActionSet"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <action name="produceActionSet">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Save the action set grouping results with the same id</name>
+            <class>eu.dnetlib.dhp.actionmanager.sdgnodoi.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/prepared/sdg</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

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

@@ -1,3 +1,11 @@
-sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
-outputPath=/tmp/miriam/webcrawlComplete/
-blackListPath=/user/miriam.baglioni/openalex-blackList
+#PROPERTIES TO CREATE THE ACTION SET
+#sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
+#outputPath=/tmp/miriam/webcrawlComplete/
+#blackListPath=/user/miriam.baglioni/openalex-blackList
+#resumeFrom=create
+
+#PROPERTIES TO REMOVE FROM THE ACTION SET
+sourcePath=/var/lib/dnet/actionManager_PROD/webcrawl/rawset_28247629-468b-478e-9a42-bc540877125d_1718121542061/
+outputPath=/tmp/miriam/webcrawlRemoved/
+blackListPath=/user/miriam.baglioni/oalexBlackListNormalized
+resumeFrom=remove

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

@@ -20,12 +20,19 @@
         </configuration>
     </global>
 
-    <start to="create_actionset"/>
+    <start to="resumeFrom"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <decision name="resumeFrom">
+        <switch>
+            <case to="create_actionset">${wf:conf('resumeFrom') eq 'create'}</case>
+            <default to="remove_from_actionset"/>
+        </switch>
+    </decision>
+
     <action name="create_actionset">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -50,5 +57,30 @@
         <ok to="End"/>
         <error to="Kill"/>
     </action>
+
+    <action name="remove_from_actionset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Removes some relations found to be wrong from the AS</name>
+            <class>eu.dnetlib.dhp.actionmanager.webcrawl.RemoveRelationFromActionSet</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--blackListPath</arg><arg>${blackListPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml

@@ -1,4 +1,4 @@
-<workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
+    <workflow-app name="Transform_BioEntity_Workflow" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>sourcePath</name>
@@ -8,40 +8,19 @@
             <name>database</name>
             <description>the PDB Database Working Path</description>
         </property>
+
         <property>
-            <name>mdStoreOutputId</name>
-            <description>the identifier of the cleaned MDStore</description>
-        </property>
-        <property>
-            <name>mdStoreManagerURI</name>
-            <description>the path of the cleaned mdstore</description>
+            <name>targetPath</name>
+            <description>the Target Working dir path</description>
         </property>
     </parameters>
 
-    <start to="StartTransaction"/>
-
+    <start to="ConvertDB"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <action name="StartTransaction">
-        <java>
-            <configuration>
-                <property>
-                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                    <value>true</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-            <arg>--action</arg><arg>NEW_VERSION</arg>
-            <arg>--mdStoreID</arg><arg>${mdStoreOutputId}</arg>
-            <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-            <capture-output/>
-        </java>
-        <ok to="ConvertDB"/>
-        <error to="RollBack"/>
-    </action>
     <action name="ConvertDB">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -62,48 +41,11 @@
             <arg>--master</arg><arg>yarn</arg>
             <arg>--dbPath</arg><arg>${sourcePath}</arg>
             <arg>--database</arg><arg>${database}</arg>
-            <arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
         </spark>
-        <ok to="CommitVersion"/>
-        <error to="RollBack"/>
-
+        <ok to="End"/>
+        <error to="Kill"/>
     </action>
-        <action name="CommitVersion">
-            <java>
-                <configuration>
-                    <property>
-                        <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                        <value>true</value>
-                    </property>
-                </configuration>
-                <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-                <arg>--action</arg><arg>COMMIT</arg>
-                <arg>--namenode</arg><arg>${nameNode}</arg>
-                <arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
-                <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-            </java>
-            <ok to="End"/>
-            <error to="Kill"/>
-        </action>
-
-        <action name="RollBack">
-            <java>
-                <configuration>
-                    <property>
-                        <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                        <value>true</value>
-                    </property>
-                </configuration>
-                <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-                <arg>--action</arg><arg>ROLLBACK</arg>
-                <arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
-                <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-            </java>
-            <ok to="Kill"/>
-            <error to="Kill"/>
-        </action>
-
-
-        <end name="End"/>
+    <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json

