[AffiliationIngestion]refactoring

Reviewed-on: D-Net/dnet-hadoop#450

.gitignore

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

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

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

dhp-common/pom.xml

@@ -70,10 +70,7 @@
 			<groupId>com.ibm.icu</groupId>
 			<artifactId>icu4j</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.hadoop</groupId>
-			<artifactId>hadoop-common</artifactId>
-		</dependency>
+
 		<dependency>
 			<groupId>com.github.sisyphsu</groupId>
 			<artifactId>dateparser</artifactId>
@@ -163,7 +160,7 @@
 
 		<dependency>
 			<groupId>eu.dnetlib.dhp</groupId>
-			<artifactId>${dhp-schemas.artifact}</artifactId>
+			<artifactId>dhp-schemas</artifactId>
 		</dependency>
 
 		<dependency>
@@ -172,4 +169,23 @@
 		</dependency>
 	</dependencies>
 
+	<!-- dependencies required on JDK9+ because J2EE has been removed -->
+	<profiles>
+		<profile>
+			<id>spark-34</id>
+			<dependencies>
+				<dependency>
+					<groupId>javax.xml.bind</groupId>
+					<artifactId>jaxb-api</artifactId>
+					<version>2.2.11</version>
+				</dependency>
+				<dependency>
+					<groupId>com.sun.xml.ws</groupId>
+					<artifactId>jaxws-ri</artifactId>
+					<version>2.3.3</version>
+					<type>pom</type>
+				</dependency>
+			</dependencies>
+		</profile>
+	</profiles>
 </project>

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

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

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

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

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

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

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

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

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

@@ -0,0 +1,363 @@
+
+package eu.dnetlib.dhp.common.api;
+
+import java.io.*;
+import java.io.IOException;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.util.concurrent.TimeUnit;
+
+import org.apache.http.HttpHeaders;
+import org.apache.http.entity.ContentType;
+import org.jetbrains.annotations.NotNull;
+
+import com.google.gson.Gson;
+
+import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
+import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList;
+import okhttp3.*;
+
+public class ZenodoAPIClient implements Serializable {
+
+	String urlString;
+	String bucket;
+
+	String deposition_id;
+	String access_token;
+
+	public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8");
+
+	private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip");
+
+	public String getUrlString() {
+		return urlString;
+	}
+
+	public void setUrlString(String urlString) {
+		this.urlString = urlString;
+	}
+
+	public String getBucket() {
+		return bucket;
+	}
+
+	public void setBucket(String bucket) {
+		this.bucket = bucket;
+	}
+
+	public void setDeposition_id(String deposition_id) {
+		this.deposition_id = deposition_id;
+	}
+
+	public ZenodoAPIClient(String urlString, String access_token) {
+
+		this.urlString = urlString;
+		this.access_token = access_token;
+	}
+
+	/**
+	 * Brand new deposition in Zenodo. It sets the deposition_id and the bucket where to store the files to upload
+	 *
+	 * @return response code
+	 * @throws IOException
+	 */
+	public int newDeposition() throws IOException {
+		String json = "{}";
+
+		URL url = new URL(urlString);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setRequestMethod("POST");
+		conn.setDoOutput(true);
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+		conn.disconnect();
+
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
+		this.bucket = newSubmission.getLinks().getBucket();
+		this.deposition_id = newSubmission.getId();
+
+		return responseCode;
+	}
+
+	/**
+	 * Upload files in Zenodo.
+	 *
+	 * @param is the inputStream for the file to upload
+	 * @param file_name the name of the file as it will appear on Zenodo
+	 * @return the response code
+	 */
+	public int uploadIS(InputStream is, String file_name) throws IOException {
+
+		URL url = new URL(bucket + "/" + file_name);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/zip");
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("PUT");
+
+		byte[] buf = new byte[8192];
+		int length;
+		try (OutputStream os = conn.getOutputStream()) {
+			while ((length = is.read(buf)) != -1) {
+				os.write(buf, 0, length);
+			}
+
+		}
+		int responseCode = conn.getResponseCode();
+		if (!checkOKStatus(responseCode)) {
+			throw new IOException("Unexpected code " + responseCode + getBody(conn));
+		}
+
+		return responseCode;
+	}
+
+	@NotNull
+	private String getBody(HttpURLConnection conn) throws IOException {
+		String body = "{}";
+		try (BufferedReader br = new BufferedReader(
+			new InputStreamReader(conn.getInputStream(), "utf-8"))) {
+			StringBuilder response = new StringBuilder();
+			String responseLine = null;
+			while ((responseLine = br.readLine()) != null) {
+				response.append(responseLine.trim());
+			}
+
+			body = response.toString();
+
+		}
+		return body;
+	}
+
+	/**
+	 * Associates metadata information to the current deposition
+	 *
+	 * @param metadata the metadata
+	 * @return response code
+	 * @throws IOException
+	 */
+	public int sendMretadata(String metadata) throws IOException {
+
+		URL url = new URL(urlString + "/" + deposition_id);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("PUT");
+
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = metadata.getBytes("utf-8");
+			os.write(input, 0, input.length);
+
+		}
+
+		final int responseCode = conn.getResponseCode();
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + getBody(conn));
+
+		return responseCode;
+
+	}
+
+	private boolean checkOKStatus(int responseCode) {
+
+		if (HttpURLConnection.HTTP_OK != responseCode ||
+			HttpURLConnection.HTTP_CREATED != responseCode)
+			return true;
+		return false;
+	}
+
+	/**
+	 * To publish the current deposition. It works for both new deposition or new version of an old deposition
+	 *
+	 * @return response code
+	 * @throws IOException
+	 */
+	@Deprecated
+	public int publish() throws IOException {
+
+		String json = "{}";
+
+		OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
+
+		RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
+
+		Request request = new Request.Builder()
+			.url(urlString + "/" + deposition_id + "/actions/publish")
+			.addHeader("Authorization", "Bearer " + access_token)
+			.post(body)
+			.build();
+
+		try (Response response = httpClient.newCall(request).execute()) {
+
+			if (!response.isSuccessful())
+				throw new IOException("Unexpected code " + response + response.body().string());
+
+			return response.code();
+
+		}
+	}
+
+	/**
+	 * To create a new version of an already published deposition. It sets the deposition_id and the bucket to be used
+	 * for the new version.
+	 *
+	 * @param concept_rec_id the concept record id of the deposition for which to create a new version. It is the last
+	 *            part of the url for the DOI Zenodo suggests to use to cite all versions: DOI: 10.xxx/zenodo.656930
+	 *            concept_rec_id = 656930
+	 * @return response code
+	 */
+	public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
+		setDepositionId(concept_rec_id, 1);
+		String json = "{}";
+
+		URL url = new URL(urlString + "/" + deposition_id + "/actions/newversion");
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("POST");
+
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+		String latest_draft = zenodoModel.getLinks().getLatest_draft();
+		deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1);
+		bucket = getBucket(latest_draft);
+
+		return responseCode;
+
+	}
+
+	/**
+	 * To finish uploading a version or new deposition not published
+	 * It sets the deposition_id and the bucket to be used
+	 *
+	 *
+	 * @param deposition_id the deposition id of the not yet published upload
+	 *            concept_rec_id = 656930
+	 * @return response code
+	 * @throws IOException
+	 * @throws MissingConceptDoiException
+	 */
+	public int uploadOpenDeposition(String deposition_id) throws IOException, MissingConceptDoiException {
+
+		this.deposition_id = deposition_id;
+
+		String json = "{}";
+
+		URL url = new URL(urlString + "/" + deposition_id);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setRequestMethod("POST");
+		conn.setDoOutput(true);
+		try (OutputStream os = conn.getOutputStream()) {
+			byte[] input = json.getBytes("utf-8");
+			os.write(input, 0, input.length);
+		}
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+		conn.disconnect();
+
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+		bucket = zenodoModel.getLinks().getBucket();
+
+		return responseCode;
+
+	}
+
+	private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException {
+
+		ZenodoModelList zenodoModelList = new Gson()
+			.fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class);
+
+		for (ZenodoModel zm : zenodoModelList) {
+			if (zm.getConceptrecid().equals(concept_rec_id)) {
+				deposition_id = zm.getId();
+				return;
+			}
+		}
+		if (zenodoModelList.size() == 0)
+			throw new MissingConceptDoiException(
+				"The concept record id specified was missing in the list of depositions");
+		setDepositionId(concept_rec_id, page + 1);
+
+	}
+
+	private String getPrevDepositions(String page) throws IOException {
+
+		HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder();
+		urlBuilder.addQueryParameter("page", page);
+
+		URL url = new URL(urlBuilder.build().toString());
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("GET");
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		return body;
+
+	}
+
+	private String getBucket(String inputUurl) throws IOException {
+
+		URL url = new URL(inputUurl);
+		HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
+		conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
+		conn.setDoOutput(true);
+		conn.setRequestMethod("GET");
+
+		String body = getBody(conn);
+
+		int responseCode = conn.getResponseCode();
+
+		conn.disconnect();
+		if (!checkOKStatus(responseCode))
+			throw new IOException("Unexpected code " + responseCode + body);
+
+		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
+
+		return zenodoModel.getLinks().getBucket();
+
+	}
+
+}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -328,7 +328,7 @@ public class MergeUtils {
 		final T merged = mergeOafFields(original, enrich, trust);
 
