Merge pull request 'mergeResultsOfDifferentTypes only when checkDelegatedAuthority is true' (#478) from merge_by_id_fix into main

Reviewed-on: #478

.gitignore

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

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

@@ -80,15 +80,7 @@ class WritePredefinedProjectPropertiesTest {
 		mojo.outputFile = testFolder;
 
 		// execute
-		try {
-			mojo.execute();
-			Assertions.assertTrue(false); // not reached
-		} catch (Exception e) {
-			Assertions
-				.assertTrue(
-					MojoExecutionException.class.isAssignableFrom(e.getClass()) ||
-						IllegalArgumentException.class.isAssignableFrom(e.getClass()));
-		}
+		Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
 	}
 
 	@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.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class DbClient implements Closeable {
 
-	private static final Log log = LogFactory.getLog(DbClient.class);
+	private static final Logger log = LoggerFactory.getLogger(DbClient.class);
 
 	private final Connection connection;
 
@@ -37,6 +37,8 @@ public class DbClient implements Closeable {
 		try (final Statement stmt = connection.createStatement()) {
 			stmt.setFetchSize(100);
 
+			log.info("running SQL:\n\n{}\n\n", sql);
+
 			try (final ResultSet rs = stmt.executeQuery(sql)) {
 				while (rs.next()) {
 					consumer.accept(rs);

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

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

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

@@ -1,53 +0,0 @@
-
-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

@@ -1,8 +0,0 @@
-
-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

@@ -1,363 +0,0 @@
-
-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

@@ -1,14 +0,0 @@
-
-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

@@ -1,47 +0,0 @@
-
-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

@@ -1,44 +0,0 @@
-
-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

@@ -1,23 +0,0 @@
-
-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

@@ -1,92 +0,0 @@
-
-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

@@ -1,153 +0,0 @@
-
-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

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

@@ -1,43 +0,0 @@
-
-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

@@ -1,118 +0,0 @@
-
-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

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

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

@@ -12,7 +12,9 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.commons.lang3.time.DateUtils;
 import org.apache.http.HttpHeaders;
+import org.joda.time.Instant;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 

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.toList()));
+							.collect(Collectors.toCollection(ArrayList::new)));
 			}
 			return (T) res;
 		} else {
@@ -1003,4 +1003,41 @@ 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

@@ -30,6 +30,7 @@ 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);
 	}
@@ -88,7 +89,7 @@ public class MergeUtils {
 	private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
 
 		if (sameClass(left, right, Result.class)) {
-			if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
+			if (checkDelegatedAuthority) {
 				return mergeResultsOfDifferentTypes((Result) left, (Result) right);
 			}
 
@@ -432,7 +433,10 @@ public class MergeUtils {
 
 		// merge datainfo for same context id
 		merge.setContext(mergeLists(merge.getContext(), enrich.getContext(), trust, Context::getId, (r, l) -> {
-			r.getDataInfo().addAll(l.getDataInfo());
+			ArrayList<DataInfo> di = new ArrayList<>();
+			di.addAll(r.getDataInfo());
+			di.addAll(l.getDataInfo());
+			r.setDataInfo(di);
 			return r;
 		}));
 
@@ -464,10 +468,6 @@ public class MergeUtils {
 		merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal()));
 		merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded()));
 
-		if (StringUtils.isBlank(merge.getTransformativeAgreement())) {
-			merge.setTransformativeAgreement(enrich.getTransformativeAgreement());
-		}
-
 		return merge;
 	}
 

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

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

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

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

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

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

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

@@ -1,109 +0,0 @@
-
-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>process-resources</phase>
+						<phase>initialize</phase>
 						<goals>
 							<goal>add-source</goal>
 							<goal>compile</goal>
@@ -59,6 +59,14 @@
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
@@ -83,6 +91,10 @@
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.commons</groupId>
+			<artifactId>commons-math3</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>
 			<artifactId>json-path</artifactId>
@@ -101,90 +113,4 @@
 		</dependency>
 	</dependencies>
 
-	<profiles>
-		<profile>
-			<id>spark-24</id>
-			<activation>
-				<activeByDefault>true</activeByDefault>
-			</activation>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-2</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-
-		<profile>
-			<id>spark-34</id>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-2</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-
-		<profile>
-			<id>spark-35</id>
-
-			<build>
-				<plugins>
-					<plugin>
-						<groupId>org.codehaus.mojo</groupId>
-						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.4.0</version>
-						<executions>
-							<execution>
-								<phase>generate-sources</phase>
-								<goals>
-									<goal>add-source</goal>
-								</goals>
-								<configuration>
-									<sources>
-										<source>src/main/spark-35</source>
-									</sources>
-								</configuration>
-							</execution>
-						</executions>
-					</plugin>
-				</plugins>
-			</build>
-		</profile>
-	</profiles>
-
 </project>