@@ -2,5 +2,5 @@
   {"paramName":"mt",  "paramLongName":"master",       "paramDescription": "should be local or yarn",                  "paramRequired": true},
   {"paramName":"db",  "paramLongName":"database",     "paramDescription": "should be PDB or UNIPROT",                 "paramRequired": true},
   {"paramName":"p",   "paramLongName":"dbPath",       "paramDescription": "the path of the database to transform",    "paramRequired": true},
-  {"paramName":"mo",   "paramLongName":"mdstoreOutputVersion",     "paramDescription": "the oaf path ",                "paramRequired": true}
+  {"paramName":"t",   "paramLongName":"targetPath",   "paramDescription": "the OAF target path ",                     "paramRequired": true}
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json

@@ -1,20 +1,5 @@
 [
-  {
-    "paramName": "mt",
-    "paramLongName": "master",
-    "paramDescription": "should be local or yarn",
-    "paramRequired": true
-  },
-  {
-    "paramName": "s",
-    "paramLongName": "sourcePath",
-    "paramDescription": "the source Path",
-    "paramRequired": true
-  },
-  {
-    "paramName": "mo",
-    "paramLongName": "mdstoreOutputVersion",
-    "paramDescription": "the oaf path ",
-    "paramRequired": true
-  }
+  {"paramName":"mt",  "paramLongName":"master",     "paramDescription": "should be local or yarn",                  "paramRequired": true},
+  {"paramName":"s",   "paramLongName":"sourcePath","paramDescription": "the source Path",                              "paramRequired": true},
+  {"paramName":"t",   "paramLongName":"targetPath","paramDescription": "the  oaf path ",  "paramRequired": true}
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml

@@ -9,26 +9,34 @@
             <description>the Working Path</description>
         </property>
         <property>
-            <name>mdStoreOutputId</name>
-            <description>the identifier of the cleaned MDStore</description>
+            <name>targetPath</name>
+            <description>the OAF MDStore Path</description>
         </property>
         <property>
-            <name>mdStoreManagerURI</name>
-            <description>the path of the cleaned mdstore</description>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
         </property>
         <property>
             <name>resumeFrom</name>
-            <value>CreateEBIDataSet</value>
+            <value>DownloadEBILinks</value>
             <description>node to start</description>
         </property>
     </parameters>
 
-    <start to="StartTransaction"/>
+    <start to="resume_from"/>
 
     <decision name="resume_from">
         <switch>
             <case to="DownloadEBILinks">${wf:conf('resumeFrom') eq 'DownloadEBILinks'}</case>
-            <case to="StartTransaction">${wf:conf('resumeFrom') eq 'CreateEBIDataSet'}</case>
+            <case to="CreateEBIDataSet">${wf:conf('resumeFrom') eq 'CreateEBIDataSet'}</case>
             <default to="DownloadEBILinks"/>
         </switch>
     </decision>
@@ -69,29 +77,9 @@
             <move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
             <move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
         </fs>
-        <ok to="StartTransaction"/>
+        <ok to="CreateEBIDataSet"/>
         <error to="Kill"/>
     </action>
-
-    <action name="StartTransaction">
-        <java>
-            <configuration>
-                <property>
-                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                    <value>true</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-            <arg>--action</arg><arg>NEW_VERSION</arg>
-            <arg>--mdStoreID</arg><arg>${mdStoreOutputId}</arg>
-            <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-            <capture-output/>
-        </java>
-        <ok to="CreateEBIDataSet"/>
-        <error to="RollBack"/>
-    </action>
-
-
     <action name="CreateEBIDataSet">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn-cluster</master>
@@ -107,49 +95,11 @@
                 ${sparkExtraOPT}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/ebi_links_dataset</arg>
-            <arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
+            <arg>--targetPath</arg><arg>${targetPath}</arg>
             <arg>--master</arg><arg>yarn</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
-
-
-    <action name="CommitVersion">
-        <java>
-            <configuration>
-                <property>
-                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                    <value>true</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-            <arg>--action</arg><arg>COMMIT</arg>
-            <arg>--namenode</arg><arg>${nameNode}</arg>
-            <arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
-            <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-        </java>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="RollBack">
-        <java>
-            <configuration>
-                <property>
-                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
-                    <value>true</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
-            <arg>--action</arg><arg>ROLLBACK</arg>
-            <arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
-            <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
-        </java>
-        <ok to="Kill"/>
-        <error to="Kill"/>
-    </action>
-
     <end name="End"/>
-
 </workflow-app>