 		merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId()));
-		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
+		merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
 			.setDateoftransformation(
@@ -432,10 +432,7 @@ public class MergeUtils {
 
 		// merge datainfo for same context id
 		merge.setContext(mergeLists(merge.getContext(), enrich.getContext(), trust, Context::getId, (r, l) -> {
-			ArrayList<DataInfo> di = new ArrayList<>();
-			di.addAll(r.getDataInfo());
-			di.addAll(l.getDataInfo());
-			r.setDataInfo(di);
+			r.getDataInfo().addAll(l.getDataInfo());
 			return r;
 		}));
 
@@ -658,13 +655,6 @@ public class MergeUtils {
 			return d1;
 		}
 
-		if (StringUtils.contains(d1.getValue(), "null")) {
-			return d2;
-		}
-		if (StringUtils.contains(d2.getValue(), "null")) {
-			return d1;
-		}
-
 		return Stream
 			.of(d1, d2)
 			.min(

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

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

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

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

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

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

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

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

dhp-pace-core/pom.xml

@@ -24,7 +24,7 @@
 				<executions>
 					<execution>
 						<id>scala-compile-first</id>
-						<phase>initialize</phase>
+						<phase>process-resources</phase>
 						<goals>
 							<goal>add-source</goal>
 							<goal>compile</goal>
@@ -59,14 +59,6 @@
 			<groupId>edu.cmu</groupId>
 			<artifactId>secondstring</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>com.google.guava</groupId>
-			<artifactId>guava</artifactId>
-		</dependency>
-		<dependency>
-			<groupId>com.google.code.gson</groupId>
-			<artifactId>gson</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
@@ -91,10 +83,6 @@
 			<groupId>com.fasterxml.jackson.core</groupId>
 			<artifactId>jackson-databind</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>com.jayway.jsonpath</groupId>
 			<artifactId>json-path</artifactId>
@@ -113,4 +101,90 @@
 		</dependency>
 	</dependencies>
 
+	<profiles>
+		<profile>
+			<id>spark-24</id>
+			<activation>
+				<activeByDefault>true</activeByDefault>
+			</activation>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-2</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+
+		<profile>
+			<id>spark-34</id>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-2</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+
+		<profile>
+			<id>spark-35</id>
+
+			<build>
+				<plugins>
+					<plugin>
+						<groupId>org.codehaus.mojo</groupId>
+						<artifactId>build-helper-maven-plugin</artifactId>
+						<version>3.4.0</version>
+						<executions>
+							<execution>
+								<phase>generate-sources</phase>
+								<goals>
+									<goal>add-source</goal>
+								</goals>
+								<configuration>
+									<sources>
+										<source>src/main/spark-35</source>
+									</sources>
+								</configuration>
+							</execution>
+						</executions>
+					</plugin>
+				</plugins>
+			</build>
+		</profile>
+	</profiles>
+
 </project>

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

@@ -3,7 +3,7 @@ package eu.dnetlib.pace.model
 import com.jayway.jsonpath.{Configuration, JsonPath}
 import eu.dnetlib.pace.common.AbstractPaceFunctions
 import eu.dnetlib.pace.config.{DedupConfig, Type}
-import eu.dnetlib.pace.util.MapDocumentUtil
+import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
 import org.apache.commons.lang3.StringUtils
 import org.apache.spark.sql.catalyst.encoders.RowEncoder
 import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
@@ -52,7 +52,7 @@ case class SparkModel(conf: DedupConfig) {
   val orderingFieldPosition: Int = schema.fieldIndex(orderingFieldName)
 
   val parseJsonDataset: (Dataset[String] => Dataset[Row]) = df => {
-    df.map(r => rowFromJson(r))(RowEncoder(schema))
+    df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
   }
 
   def rowFromJson(json: String): Row = {

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

@@ -1,48 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-
-import com.wcohen.ss.AbstractStringDistance;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("countryMatch")
-public class CountryMatch extends AbstractStringComparator {
-
-	public CountryMatch(Map<String, String> params) {
-		super(params, new com.wcohen.ss.JaroWinkler());
-	}
-
-	public CountryMatch(final double weight) {
-		super(weight, new com.wcohen.ss.JaroWinkler());
-	}
-
-	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
-		super(weight, ssalgo);
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-		if (a.isEmpty() || b.isEmpty()) {
-			return -1.0; // return -1 if a field is missing
-		}
-		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
-			return -1.0; // return -1 if a country is UNKNOWN
-		}
-
-		return a.equals(b) ? 1.0 : 0;
-	}
-
-	@Override
-	public double getWeight() {
-		return super.weight;
-	}
-
-	@Override
-	protected double normalize(final double d) {
-		return d;
-	}
-}

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

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

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

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

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

@@ -336,23 +336,4 @@ public class ComparatorTest extends AbstractPaceTest {
 		System.out.println("compare = " + compare);
 	}
 