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

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

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

@@ -27,14 +27,6 @@ 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");
@@ -82,64 +74,6 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return s12;
 	}
 
-	public static String countryInference(final String original, String inferFrom) {
-		if (!original.equalsIgnoreCase("unknown"))
-			return original;
-
-		inferFrom = cleanup(inferFrom);
-		inferFrom = normalize(inferFrom);
-		inferFrom = filterAllStopWords(inferFrom);
-		Set<String> cities = getCities(inferFrom, 4);
-		return citiesToCountry(cities).stream().findFirst().orElse("UNKNOWN");
-	}
-
-	public static String cityInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> cities = getCities(original, 4);
-
-		for (String city : cities) {
-			original = original.replaceAll(city, cityMap.get(city));
-		}
-
-		return original;
-	}
-
-	public static String keywordInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> keywords = getKeywords(original, keywordMap, 4);
-
-		for (String keyword : keywords) {
-			original = original.replaceAll(keyword, keywordMap.get(keyword));
-		}
-
-		return original;
-	}
-
-	public static String cityKeywordInference(String original) {
-		original = cleanup(original);
-		original = normalize(original);
-		original = filterAllStopWords(original);
-
-		Set<String> keywords = getKeywords(original, keywordMap, 4);
-		Set<String> cities = getCities(original, 4);
-
-		for (String keyword : keywords) {
-			original = original.replaceAll(keyword, keywordMap.get(keyword));
-		}
-
-		for (String city : cities) {
-			original = original.replaceAll(city, cityMap.get(city));
-		}
-
-		return original;
-	}
-
 	protected static String fixXML(final String a) {
 
 		return a
@@ -274,30 +208,6 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return m;
 	}
 
-	public static Map<String, String> loadCountryMapFromClasspath(final String classpath) {
-
-		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
-
-		final Map<String, String> m = new HashMap<>();
-		try {
-			for (final String s : IOUtils
-				.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
-				// string is like this: country_code;city1;city2;city3
-				String[] line = s.split(";");
-				String value = line[0];
-				for (int i = 1; i < line.length; i++) {
-					String city = fixAliases(transliterator.transliterate(line[i].toLowerCase()));
-					String code = cityMap.get(city);
-					m.put(code, value);
-				}
-			}
-		} catch (final Throwable e) {
-			return new HashMap<>();
-		}
-		return m;
-
-	}
-
 	public static String removeKeywords(String s, Set<String> keywords) {
 
 		s = " " + s + " ";
@@ -327,10 +237,6 @@ 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

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

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

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

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

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

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

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

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

@@ -2,7 +2,6 @@
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
-import java.util.Set;
 
 import com.wcohen.ss.AbstractStringDistance;
 
@@ -13,11 +12,8 @@ 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) {
@@ -30,7 +26,6 @@ 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
 		}
@@ -50,5 +45,4 @@ 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

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

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

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

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

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

dhp-pace-core/src/main/java/eu/dnetlib/pace/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(ignoreUndefined);
+		TreeNodeStats stats = new TreeNodeStats();
 
 		// 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

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

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

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

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

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

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

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

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

@@ -8,7 +8,6 @@ import org.junit.jupiter.api.Test;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
-import com.mongodb.connection.Cluster;
 
 import eu.dnetlib.pace.AbstractPaceTest;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
@@ -178,16 +177,41 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void legalnameClustering() {
+	public void testKeywordsClustering() {
 
-		final ClusteringFunction cf = new LegalnameClustering(params);
-		String s = "key::1 key::2 city::1";
+		final ClusteringFunction cf = new KeywordsClustering(params);
+		final String s = "Polytechnic University of Turin";
 		System.out.println(s);
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 
-		s = "key::1 key::2 city::1 city::2";
-		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)));
+
 	}
 
 	@Test

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

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

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

@@ -35,7 +35,6 @@ public class ComparatorTest extends AbstractPaceTest {
 		params.put("name_th", "0.95");
 		params.put("jpath_value", "$.value");
 		params.put("jpath_classid", "$.qualifier.classid");
-		params.put("codeRegex", "key::\\d+");
 	}
 