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

@@ -888,7 +888,11 @@ case object Crossref2Oaf {
               val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
-
+//              Added mapping for DFG
+            case "10.13039/501100001659" =>
+              val targetId = getProjectId("dfgf________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             case "10.13039/100020031" =>
               val targetId = getProjectId("tara________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
@@ -1025,6 +1029,7 @@ case object Crossref2Oaf {
             tp._1 match {
               case "electronic" => journal.setIssnOnline(tp._2)
               case "print"      => journal.setIssnPrinted(tp._2)
+              case _            =>
             }
           })
         }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala

@@ -231,7 +231,7 @@ object BioDBToOAF {
   def uniprotToOAF(input: String): List[Oaf] = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json = parse(input)
-    val pid = (json \ "pid").extract[String].trim()
+    val pid = (json \ "pid").extract[String]
 
     val d = new Dataset
 

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala

@@ -2,15 +2,12 @@ package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.collection.CollectionUtils
-import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
-import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
 import eu.dnetlib.dhp.schema.oaf.Oaf
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
-import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
 
 object SparkTransformBioDatabaseToOAF {
 
@@ -28,13 +25,8 @@ object SparkTransformBioDatabaseToOAF {
 
     val dbPath: String = parser.get("dbPath")
     log.info("dbPath: {}", database)
-
-    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
-    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
-
-    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-    log.info("outputBasePath: {}", outputBasePath)
+    val targetPath: String = parser.get("targetPath")
+    log.info("targetPath: {}", database)
 
     val spark: SparkSession =
       SparkSession
@@ -51,28 +43,24 @@ object SparkTransformBioDatabaseToOAF {
       case "UNIPROT" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))),
-          s"$outputBasePath/$MDSTORE_DATA_PATH"
+          targetPath
         )
       case "PDB" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))),
-          s"$outputBasePath/$MDSTORE_DATA_PATH"
+          targetPath
         )
       case "SCHOLIX" =>
         CollectionUtils.saveDataset(
           spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)),
-          s"$outputBasePath/$MDSTORE_DATA_PATH"
+          targetPath
         )
       case "CROSSREF_LINKS" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))),
-          s"$outputBasePath/$MDSTORE_DATA_PATH"
+          targetPath
         )
     }
-
-    val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
-    val mdStoreSize = df.count
-    writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
   }
 
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala

@@ -2,12 +2,9 @@ package eu.dnetlib.dhp.sx.bio.ebi
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.collection.CollectionUtils
-import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
-import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import eu.dnetlib.dhp.schema.oaf.Oaf
 import eu.dnetlib.dhp.sx.bio.pubmed._
-import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop.conf.Configuration
@@ -17,13 +14,13 @@ import org.apache.http.client.methods.HttpGet
 import org.apache.http.impl.client.HttpClientBuilder
 import org.apache.spark.SparkConf
 import org.apache.spark.rdd.RDD
-import org.apache.spark.sql.expressions.Aggregator
 import org.apache.spark.sql._
+import org.apache.spark.sql.expressions.Aggregator
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.io.InputStream
-import scala.io.Source
-import scala.xml.pull.XMLEventReader
+import java.io.{ByteArrayInputStream, InputStream}
+import java.nio.charset.Charset
+import javax.xml.stream.XMLInputFactory
 
 object SparkCreateBaselineDataFrame {
 
@@ -86,7 +83,7 @@ object SparkCreateBaselineDataFrame {
           if (response.getStatusLine.getStatusCode > 400) {
             tries -= 1
           } else
-            return IOUtils.toString(response.getEntity.getContent)
+            return IOUtils.toString(response.getEntity.getContent, Charset.defaultCharset())
         } catch {
           case e: Throwable =>
             println(s"Error on requesting ${r.getURI}")
@@ -158,7 +155,8 @@ object SparkCreateBaselineDataFrame {
       IOUtils.toString(
         SparkEBILinksToOaf.getClass.getResourceAsStream(
           "/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
-        )
+        ),
+        Charset.defaultCharset()
       )
     )
     parser.parseArgument(args)
@@ -167,15 +165,11 @@ object SparkCreateBaselineDataFrame {
     val workingPath = parser.get("workingPath")
     log.info("workingPath: {}", workingPath)
 