-	@Test
-	public void countryMatch() {
-
-		CountryMatch countryMatch = new CountryMatch(params);
-
-		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
-		assertEquals(-1.0, result);
-
-		result = countryMatch.distance("CHILE", "UNKNOWN", conf);
-		assertEquals(-1.0, result);
-
-		result = countryMatch.distance("CHILE", "ITALY", conf);
-		assertEquals(0.0, result);
-
-		result = countryMatch.distance("CHILE", "CHILE", conf);
-		assertEquals(1.0, result);
-
-	}
-
 }

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

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

dhp-shade-package/pom.xml

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

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

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

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

@@ -105,8 +105,8 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				final String ror = ROR_PREFIX
 					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
-//				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
-//				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
+				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
+				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
 
 				return ret
 					.iterator();
@@ -140,17 +140,11 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				"institution", functions
 					.explode(
 						functions.col("institutions")))
-
 			.selectExpr(
-				"id", "doi", "institution.ror as ror",
+				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
 				"institution.country_code as country_code", "publication_year")
 			.distinct();
 
-//			.selectExpr(
-//				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
-//				"institution.country_code as country_code", "publication_year")
-//			.distinct();
-
 	}
 
 	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {

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

@@ -1,6 +1,7 @@
 
 package eu.dnetlib.dhp.collection.plugin.rest;
 
+import java.util.Map;
 import java.util.Optional;
 import java.util.Spliterator;
 import java.util.Spliterators;
@@ -9,6 +10,8 @@ import java.util.stream.StreamSupport;
 
 import org.apache.commons.lang3.StringUtils;
 
+import com.google.gson.Gson;
+
 import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
@@ -47,6 +50,9 @@ public class RestCollectorPlugin implements CollectorPlugin {
 		final String entityXpath = api.getParams().get("entityXpath");
 		final String authMethod = api.getParams().get("authMethod");
 		final String authToken = api.getParams().get("authToken");
+		final String requestHeaderMap = api.getParams().get("requestHeaderMap");
+		Gson gson = new Gson();
+		Map requestHeaders = gson.fromJson(requestHeaderMap, Map.class);
 		final String resultSizeValue = Optional
 			.ofNullable(api.getParams().get("resultSizeValue"))
 			.filter(StringUtils::isNotBlank)
@@ -64,9 +70,6 @@ public class RestCollectorPlugin implements CollectorPlugin {
 		if (StringUtils.isBlank(resultFormatValue)) {
 			throw new CollectorException("Param 'resultFormatValue' is null or empty");
 		}
-		if (StringUtils.isBlank(queryParams)) {
-			throw new CollectorException("Param 'queryParams' is null or empty");
-		}
 		if (StringUtils.isBlank(entityXpath)) {
 			throw new CollectorException("Param 'entityXpath' is null or empty");
 		}
@@ -92,7 +95,8 @@ public class RestCollectorPlugin implements CollectorPlugin {
 			entityXpath,
 			authMethod,
 			authToken,
-			resultOutputFormat);
+			resultOutputFormat,
+			requestHeaders);
 
 		return StreamSupport
 			.stream(

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

@@ -9,8 +9,11 @@ import java.net.URL;
 import java.net.URLEncoder;
 import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
+import java.util.Map;
 import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
@@ -18,22 +21,18 @@ import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpression;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
+import javax.xml.xpath.*;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.http.HttpHeaders;
-import org.apache.http.entity.ContentType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 
+import com.google.common.collect.Maps;
+
 import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
@@ -48,20 +47,23 @@ import eu.dnetlib.dhp.common.collection.HttpClientParams;
  *
  */
 public class RestIterator implements Iterator<String> {
-
 	private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
 	public static final String UTF_8 = "UTF-8";
 	private static final int MAX_ATTEMPTS = 5;
 
 	private final HttpClientParams clientParams;
 
-	private final String BASIC = "basic";
+	private final String AUTHBASIC = "basic";
+
+	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
+		+ ">";
 
 	private final String baseUrl;
 	private final String resumptionType;
 	private final String resumptionParam;
 	private final String resultFormatValue;
-	private String queryParams;
+	private String queryParams = "";
 	private final int resultSizeValue;
 	private int resumptionInt = 0; // integer resumption token (first record to harvest)
 	private int resultTotal = -1;
@@ -89,6 +91,11 @@ public class RestIterator implements Iterator<String> {
 	 */
 	private final String resultOutputFormat;
 
+	/*
+	 * Can be used to set additional request headers, like for content negotiation
+	 */
+	private Map<String, String> requestHeaders;
+
 	/**
 	 * RestIterator class compatible to version 1.3.33
 	 */
@@ -107,7 +114,8 @@ public class RestIterator implements Iterator<String> {
 		final String entityXpath,
 		final String authMethod,
 		final String authToken,
-		final String resultOutputFormat) {
+		final String resultOutputFormat,
+		final Map<String, String> requestHeaders) {
 
 		this.clientParams = clientParams;
 		this.baseUrl = baseUrl;
@@ -119,6 +127,7 @@ public class RestIterator implements Iterator<String> {
 		this.authMethod = authMethod;
 		this.authToken = authToken;
 		this.resultOutputFormat = resultOutputFormat;
+		this.requestHeaders = requestHeaders != null ? requestHeaders : Maps.newHashMap();
 
 		this.queryFormat = StringUtils.isNotBlank(resultFormatParam) ? "&" + resultFormatParam + "=" + resultFormatValue
 			: "";
@@ -148,7 +157,12 @@ public class RestIterator implements Iterator<String> {
 	}
 
 	private void initQueue() {
-		this.query = this.baseUrl + "?" + this.queryParams + this.querySize + this.queryFormat;
+		if (queryParams.equals("") && querySize.equals("") && queryFormat.equals("")) {
+			query = baseUrl;
+		} else {
+			query = baseUrl + "?" + queryParams + querySize + queryFormat;
+		}
+
 		log.info("REST calls starting with {}", this.query);
 	}
 
@@ -162,19 +176,6 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public boolean hasNext() {
-		if (this.recordQueue.isEmpty() && this.query.isEmpty()) {
-			disconnect();
-			return false;
-		}
-		return true;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * @see java.util.Iterator#next()
-	 */
-	@Override
-	public String next() {
 		synchronized (this.recordQueue) {
 			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
 				try {
@@ -184,6 +185,23 @@ public class RestIterator implements Iterator<String> {
 					throw new RuntimeException(e);
 				}
 			}
+
+			if (!this.recordQueue.isEmpty()) {
+				return true;
+			}
+
+			disconnect();
+			return false;
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * @see java.util.Iterator#next()
+	 */
+	@Override
+	public String next() {
+		synchronized (this.recordQueue) {
 			return this.recordQueue.poll();
 		}
 	}
@@ -209,9 +227,8 @@ public class RestIterator implements Iterator<String> {
 
 		try {
 			String resultJson;
-			String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+			String resultXml = XML_HEADER;
 			String nextQuery = "";
-			final String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
 			Node resultNode = null;
 			NodeList nodeList = null;
 			String qUrlArgument = "";
@@ -226,37 +243,48 @@ public class RestIterator implements Iterator<String> {
 				}
 			}
 