 	@Test
@@ -45,23 +44,52 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void codeMatchTest() {
-		CodeMatch codeMatch = new CodeMatch(params);
+	public void cityMatchTest() {
+		final CityMatch cityMatch = new CityMatch(params);
 
-		// both names with no codes
-		assertEquals(1.0, codeMatch.distance("testing1", "testing2", conf));
+		// both names with no cities
+		assertEquals(1.0, cityMatch.distance("Università", "Centro di ricerca", conf));
 
-		// one of the two names with no codes
-		assertEquals(-1.0, codeMatch.distance("testing1 key::1", "testing", conf));
+		// one of the two names with no cities
+		assertEquals(-1.0, cityMatch.distance("Università di Bologna", "Centro di ricerca", conf));
 
-		// both names with codes (same)
-		assertEquals(1.0, codeMatch.distance("testing1 key::1", "testing2 key::1", conf));
+		// both names with cities (same)
+		assertEquals(1.0, cityMatch.distance("Universita di Bologna", "Biblioteca di Bologna", conf));
 
-		// both names with codes (different)
-		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", 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 (1 same, 1 different)
-		assertEquals(0.5, codeMatch.distance("key::1 key::2 testing1", "key::1 testing", 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));
 
 	}
 
@@ -127,15 +155,15 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void jaroWinklerLegalnameTest() {
+	public void jaroWinklerNormalizedNameTest() {
 
-		final JaroWinklerLegalname jaroWinklerLegalname = new JaroWinklerLegalname(params);
+		final JaroWinklerNormalizedName jaroWinklerNormalizedName = new JaroWinklerNormalizedName(params);
 
-		double result = jaroWinklerLegalname
-			.distance("AT&T (United States)", "United States key::2 key::1", conf);
+		double result = jaroWinklerNormalizedName
+			.distance("AT&T (United States)", "United States Military Academy", conf);
 		System.out.println("result = " + result);
 
-		result = jaroWinklerLegalname.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
+		result = jaroWinklerNormalizedName.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
 		System.out.println("result = " + result);
 
 	}
@@ -316,13 +344,13 @@ public class ComparatorTest extends AbstractPaceTest {
 		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CL", "UNKNOWN", conf);
+		result = countryMatch.distance("CHILE", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CL", "IT", conf);
+		result = countryMatch.distance("CHILE", "ITALY", conf);
 		assertEquals(0.0, result);
 
-		result = countryMatch.distance("CL", "CL", conf);
+		result = countryMatch.distance("CHILE", "CHILE", conf);
 		assertEquals(1.0, result);
 
 	}

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

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

dhp-shade-package/pom.xml

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

dhp-workflows/dhp-actionmanager/pom.xml

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

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

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

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

@@ -0,0 +1,210 @@
+/*
+ * 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

@@ -0,0 +1,3 @@
+{"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

@@ -6,18 +6,7 @@
         <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>
@@ -54,28 +43,6 @@
                     <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

@@ -44,6 +44,8 @@ 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 {
 
@@ -74,6 +76,9 @@ 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);
 
@@ -84,43 +89,68 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, 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);
-
+				createActionSet(
+					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
+					publisherInputPath, outputPath);
 			});
 	}
 
+	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) {
@@ -132,6 +162,10 @@ 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

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

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

@@ -6,23 +6,26 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.*;
-import org.jetbrains.annotations.NotNull;
+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.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class PrepareSDGSparkJob implements Serializable {
@@ -49,91 +52,42 @@ public class PrepareSDGSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
-		final Boolean distributeDOI = Optional
-			.ofNullable(parser.get("distributeDoi"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("distribute doi {}", distributeDOI);
-
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				if (distributeDOI)
-					doPrepare(
-						spark,
-						sourcePath,
-
-						outputPath);
-				else
-					doPrepareoaid(spark, sourcePath, outputPath);
+				doPrepare(
+					spark,
+					sourcePath,
 
+					outputPath);
 			});
 	}
 
 	private static void doPrepare(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);
+		Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
 
 		sdgDataset
-			.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))
+			.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))
 			.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

@@ -13,6 +13,9 @@ import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
@@ -21,9 +24,13 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.*;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {

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

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

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

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

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

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

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

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

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

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

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

@@ -1,91 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.sdgnodoi;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.Objects;
-import java.util.Optional;
-
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.fs.Hdfs;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.GzipCodec;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import scala.Tuple2;
-
-public class CreateActionSetSparkJob implements Serializable {
-
-	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(final String[] args) throws IOException, ParseException {
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							CreateActionSetSparkJob.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json"))));
-
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		final String inputPath = parser.get("sourcePath");
-		log.info("inputPath {}", inputPath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}", outputPath);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				createActionSet(spark, inputPath, outputPath);
-			});
-
-	}
-
-	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
-		spark
-			.read()
-			.textFile(inputPath)
-			.map(
-				(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
-				Encoders.bean(Result.class))
-			.toJavaRDD()
-			.map(p -> new AtomicAction(p.getClass(), p))
-			.mapToPair(
-				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(
-				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
-	}
-
-}

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

@@ -5,10 +5,11 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.BZip2Codec;
+import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FilterFunction;
@@ -112,7 +113,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
 
 	}
 
@@ -152,40 +153,11 @@ 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) {
-		switch (pidType) {
-			case "PMID":
-				return pid.substring(33);
-			case "PMC":
-				return "PMC" + pid.substring(43);
-			case "DOI":
-				return pid.substring(16);
+		if (pidType.equals("DOI")) {
+			return pid.substring(16);
 		}
-
-		throw new RuntimeException();
-
+		throw new IllegalArgumentException("DOI is the only supported PID type");
 	}
 
 	private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {

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

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

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

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

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

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

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

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

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

@@ -1,76 +0,0 @@
-
-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

@@ -1,117 +0,0 @@
-
-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

@@ -8,10 +8,7 @@ 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;
@@ -22,7 +19,6 @@ 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;
 
@@ -62,23 +58,13 @@ 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) {
@@ -127,7 +113,7 @@ public class XMLIterator implements Iterator<String> {
 				final XMLEvent event = parser.nextEvent();
 
 				// TODO: replace with depth tracking instead of close tag tracking.
-				if (event.isEndElement() && isCheckTag(event.asEndElement().getName().getLocalPart())) {
+				if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
 					writer.add(event);
 					break;
 				}
@@ -156,16 +142,18 @@ public class XMLIterator implements Iterator<String> {
 		XMLEvent peek = parser.peek();
 		if (peek != null && peek.isStartElement()) {
 			String name = peek.asStartElement().getName().getLocalPart();
-			if (isCheckTag(name))
+			if (element.equals(name)) {
 				return peek;
+			}
 		}
 
 		while (parser.hasNext()) {
-			XMLEvent event = parser.nextEvent();
+			final XMLEvent event = parser.nextEvent();
 			if (event != null && event.isStartElement()) {
 				String name = event.asStartElement().getName().getLocalPart();
-				if (isCheckTag(name))
+				if (element.equals(name)) {
 					return event;
+				}
 			}
 		}
 		return null;
@@ -173,31 +161,12 @@ public class XMLIterator implements Iterator<String> {
 
 	private XMLEventReader getParser() {
 		try {
-			XMLInputFactory xif = inputFactory.get();
-			xif.setProperty(XMLInputFactory.SUPPORT_DTD, false);
-			return xif.createXMLEventReader(sanitize(inputStream));
+			return inputFactory.get().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

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

@@ -1,30 +0,0 @@
-<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

@@ -1,100 +0,0 @@
-<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

@@ -28,13 +28,19 @@
     "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": "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": "o",
     "paramLongName": "outputPath",

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

@@ -35,5 +35,6 @@ 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

@@ -21,6 +21,10 @@
             <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>
@@ -117,6 +121,7 @@
             <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

@@ -1,25 +0,0 @@
-[
-  {
-    "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

@@ -1,2 +0,0 @@
-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

@@ -1,30 +0,0 @@
-<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

@@ -1,111 +0,0 @@
-<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

@@ -1,20 +0,0 @@
-[
-  {
-    "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

@@ -1,30 +0,0 @@
-<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

@@ -1,125 +0,0 @@
-
-<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

@@ -1,11 +1,3 @@
-#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
+sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
+outputPath=/tmp/miriam/webcrawlComplete/
+blackListPath=/user/miriam.baglioni/openalex-blackList