-    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
-    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
-
-    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-    log.info("outputBasePath: {}", outputBasePath)
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
 
     val hdfsServerUri = parser.get("hdfsServerUri")
-    log.info("hdfsServerUri: {}", hdfsServerUri)
+    log.info("hdfsServerUri: {}", targetPath)
 
     val skipUpdate = parser.get("skipUpdate")
     log.info("skipUpdate: {}", skipUpdate)
@@ -201,10 +195,11 @@ object SparkCreateBaselineDataFrame {
     if (!"true".equalsIgnoreCase(skipUpdate)) {
       downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
       val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
+      val inputFactory = XMLInputFactory.newInstance
       val ds: Dataset[PMArticle] = spark.createDataset(
         k.filter(i => i._1.endsWith(".gz"))
           .flatMap(i => {
-            val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
+            val xml = inputFactory.createXMLEventReader(new ByteArrayInputStream(i._2.getBytes()))
             new PMParser(xml)
           })
       )
@@ -223,11 +218,8 @@ object SparkCreateBaselineDataFrame {
         .map(a => PubMedToOaf.convert(a, vocabularies))
         .as[Oaf]
         .filter(p => p != null),
-      s"$outputBasePath/$MDSTORE_DATA_PATH"
+      targetPath
     )
 
-    val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
-    val mdStoreSize = df.count
-    writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
   }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala

@@ -9,9 +9,6 @@ import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
 import org.apache.spark.sql._
 import org.slf4j.{Logger, LoggerFactory}
-import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
-import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
-import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile}
 
 object SparkEBILinksToOaf {
 
@@ -35,13 +32,8 @@ object SparkEBILinksToOaf {
     import spark.implicits._
     val sourcePath = parser.get("sourcePath")
     log.info(s"sourcePath  -> $sourcePath")
-    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
-    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
-
-    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-    log.info("outputBasePath: {}", outputBasePath)
-
+    val targetPath = parser.get("targetPath")
+    log.info(s"targetPath  -> $targetPath")
     implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
 
     val ebLinks: Dataset[EBILinkItem] = spark.read
@@ -54,10 +46,7 @@ object SparkEBILinksToOaf {
         .flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
         .filter(p => BioDBToOAF.EBITargetLinksFilter(p))
         .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
-      s"$outputBasePath/$MDSTORE_DATA_PATH"
+      targetPath
     )
-    val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH")
-    val mdStoreSize = df.count
-    writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH")
   }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala

@@ -1,7 +1,8 @@
 package eu.dnetlib.dhp.sx.bio.pubmed
 
 import scala.xml.MetaData
-import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
+import javax.xml.stream.XMLEventReader
+import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
 
 /** @param xml
   */

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

@@ -78,10 +78,6 @@ public class PrepareAffiliationRelationsTest {
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
-		String publisherAffiliationRelationPath = getClass()
-			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
-			.getPath();
-
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
@@ -93,7 +89,6 @@ public class PrepareAffiliationRelationsTest {
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
-					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -110,7 +105,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(138, tmp.count());
+		assertEquals(120, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -121,7 +116,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				69, execVerification
+				60, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -129,7 +124,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				69, execVerification
+				60, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
@@ -150,12 +145,5 @@ public class PrepareAffiliationRelationsTest {
 					.get(0)
 					.getString(4));
 
-		final String publisherid = ID_PREFIX
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s00217-010-1268-9"));
-		final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/03265fv13");
-
-		Assertions
-			.assertEquals(
-				1, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
 	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java

@@ -15,10 +15,7 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.AfterAll;
-import org.junit.jupiter.api.Assertions;
-import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCITest.java

@@ -119,7 +119,9 @@ public class ReadCOCITest {
 					workingDir.toString() + "/COCI",
 					"-outputPath",
 					workingDir.toString() + "/COCI_json/",
-					"-inputFile", "input1;input2;input3;input4;input5"
+					"-inputFile", "input1;input2;input3;input4;input5",
+					"-format",
+					"COCI"
 				});
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java