+			// find pagination page start number in queryParam and remove before start the first query
+			if ((resumptionType.toLowerCase().equals("pagination") || resumptionType.toLowerCase().equals("page"))
+				&& (query.contains("paginationStart="))) {
+
+				final Matcher m = Pattern.compile("paginationStart=([0-9]+)").matcher(query);
+				m.find(); // guaranteed to be true for this regex
+
+				String[] pageVal = m.group(0).split("=");
+				pagination = Integer.parseInt(pageVal[1]);
+
+				// remove page start number from query and queryParams
+				queryParams = queryParams.replaceFirst("&?paginationStart=[0-9]+", "");
+				query = query.replaceFirst("&?paginationStart=[0-9]+", "");
+
+			}
+
 			try {
 				log.info("requesting URL [{}]", query);
 
 				final URL qUrl = new URL(query);
 				log.debug("authMethod: {}", this.authMethod);
-				if ("bearer".equalsIgnoreCase(this.authMethod)) {
-					log.trace("authMethod before inputStream: {}", resultXml);
-					final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-					conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + this.authToken);
-					conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
-					conn.setRequestMethod("GET");
-					theHttpInputStream = conn.getInputStream();
-				} else if (this.BASIC.equalsIgnoreCase(this.authMethod)) {
-					log.trace("authMethod before inputStream: {}", resultXml);
-					final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-					conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + this.authToken);
-					conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
-					conn.setRequestMethod("GET");
-					theHttpInputStream = conn.getInputStream();
-				} else {
-					theHttpInputStream = qUrl.openStream();
+				if (this.authMethod == "bearer") {
+					log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
+					requestHeaders.put("Authorization", "Bearer " + authToken);
+					// requestHeaders.put("Content-Type", "application/json");
+				} else if (AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
+					log.trace("RestIterator.downloadPage():: authMethod before inputStream: " + resultXml);
+					requestHeaders.put("Authorization", "Basic " + authToken);
+					// requestHeaders.put("accept", "application/xml");
 				}
+				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
+				conn.setRequestMethod("GET");
+				this.setRequestHeader(conn);
+				resultStream = conn.getInputStream();
 
-				this.resultStream = theHttpInputStream;
 				if ("json".equals(this.resultOutputFormat)) {
 					resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
 					resultXml = JsonUtils.convertToXML(resultJson);
 					this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
 				}
 
-				if (!(emptyXml).equalsIgnoreCase(resultXml)) {
+				if (!isEmptyXml(resultXml)) {
 					resultNode = (Node) this.xpath
 						.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
 					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
@@ -265,8 +293,7 @@ public class RestIterator implements Iterator<String> {
 						final StringWriter sw = new StringWriter();
 						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
 						final String toEnqueue = sw.toString();
-						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue)
-							|| emptyXml.equalsIgnoreCase(toEnqueue)) {
+						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
 							log
 								.warn(
 									"The following record resulted in empty item for the feeding queue: {}", resultXml);
@@ -294,6 +321,7 @@ public class RestIterator implements Iterator<String> {
 							throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
 						}
 						qUrlArgument = qUrl.getQuery();
+
 						final String[] arrayQUrlArgument = qUrlArgument.split("&");
 						for (final String arrayUrlArgStr : arrayQUrlArgument) {
 							if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
@@ -307,7 +335,7 @@ public class RestIterator implements Iterator<String> {
 							}
 						}
 
-						if (((emptyXml).equalsIgnoreCase(resultXml))
+						if (isEmptyXml(resultXml)
 							|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
 							// resumptionStr = "";
 							if (nodeList != null) {
@@ -326,13 +354,13 @@ public class RestIterator implements Iterator<String> {
 
 					case "pagination":
 					case "page": // pagination, iterate over page numbers
-						this.pagination += 1;
-						if (nodeList != null) {
+						if (nodeList != null && nodeList.getLength() > 0) {
 							this.discoverResultSize += nodeList.getLength();
 						} else {
 							this.resultTotal = this.discoverResultSize;
 							this.pagination = this.discoverResultSize;
 						}
+						this.pagination += 1;
 						this.resumptionInt = this.pagination;
 						this.resumptionStr = Integer.toString(this.resumptionInt);
 						break;
@@ -380,7 +408,8 @@ public class RestIterator implements Iterator<String> {
 			try {
 				if (this.resultTotal == -1) {
 					this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
-					if ("page".equalsIgnoreCase(this.resumptionType) && !this.BASIC.equalsIgnoreCase(this.authMethod)) {
+					if ("page".equalsIgnoreCase(this.resumptionType)
+						&& !this.AUTHBASIC.equalsIgnoreCase(this.authMethod)) {
 						this.resultTotal += 1;
 					} // to correct the upper bound
 					log.info("resultTotal was -1 is now: " + this.resultTotal);
@@ -409,6 +438,10 @@ public class RestIterator implements Iterator<String> {
 
 	}
 
+	private boolean isEmptyXml(String s) {
+		return EMPTY_XML.equalsIgnoreCase(s);
+	}
+
 	private boolean isInteger(final String s) {
 		boolean isValidInteger = false;
 		try {
@@ -433,6 +466,22 @@ public class RestIterator implements Iterator<String> {
 		}
 	}
 
+	/**
+	 * setRequestHeader
+	 *
+	 * setRequestProperty: Sets the general request property. If a property with the key already exists, overwrite its value with the new value.
+	 * @param conn
+	 */
+	private void setRequestHeader(HttpURLConnection conn) {
+		if (requestHeaders != null) {
+			for (String key : requestHeaders.keySet()) {
+				conn.setRequestProperty(key, requestHeaders.get(key));
+			}
+			log.debug("Set Request Header with: " + requestHeaders);
+		}
+
+	}
+
 	public String getResultFormatValue() {
 		return this.resultFormatValue;
 	}

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

@@ -8,7 +8,10 @@ import java.io.StringWriter;
 import java.nio.charset.Charset;
 import java.nio.charset.CharsetDecoder;
 import java.nio.charset.CodingErrorAction;
+import java.util.Arrays;
 import java.util.Iterator;
+import java.util.List;
+import java.util.stream.Collectors;
 
 import javax.xml.stream.XMLEventFactory;
 import javax.xml.stream.XMLEventReader;
@@ -19,6 +22,7 @@ import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -58,13 +62,23 @@ public class XMLIterator implements Iterator<String> {
 
 	private String element;
 
+	private List<String> elements;
+
 	private InputStream inputStream;
 
 	public XMLIterator(final String element, final InputStream inputStream) {
 		super();
 		this.element = element;
+		if (element.contains(",")) {
+			elements = Arrays
+				.stream(element.split(","))
+				.filter(StringUtils::isNoneBlank)
+				.map(String::toLowerCase)
+				.collect(Collectors.toList());
+		}
 		this.inputStream = inputStream;
 		this.parser = getParser();
+
 		try {
 			this.current = findElement(parser);
 		} catch (XMLStreamException e) {
@@ -113,7 +127,7 @@ public class XMLIterator implements Iterator<String> {
 				final XMLEvent event = parser.nextEvent();
 