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

@@ -20,19 +20,12 @@
         </configuration>
     </global>
 
-    <start to="resumeFrom"/>
+    <start to="create_actionset"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-    <decision name="resumeFrom">
-        <switch>
-            <case to="create_actionset">${wf:conf('resumeFrom') eq 'create'}</case>
-            <default to="remove_from_actionset"/>
-        </switch>
-    </decision>
-
     <action name="create_actionset">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -57,30 +50,5 @@
         <ok to="End"/>
         <error to="Kill"/>
     </action>
-
-    <action name="remove_from_actionset">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Removes some relations found to be wrong from the AS</name>
-            <class>eu.dnetlib.dhp.actionmanager.webcrawl.RemoveRelationFromActionSet</class>
-            <jar>dhp-aggregation-${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>
@@ -8,19 +8,40 @@
             <name>database</name>
             <description>the PDB Database Working Path</description>
         </property>
-
         <property>
-            <name>targetPath</name>
-            <description>the Target Working dir path</description>
+            <name>mdStoreOutputId</name>
+            <description>the identifier of the cleaned MDStore</description>
+        </property>
+        <property>
+            <name>mdStoreManagerURI</name>
+            <description>the path of the cleaned mdstore</description>
         </property>
     </parameters>
 
-    <start to="ConvertDB"/>
+    <start to="StartTransaction"/>
+
 
     <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>
@@ -41,11 +62,48 @@
             <arg>--master</arg><arg>yarn</arg>
             <arg>--dbPath</arg><arg>${sourcePath}</arg>
             <arg>--database</arg><arg>${database}</arg>
-            <arg>--targetPath</arg><arg>${targetPath}</arg>
+            <arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
         </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
+        <ok to="CommitVersion"/>
+        <error to="RollBack"/>
+
     </action>
-    <end name="End"/>
+        <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/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":"t",   "paramLongName":"targetPath",   "paramDescription": "the OAF target path ",                     "paramRequired": true}
+  {"paramName":"mo",   "paramLongName":"mdstoreOutputVersion",     "paramDescription": "the oaf path ",                "paramRequired": true}
 ]

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

@@ -1,5 +1,20 @@
 [
-  {"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}
+  {
+    "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
+  }
 ]

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

@@ -9,34 +9,26 @@
             <description>the Working Path</description>
         </property>
         <property>
-            <name>targetPath</name>
-            <description>the OAF MDStore Path</description>
+            <name>mdStoreOutputId</name>
+            <description>the identifier of the cleaned MDStore</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>
+            <name>mdStoreManagerURI</name>
+            <description>the path of the cleaned mdstore</description>
         </property>
         <property>
             <name>resumeFrom</name>
-            <value>DownloadEBILinks</value>
+            <value>CreateEBIDataSet</value>
             <description>node to start</description>
         </property>
     </parameters>
 
-    <start to="resume_from"/>
+    <start to="StartTransaction"/>
 
     <decision name="resume_from">
         <switch>
             <case to="DownloadEBILinks">${wf:conf('resumeFrom') eq 'DownloadEBILinks'}</case>
-            <case to="CreateEBIDataSet">${wf:conf('resumeFrom') eq 'CreateEBIDataSet'}</case>
+            <case to="StartTransaction">${wf:conf('resumeFrom') eq 'CreateEBIDataSet'}</case>
             <default to="DownloadEBILinks"/>
         </switch>
     </decision>
@@ -77,9 +69,29 @@
             <move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
             <move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
         </fs>
-        <ok to="CreateEBIDataSet"/>
+        <ok to="StartTransaction"/>
         <error to="Kill"/>
     </action>
+
+    <action name="StartTransaction">
+        <java>
+            <configuration>
+                <property>
+                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
+                    <value>true</value>
+                </property>
+            </configuration>
+            <main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
+            <arg>--action</arg><arg>NEW_VERSION</arg>
+            <arg>--mdStoreID</arg><arg>${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>
@@ -95,11 +107,49 @@
                 ${sparkExtraOPT}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${sourcePath}/ebi_links_dataset</arg>
-            <arg>--targetPath</arg><arg>${targetPath}</arg>
+            <arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</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