@@ -0,0 +1,213 @@
+
+package eu.dnetlib.dhp.actionmanager.person;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.utils.DHPUtils;
+
+public class CreatePersonAS {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(CreatePersonAS.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(CreatePersonAS.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CreatePersonAS.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.codegen.wholeStage", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(CreatePersonAS.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testAuthors() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/person/")
+			.getPath();
+
+//		spark
+//				.read()
+//				.parquet(inputPath + "Authors")
+//				.as(Encoders.bean(Author.class))
+//						.filter((FilterFunction<Author>) a -> Optional.ofNullable(a.getOtherNames()).isPresent() &&
+//								Optional.ofNullable(a.getBiography()).isPresent())
+//								.write()
+//										.mode(SaveMode.Overwrite)
+//												.parquet(workingDir.toString() + "AuthorsSubset");
+
+		ExtractPerson
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet1",
+					"-workingDir",
+					workingDir.toString() + "/working"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> relations = sc
+			.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
+			.filter(v -> "eu.dnetlib.dhp.schema.oaf.Relation".equalsIgnoreCase(v._1().toString()))
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+//
+		JavaRDD<Person> people = sc
+			.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
+			.filter(v -> "eu.dnetlib.dhp.schema.oaf.Person".equalsIgnoreCase(v._1().toString()))
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Person) aa.getPayload()));
+//
+		Assertions.assertEquals(7, people.count());
+		Assertions
+			.assertEquals(
+				"Paulo",
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getGivenName());
+		Assertions
+			.assertEquals(
+				"Tavares",
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getFamilyName());
+		Assertions
+			.assertEquals(
+				4,
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getAlternativeNames()
+					.size());
+		Assertions
+			.assertEquals(
+				4,
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getPid()
+					.size());
+		Assertions
+			.assertTrue(
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getPid()
+					.stream()
+					.anyMatch(
+						p -> p.getQualifier().getSchemename().equalsIgnoreCase("Scopus Author ID")
+							&& p.getValue().equalsIgnoreCase("15119405200")));
+
+		Assertions
+			.assertEquals(
+				16,
+				relations
+					.filter(r -> r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				14,
+				relations
+					.filter(r -> r.getRelClass().equalsIgnoreCase(ModelConstants.PERSON_PERSON_HASCOAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				3,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				2,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED)
+							&& r.getTarget().startsWith("50|doi"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED)
+							&& r.getTarget().startsWith("50|arXiv"))
+					.count());
+
+		Assertions
+			.assertEquals(
+				1,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.PERSON_PERSON_HASCOAUTHORED))
+					.count());
+		Assertions.assertEquals(33, relations.count());
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.actionmanager.webcrawl;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -101,7 +102,10 @@ public class CreateASTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-		Assertions.assertEquals(58, tmp.count());
+		tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
+		tmp.foreach(r -> assertTrue(r.getSource().startsWith("20|ror") || r.getSource().startsWith("50|doi")));
+		tmp.foreach(r -> assertTrue(r.getTarget().startsWith("20|ror") || r.getTarget().startsWith("50|doi")));
+		Assertions.assertEquals(24, tmp.count());
 
 	}
 
@@ -112,7 +116,7 @@ public class CreateASTest {
 
 		String inputPath = getClass()
 			.getResource(
-				"/eu/dnetlib/dhp/actionmanager/webcrawl/")
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
 			.getPath();
 		String blackListPath = getClass()
 			.getResource(
@@ -194,7 +198,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getSource()
@@ -207,7 +211,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -228,13 +232,13 @@ public class CreateASTest {
 								"20|ror_________::" + IdentifierFactory
 									.md5(
 										PidCleaner
-											.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
+											.normalizePidValue("ROR", "https://ror.org/03265fv13")))
 							&& r.getSource().startsWith("50|doi"))
 					.count());
 
 		Assertions
 			.assertEquals(
-				1, tmp
+				0, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -268,6 +272,10 @@ public class CreateASTest {
 			.getResource(
 				"/eu/dnetlib/dhp/actionmanager/webcrawl")
 			.getPath();
+		String blackListPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
+			.getPath();
 
 		CreateActionSetFromWebEntries
 			.main(
@@ -277,7 +285,8 @@ public class CreateASTest {
 					"-sourcePath",
 					inputPath,
 					"-outputPath",
-					workingDir.toString() + "/actionSet1"
+					workingDir.toString() + "/actionSet1",
+					"-blackListPath", blackListPath
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());