 				// TODO: replace with depth tracking instead of close tag tracking.
-				if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) {
+				if (event.isEndElement() && isCheckTag(event.asEndElement().getName().getLocalPart())) {
 					writer.add(event);
 					break;
 				}
@@ -142,31 +156,48 @@ public class XMLIterator implements Iterator<String> {
 		XMLEvent peek = parser.peek();
 		if (peek != null && peek.isStartElement()) {
 			String name = peek.asStartElement().getName().getLocalPart();
-			if (element.equals(name)) {
+			if (isCheckTag(name))
 				return peek;
 		}
-		}
 
 		while (parser.hasNext()) {
-			final XMLEvent event = parser.nextEvent();
+			XMLEvent event = parser.nextEvent();
 			if (event != null && event.isStartElement()) {
 				String name = event.asStartElement().getName().getLocalPart();
-				if (element.equals(name)) {
+				if (isCheckTag(name))
 					return event;
 			}
 		}
-		}
 		return null;
 	}
 
 	private XMLEventReader getParser() {
 		try {
-			return inputFactory.get().createXMLEventReader(sanitize(inputStream));
+			XMLInputFactory xif = inputFactory.get();
+			xif.setProperty(XMLInputFactory.SUPPORT_DTD, false);
+			return xif.createXMLEventReader(sanitize(inputStream));
 		} catch (XMLStreamException e) {
 			throw new RuntimeException(e);
 		}
 	}
 
+	private boolean isCheckTag(final String tagName) {
+		if (elements != null) {
+			final String found = elements
+				.stream()
+				.filter(e -> e.equalsIgnoreCase(tagName))
+				.findFirst()
+				.orElse(null);
+			if (found != null)
+				return true;
+		} else {
+			if (element.equalsIgnoreCase(tagName)) {
+				return true;
+			}
+		}
+		return false;
+	}
+
 	private Reader sanitize(final InputStream in) {
 		final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder();
 		charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/DataFetcher.java

@@ -1,134 +0,0 @@
-package eu.dnetlib.dhp.transformation.xslt;
-
-import java.io.Serializable;
-import net.sf.saxon.s9api.*;
-
-import org.apache.commons.io.IOUtils;
-import org.json.JSONObject;
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * This class fetches JSON from a provided link and returns
- * a Dublin Core. This functionality is particularly needed for OSF Preprints
- */
-
-
-public class DataFetcher implements ExtensionFunction, Serializable {
-
-    /**
-     * This method fetches JSON object from a given URL
-     * @param url a url in the metadata for fetching authors in JSON format
-     * @return
-     * @throws IOException
-     */
-    static JSONObject getJson(URL url) throws IOException {
-
-        String json = IOUtils.toString(url);
-        return new JSONObject(json);
-    }
-
-    /**
-     * This method extracts authors from a given JSON
-     *
-     * @param jsonObject
-     * @return
-     */
-    static List<String> getAuthorsFromJson(JSONObject jsonObject) {
-        List<String> authors = new ArrayList<>();
-        // count of authors
-        int countOfAuthors = jsonObject.getJSONArray("data").length();
-        for (int i = 0; i < countOfAuthors; i++) {
-
-            authors.add(jsonObject
-                    .getJSONArray("data")
-                    .getJSONObject(i)
-                    .getJSONObject("embeds")
-                    .getJSONObject("users")
-                    .getJSONObject("data")
-                    .getJSONObject("attributes")
-                    .getString("full_name"));
-        }
-        return authors;
-    }
-
-    /**
-     * This method transforms list of authors into Dublin Core
-     * @param authors
-     * @return Dublin Core list of authors
-     */
-    static List<String> transformListToDublinCore(List<String> authors) {
-
-        List<String> dublinCoreAuthors = new ArrayList<>();
-        for (String author : authors){
-
-            //splitting full name into first and last names according to OpenAIRE v3 guidelines at:
-            // https://guidelines.openaire.eu/en/latest/literature/field_creator.html
-            // “surname”, “initials” (“first name”) “prefix”.
-            String[] parts = author.split(" ");
-            String firstName = parts[0];
-            String lastName = parts[1];
-            char initialOfFirstName = firstName.charAt(0);
-
-            dublinCoreAuthors.add(
-                    "<dc:creator>" + lastName + ", " + initialOfFirstName +  ". (" + firstName + ")" + "</dc:creator>");
-        }
-        return dublinCoreAuthors;
-    }
-
-     /**
-     * This is a public method which fetches authors and transform them into Dublin Core
-     */
-    public static String getAndTransformAuthors(URL url) throws IOException{
-        return String.join(", ", transformListToDublinCore(getAuthorsFromJson(getJson(url))));
-    }
-
-
-    /**
-     * This method extracts link to fulltext from a given JSON
-     *
-     * @return
-     */
-    static private String getLinkToFulltextFromJson(JSONObject jsonObject) throws MalformedURLException {
-
-        // note: Link to JSON containing fulltextlink is in "primary_file" attribute.
-        // And in the resultant JSON,  “links->download” contains the URL to fulltext
-
-        return jsonObject
-                .getJSONObject("data")
-                .getJSONObject("links")
-                .getString("download");
-    }
-
-    /**
-     * This is a public method which fetches link to full text and returns it as a suitable format
-     */
-    public static String getFullTextLinkAndTransform (URL url )throws IOException{
-
-        return getLinkToFulltextFromJson(getJson(url));
-    }
-
-
-    @Override
-    public QName getName() {
-        return null;
-    }
-
-    @Override
-    public SequenceType getResultType() {
-        return null;
-    }
-
-    @Override
-    public SequenceType[] getArgumentTypes() {
-        return new SequenceType[0];
-    }
-
-    @Override
-    public XdmValue call(XdmValue[] xdmValues) throws SaxonApiException {
-        return null;
-    }
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/transformation/xslt/XSLTTransformationFunction.java

@@ -55,8 +55,6 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
 		processor.registerExtensionFunction(new DateCleaner());
 		processor.registerExtensionFunction(new PersonCleaner());
 
-		processor.registerExtensionFunction(new DataFetcher());
-
 		final XsltCompiler comp = processor.newXsltCompiler();
 		QName datasourceIDParam = new QName(DATASOURCE_ID_PARAM);
 		comp.setParameter(datasourceIDParam, new XdmAtomicValue(value.getProvenance().getDatasourceId()));