@@ -888,11 +888,7 @@ 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)
@@ -1029,7 +1025,6 @@ 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]
+    val pid = (json \ "pid").extract[String].trim()
 
     val d = new Dataset
 

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

@@ -2,12 +2,15 @@ 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 {
 
@@ -25,8 +28,13 @@ object SparkTransformBioDatabaseToOAF {
 
     val dbPath: String = parser.get("dbPath")
     log.info("dbPath: {}", database)
-    val targetPath: String = parser.get("targetPath")
-    log.info("targetPath: {}", 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 spark: SparkSession =
       SparkSession
@@ -43,24 +51,28 @@ object SparkTransformBioDatabaseToOAF {
       case "UNIPROT" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))),
-          targetPath
+          s"$outputBasePath/$MDSTORE_DATA_PATH"
         )
       case "PDB" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))),
-          targetPath
+          s"$outputBasePath/$MDSTORE_DATA_PATH"
         )
       case "SCHOLIX" =>
         CollectionUtils.saveDataset(
           spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)),
-          targetPath
+          s"$outputBasePath/$MDSTORE_DATA_PATH"
         )
       case "CROSSREF_LINKS" =>
         CollectionUtils.saveDataset(
           spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))),
-          targetPath
+          s"$outputBasePath/$MDSTORE_DATA_PATH"
         )
     }
+
+    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

@@ -2,9 +2,12 @@ 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.oaf.Oaf
+import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
+import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
 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
@@ -14,13 +17,13 @@ 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._
 import org.apache.spark.sql.expressions.Aggregator
+import org.apache.spark.sql._
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.io.{ByteArrayInputStream, InputStream}
-import java.nio.charset.Charset
-import javax.xml.stream.XMLInputFactory
+import java.io.InputStream
+import scala.io.Source
+import scala.xml.pull.XMLEventReader
 
 object SparkCreateBaselineDataFrame {
 
@@ -83,7 +86,7 @@ object SparkCreateBaselineDataFrame {
           if (response.getStatusLine.getStatusCode > 400) {
             tries -= 1
           } else
-            return IOUtils.toString(response.getEntity.getContent, Charset.defaultCharset())
+            return IOUtils.toString(response.getEntity.getContent)
         } catch {
           case e: Throwable =>
             println(s"Error on requesting ${r.getURI}")
@@ -155,8 +158,7 @@ object SparkCreateBaselineDataFrame {
       IOUtils.toString(
         SparkEBILinksToOaf.getClass.getResourceAsStream(
           "/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
-        ),
-        Charset.defaultCharset()
+        )
       )
     )
     parser.parseArgument(args)
@@ -165,11 +167,15 @@ object SparkCreateBaselineDataFrame {
     val workingPath = parser.get("workingPath")
     log.info("workingPath: {}", workingPath)
 
-    val targetPath = parser.get("targetPath")
-    log.info("targetPath: {}", targetPath)
+    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 hdfsServerUri = parser.get("hdfsServerUri")
-    log.info("hdfsServerUri: {}", targetPath)
+    log.info("hdfsServerUri: {}", hdfsServerUri)
 
     val skipUpdate = parser.get("skipUpdate")
     log.info("skipUpdate: {}", skipUpdate)
@@ -195,11 +201,10 @@ 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 = inputFactory.createXMLEventReader(new ByteArrayInputStream(i._2.getBytes()))
+            val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
             new PMParser(xml)
           })
       )
@@ -218,8 +223,11 @@ object SparkCreateBaselineDataFrame {
         .map(a => PubMedToOaf.convert(a, vocabularies))
         .as[Oaf]
         .filter(p => p != null),
-      targetPath
+      s"$outputBasePath/$MDSTORE_DATA_PATH"
     )
 
+    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

@@ -9,6 +9,9 @@ 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 {
 
@@ -32,8 +35,13 @@ object SparkEBILinksToOaf {
     import spark.implicits._
     val sourcePath = parser.get("sourcePath")
     log.info(s"sourcePath  -> $sourcePath")
-    val targetPath = parser.get("targetPath")
-    log.info(s"targetPath  -> $targetPath")
+    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
+    log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion)
+
+    val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
+    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
+    log.info("outputBasePath: {}", outputBasePath)
+
     implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
 
     val ebLinks: Dataset[EBILinkItem] = spark.read
@@ -46,7 +54,10 @@ object SparkEBILinksToOaf {
         .flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
         .filter(p => BioDBToOAF.EBITargetLinksFilter(p))
         .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
-      targetPath
+      s"$outputBasePath/$MDSTORE_DATA_PATH"
     )
+    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

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

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

@@ -78,6 +78,10 @@ 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
@@ -89,6 +93,7 @@ public class PrepareAffiliationRelationsTest {
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
+					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -105,7 +110,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(120, tmp.count());
+		assertEquals(138, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -116,7 +121,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -124,7 +129,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
@@ -145,5 +150,12 @@ 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

@@ -15,7 +15,10 @@ 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.*;
+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;
 

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

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

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

@@ -1,213 +0,0 @@
-
-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

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