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

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

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json

@@ -1,5 +1,10 @@
 [
-
+  {
+    "id": "100007630",
+    "uri": "http://dx.doi.org/10.13039/100007630",
+    "name": "College of Engineering and Informatics, National University of Ireland, Galway",
+    "synonym": []
+  },
   {
     "id": "100007731",
     "uri": "http://dx.doi.org/10.13039/100007731",
@@ -427,13 +432,13 @@
     "id": "501100001634",
     "uri": "http://dx.doi.org/10.13039/501100001634",
     "name": "University of Galway",
-    "synonym": ["501100019905", "100007630", "501100020570", "501100023852"]
+    "synonym": []
   },
   {
     "id": "501100001635",
     "uri": "http://dx.doi.org/10.13039/501100001635",
     "name": "University of Limerick",
-    "synonym": ["501100014531"]
+    "synonym": []
   },
   {
     "id": "501100001636",
@@ -463,7 +468,7 @@
     "id": "501100002736",
     "uri": "http://dx.doi.org/10.13039/501100002736",
     "name": "Covidien",
-    "synonym": ["501100003956"]
+    "synonym": []
   },
   {
     "id": "501100002755",
@@ -513,6 +518,12 @@
     "name": "Irish Institute of Clinical Neuroscience",
     "synonym": []
   },
+  {
+    "id": "501100003956",
+    "uri": "http://dx.doi.org/10.13039/501100003956",
+    "name": "Aspect Medical Systems",
+    "synonym": []
+  },
   {
     "id": "501100004162",
     "uri": "http://dx.doi.org/10.13039/501100004162",
@@ -633,7 +644,12 @@
     "name": "Irish Centre for High-End Computing",
     "synonym": []
   },
-
+  {
+    "id": "501100019905",
+    "uri": "http://dx.doi.org/10.13039/501100019905",
+    "name": "Galway University Foundation",
+    "synonym": []
+  },
   {
     "id": "501100020036",
     "uri": "http://dx.doi.org/10.13039/501100020036",
@@ -808,7 +824,12 @@
     "name": "Energy Policy Research Centre, Economic and Social Research Institute",
     "synonym": []
   },
-
+  {
+    "id": "501100014531",
+    "uri": "http://dx.doi.org/10.13039/501100014531",
+    "name": "Physical Education and Sport Sciences Department, University of Limerick",
+    "synonym": []
+  },
   {
     "id": "501100014745",
     "uri": "http://dx.doi.org/10.13039/501100014745",
@@ -821,11 +842,22 @@
     "name": "ADAPT - Centre for Digital Content Technology",
     "synonym": []
   },
-
+  {
+    "id": "501100020570",
+    "uri": "http://dx.doi.org/10.13039/501100020570",
+    "name": "College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway",
+    "synonym": []
+  },
   {
     "id": "501100020871",
     "uri": "http://dx.doi.org/10.13039/501100020871",
     "name": "Bernal Institute, University of Limerick",
     "synonym": []
+  },
+  {
+    "id": "501100023852",
+    "uri": "http://dx.doi.org/10.13039/501100023852",
+    "name": "Moore Institute for Research in the Humanities and Social Studies, University of Galway",
+    "synonym": []
   }
 ]

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

@@ -48,37 +48,12 @@
             <description>Used to configure the heap size for the map JVM process. Should be 80% of mapreduce.map.memory.mb.</description>
         </property>
 
-        <property>
-            <name>JAVA_HOME</name>
-            <value>/srv/java/openjdk-17</value>
-            <description>Used to configure the Java home location for oozie.launcher.mapreduce.map.env</description>
-        </property>
-
-        <property>
-            <name>JAVA_OPTS</name>
-                <value>-Dcom.sun.security.enableAIAcaIssuers=true</value>
-            <description>Used to configure the JAVA_OPTS parameter</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.launcher.mapreduce.map.env</name>
-                <value>JAVA_HOME=${JAVA_HOME}</value>
-            </property>
-        </configuration>
     </global>
 
     <start to="collection_mode"/>
@@ -124,7 +99,7 @@
     <action name="CollectionWorker">
         <java>
             <main-class>eu.dnetlib.dhp.collection.CollectorWorkerApplication</main-class>
-            <java-opts>${JAVA_OPTS} ${collection_java_xmx}</java-opts>
+            <java-opts>${collection_java_xmx}</java-opts>
             <arg>--apidescriptor</arg><arg>${apiDescription}</arg>
             <arg>--namenode</arg><arg>${nameNode}</arg>
             <arg>--workflowId</arg><arg>${workflowId}</arg>

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

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

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

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

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

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

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

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

@@ -1025,6 +1025,7 @@ case object Crossref2Oaf {
             tp._1 match {
               case "electronic" => journal.setIssnOnline(tp._2)
               case "print"      => journal.setIssnPrinted(tp._2)
+              case _            =>
             }
           })
         }

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

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

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

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

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

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

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

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

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

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

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

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

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

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

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipMultipleNodeTest.java

@@ -0,0 +1,64 @@
+
+package eu.dnetlib.dhp.collection.plugin.file;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Objects;
+import java.util.stream.Stream;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
+@ExtendWith(MockitoExtension.class)
+public class FileGZipMultipleNodeTest {
+
+	private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class);
+
+	private final ApiDescriptor api = new ApiDescriptor();
+
+	private FileGZipCollectorPlugin plugin;
+
+	private static final String SPLIT_ON_ELEMENT = "incollection,article";
+
+	@BeforeEach
+	public void setUp() throws IOException {
+
+		final String gzipFile = Objects
+			.requireNonNull(
+				this
+					.getClass()
+					.getResource("/eu/dnetlib/dhp/collection/plugin/file/dblp.gz"))
+			.getFile();
+
+		api.setBaseUrl(gzipFile);
+
+		HashMap<String, String> params = new HashMap<>();
+		params.put("splitOnElement", SPLIT_ON_ELEMENT);
+
+		api.setParams(params);
+
+		FileSystem fs = FileSystem.get(new Configuration());
+		plugin = new FileGZipCollectorPlugin(fs);
+	}
+
+	@Test
+	void test() throws CollectorException {
+
+		final Stream<String> stream = plugin.collect(api, new AggregatorReport());
+
+		stream.limit(10).forEach(s -> {
+			Assertions.assertTrue(s.length() > 0);
+			log.info(s);
+		});
+	}
+}

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

@@ -36,11 +36,11 @@ public class OsfPreprintCollectorTest {
 	private final String resultTotalXpath = "/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']";
 
 	private final String resumptionParam = "page";
-	private final String resumptionType = "page";
-	private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
+	private final String resumptionType = "scan";
+	private final String resumptionXpath = "substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')";
 
-	private final String resultSizeParam = "";
-	private final String resultSizeValue = "";
+	private final String resultSizeParam = "page[size]";
+	private final String resultSizeValue = "100";
 
 	private final String resultFormatParam = "format";
 	private final String resultFormatValue = "json";
@@ -74,7 +74,7 @@ public class OsfPreprintCollectorTest {
 		final AtomicInteger i = new AtomicInteger(0);
 		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
 
-		stream.limit(200).forEach(s -> {
+		stream.limit(2000).forEach(s -> {
 			Assertions.assertTrue(s.length() > 0);
 			i.incrementAndGet();
 			log.info(s);

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

@@ -4,6 +4,11 @@
 
 package eu.dnetlib.dhp.collection.plugin.rest;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.HttpURLConnection;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Stream;
@@ -12,6 +17,8 @@ import org.junit.jupiter.api.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.google.gson.Gson;
+
 import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
@@ -25,18 +32,18 @@ class RestCollectorPluginTest {
 
 	private static final Logger log = LoggerFactory.getLogger(RestCollectorPluginTest.class);
 
-	private final String baseUrl = "https://share.osf.io/api/v2/search/creativeworks/_search";
-	private final String resumptionType = "count";
-	private final String resumptionParam = "from";
-	private final String entityXpath = "//hits/hits";
-	private final String resumptionXpath = "//hits";
-	private final String resultTotalXpath = "//hits/total";
-	private final String resultFormatParam = "format";
+	private final String baseUrl = "https://ddh-openapi.worldbank.org/search";
+	private final String resumptionType = "discover";
+	private final String resumptionParam = "skip";
+	private final String entityXpath = "//*[local-name()='data']";
+	private final String resumptionXpath = "";
+	private final String resultTotalXpath = "//*[local-name()='count']";
+	private final String resultFormatParam = "";
 	private final String resultFormatValue = "json";
-	private final String resultSizeParam = "size";
+	private final String resultSizeParam = "top";
 	private final String resultSizeValue = "10";
 	// private String query = "q=%28sources%3ASocArXiv+AND+type%3Apreprint%29";
-	private final String query = "q=%28sources%3AengrXiv+AND+type%3Apreprint%29";
+	private final String query = "";
 	// private String query = "=(sources:engrXiv AND type:preprint)";
 
 	private final String protocolDescriptor = "rest_json2xml";
@@ -56,6 +63,7 @@ class RestCollectorPluginTest {
 		params.put("resultSizeValue", resultSizeValue);
 		params.put("queryParams", query);
 		params.put("entityXpath", entityXpath);
+		params.put("requestHeaderMap", "{\"User-Agent\": \"OpenAIRE DEV\"}");
 
 		api.setBaseUrl(baseUrl);
 		api.setParams(params);
@@ -78,4 +86,19 @@ class RestCollectorPluginTest {
 		log.info("{}", i.intValue());
 		Assertions.assertTrue(i.intValue() > 0);
 	}
+
+	@Disabled
+	@Test
+	void testUrl() throws IOException {
+		String url_s = "https://ddh-openapi.worldbank.org/search?&top=10";
+		URL url = new URL(url_s);
+		final HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+		conn.setRequestMethod("GET");
+		conn.setRequestProperty("User-Agent", "OpenAIRE");
+		Gson gson = new Gson();
+		System.out.println("Request header");
+		System.out.println(gson.toJson(conn.getHeaderFields()));
+		InputStream inputStream = conn.getInputStream();
+
+	}
 }

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

@@ -44,7 +44,7 @@ public class RestIteratorTest {
 
 		final RestIterator iterator = new RestIterator(clientParams, baseUrl, resumptionType, resumptionParam,
 			resumptionXpath, resultTotalXpath, resultFormatParam, resultFormatValue, resultSizeParam, resultSizeValue,
-			query, entityXpath, authMethod, authToken, resultOffsetParam);
+			query, entityXpath, authMethod, authToken, resultOffsetParam, null);
 		int i = 20;
 		while (iterator.hasNext() && i > 0) {
 			String result = iterator.next();

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/transformation/xslt/DataFetcherTest.java

@@ -1,68 +0,0 @@
-package eu.dnetlib.dhp.transformation.xslt;
-
-import org.json.JSONObject;
-import org.junit.jupiter.api.AfterEach;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.net.URL;
-import java.util.List;
-
-import static org.junit.jupiter.api.Assertions.*;
-
-class DataFetcherTest {
-
-    @BeforeEach
-    void setUp() {
-    }
-
-    @AfterEach
-    void tearDown() {
-    }
-
-    @Test
-    void getJson() throws IOException, URISyntaxException {
-        URL contributorsUrl = new URI("https://api.osf.io/v2/preprints/mrwqb/contributors/?format=json").toURL();
-        JSONObject testJsonObj = DataFetcher.getJson(contributorsUrl);
-
-        String x = testJsonObj
-                .getJSONArray("data")
-                .getJSONObject(0)
-                .getJSONObject("embeds")
-                .getJSONObject("users")
-                .getJSONObject("data")
-                .getJSONObject("attributes")
-                .getString("full_name");
-        System.out.println(x);
-        System.out.println(testJsonObj.getJSONArray("data").length());
-        testJsonObj.getJSONArray("data").forEach(System.out::println);
-    }
-
-    @Test
-    void getAuthorsFromJson() throws IOException, URISyntaxException {
-        URL contributorsUrl = new URI("https://api.osf.io/v2/preprints/mrwqb/contributors/?format=json").toURL();
-        JSONObject testJsonObj = DataFetcher.getJson(contributorsUrl);
-        List<String> authors = DataFetcher.getAuthorsFromJson(testJsonObj);
-        System.out.println(authors);
-        System.out.println(DataFetcher.transformListToDublinCore(authors));
-    }
-
-    @Test
-    void getAndTransformAuthors() throws IOException, URISyntaxException {
-        URL contributorsUrl = new URI("https://api.osf.io/v2/preprints/mrwqb/contributors/?format=json").toURL();
-        System.out.println(DataFetcher.getAndTransformAuthors(contributorsUrl));
-    }
-
-
-    @Test
-    void getLinkToFulltextFromJson() throws URISyntaxException, IOException {
-        URL linkToFullTextDocument = new URI("https://api.osf.io/v2/files/5de7c96f84c479000c7928af/?format=json").toURL();
-        System.out.println(DataFetcher.getFullTextLinkAndTransform(linkToFullTextDocument));
-
-
-    }
-}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/issn_pub.json

@@ -789,10 +789,6 @@
       "value": "2227-9717",
       "type": "electronic"
     },
-    {
-      "value": "VALUE",
-      "type": "PIPPO"
-    },
     {
       "value": "1063-4584",
       "type": "pu"

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump

@@ -1,44 +1,15 @@
-{"classification": "Signaling protein", "pdb": "5NM4", "deposition_date": "2017-04-05", "title": "A2a adenosine receptor room-temperature structure determined by serial Femtosecond crystallography", "Keywords": ["Oom-temperature", " serial crystallography", " signaling protein"], "authors": ["T.weinert", "R.cheng", "D.james", "D.gashi", "P.nogly", "K.jaeger", "M.hennig", "", "J.standfuss"], "pmid": "28912485", "doi": "10.1038/S41467-017-00630-4"}
-{"classification": "Oxidoreductase/oxidoreductase inhibitor", "pdb": "4KN3", "deposition_date": "2013-05-08", "title": "Structure of the y34ns91g double mutant of dehaloperoxidase from Amphitrite ornata with 2,4,6-trichlorophenol", "Keywords": ["Lobin", " oxygen storage", " peroxidase", " oxidoreductase", " oxidoreductase-", "Oxidoreductase inhibitor complex"], "authors": ["C.wang", "L.lovelace", "L.lebioda"], "pmid": "23952341", "doi": "10.1021/BI400627W"}
-{"classification": "Transport protein", "pdb": "8HKM", "deposition_date": "2022-11-27", "title": "Ion channel", "Keywords": ["On channel", " transport protein"], "authors": ["D.h.jiang", "J.t.zhang"], "pmid": "37494189", "doi": "10.1016/J.CELREP.2023.112858"}
-{"classification": "Signaling protein", "pdb": "6JT1", "deposition_date": "2019-04-08", "title": "Structure of human soluble guanylate cyclase in the heme oxidised State", "Keywords": ["Oluble guanylate cyclase", " signaling protein"], "authors": ["L.chen", "Y.kang", "R.liu", "J.-x.wu"], "pmid": "31514202", "doi": "10.1038/S41586-019-1584-6"}
-{"classification": "Immune system", "pdb": "7OW6", "deposition_date": "2021-06-16", "title": "Crystal structure of a tcr in complex with hla-a*11:01 bound to kras G12d peptide (vvvgadgvgk)", "Keywords": ["La", " kras", " tcr", " immune system"], "authors": ["V.karuppiah", "R.a.robinson"], "doi": "10.1038/S41467-022-32811-1"}
-{"classification": "Biosynthetic protein", "pdb": "5EQ8", "deposition_date": "2015-11-12", "title": "Crystal structure of medicago truncatula histidinol-phosphate Phosphatase (mthpp) in complex with l-histidinol", "Keywords": ["Istidine biosynthesis", " metabolic pathways", " dimer", " plant", "", "Biosynthetic protein"], "authors": ["M.ruszkowski", "Z.dauter"], "pmid": "26994138", "doi": "10.1074/JBC.M115.708727"}
-{"classification": "De novo protein", "pdb": "8CWA", "deposition_date": "2022-05-18", "title": "Solution nmr structure of 8-residue rosetta-designed cyclic peptide D8.21 in cdcl3 with cis/trans switching (tc conformation, 53%)", "Keywords": ["Yclic peptide", " non natural amino acids", " cis/trans", " switch peptides", "", "De novo design", "Membrane permeability", "De novo protein"], "authors": ["T.a.ramelot", "R.tejero", "G.t.montelione"], "pmid": "36041435", "doi": "10.1016/J.CELL.2022.07.019"}
-{"classification": "Hydrolase", "pdb": "3R6M", "deposition_date": "2011-03-21", "title": "Crystal structure of vibrio parahaemolyticus yeaz", "Keywords": ["Ctin/hsp70 nucleotide-binding fold", " bacterial resuscitation", " viable", "But non-culturable state", "Resuscitation promoting factor", "Ygjd", "", "Yjee", "Vibrio parahaemolyticus", "Hydrolase"], "authors": ["A.roujeinikova", "I.aydin"], "pmid": "21858042", "doi": "10.1371/JOURNAL.PONE.0023245"}
-{"classification": "Hydrolase", "pdb": "2W5J", "deposition_date": "2008-12-10", "title": "Structure of the c14-rotor ring of the proton translocating Chloroplast atp synthase", "Keywords": ["Ydrolase", " chloroplast", " atp synthase", " lipid-binding", " cf(0)", " membrane", "", "Transport", "Formylation", "Energy transduction", "Hydrogen ion transport", "", "Ion transport", "Transmembrane", "Membrane protein"], "authors": ["M.vollmar", "D.schlieper", "M.winn", "C.buechner", "G.groth"], "pmid": "19423706", "doi": "10.1074/JBC.M109.006916"}
-{"classification": "De novo protein", "pdb": "4GLU", "deposition_date": "2012-08-14", "title": "Crystal structure of the mirror image form of vegf-a", "Keywords": ["-protein", " covalent dimer", " cysteine knot protein", " growth factor", " de", "Novo protein"], "authors": ["K.mandal", "M.uppalapati", "D.ault-riche", "J.kenney", "J.lowitz", "S.sidhu", "", "S.b.h.kent"], "pmid": "22927390", "doi": "10.1073/PNAS.1210483109"}
-{"classification": "Hydrolase/hydrolase inhibitor", "pdb": "3WYL", "deposition_date": "2014-09-01", "title": "Crystal structure of the catalytic domain of pde10a complexed with 5- Methoxy-3-(1-phenyl-1h-pyrazol-5-yl)-1-(3-(trifluoromethyl)phenyl) Pyridazin-4(1h)-one", "Keywords": ["Ydrolase-hydrolase inhibitor complex"], "authors": ["H.oki", "Y.hayano"], "pmid": "25384088", "doi": "10.1021/JM5013648"}
-{"classification": "Isomerase", "pdb": "5BOR", "deposition_date": "2015-05-27", "title": "Structure of acetobacter aceti pure-s57c, sulfonate form", "Keywords": ["Cidophile", " pure", " purine biosynthesis", " isomerase"], "authors": ["K.l.sullivan", "T.j.kappock"]}
-{"classification": "Hydrolase", "pdb": "1X0C", "deposition_date": "2005-03-17", "title": "Improved crystal structure of isopullulanase from aspergillus niger Atcc 9642", "Keywords": ["Ullulan", " glycoside hydrolase family 49", " glycoprotein", " hydrolase"], "authors": ["M.mizuno", "T.tonozuka", "A.yamamura", "Y.miyasaka", "H.akeboshi", "S.kamitori", "", "A.nishikawa", "Y.sakano"], "pmid": "18155243", "doi": "10.1016/J.JMB.2007.11.098"}
-{"classification": "Oxidoreductase", "pdb": "7CUP", "deposition_date": "2020-08-23", "title": "Structure of 2,5-dihydroxypridine dioxygenase from pseudomonas putida Kt2440", "Keywords": ["On-heme dioxygenase", " oxidoreductase"], "authors": ["G.q.liu", "H.z.tang"]}
-{"classification": "Ligase", "pdb": "1VCN", "deposition_date": "2004-03-10", "title": "Crystal structure of t.th. hb8 ctp synthetase complex with sulfate Anion", "Keywords": ["Etramer", " riken structural genomics/proteomics initiative", " rsgi", "", "Structural genomics", "Ligase"], "authors": ["M.goto", "Riken structural genomics/proteomics initiative (rsgi)"], "pmid": "15296735", "doi": "10.1016/J.STR.2004.05.013"}
-{"classification": "Transferase/transferase inhibitor", "pdb": "6C9V", "deposition_date": "2018-01-28", "title": "Mycobacterium tuberculosis adenosine kinase bound to (2r,3s,4r,5r)-2- (hydroxymethyl)-5-(6-(4-phenylpiperazin-1-yl)-9h-purin-9-yl) Tetrahydrofuran-3,4-diol", "Keywords": ["Ucleoside analog", " complex", " inhibitor", " structural genomics", " psi-2", "", "Protein structure initiative", "Tb structural genomics consortium", "", "Tbsgc", "Transferase-transferase inhibitor complex"], "authors": ["R.a.crespo", "Tb structural genomics consortium (tbsgc)"], "pmid": "31002508", "doi": "10.1021/ACS.JMEDCHEM.9B00020"}
-{"classification": "De novo protein", "pdb": "4LPY", "deposition_date": "2013-07-16", "title": "Crystal structure of tencon variant g10", "Keywords": ["Ibronectin type iii fold", " alternate scaffold", " de novo protein"], "authors": ["A.teplyakov", "G.obmolova", "G.l.gilliland"], "pmid": "24375666", "doi": "10.1002/PROT.24502"}
-{"classification": "Isomerase", "pdb": "2Y88", "deposition_date": "2011-02-03", "title": "Crystal structure of mycobacterium tuberculosis phosphoribosyl Isomerase (variant d11n) with bound prfar", "Keywords": ["Romatic amino acid biosynthesis", " isomerase", " tim-barrel", " histidine", "Biosynthesis", "Tryptophan biosynthesis"], "authors": ["J.kuper", "A.v.due", "A.geerlof", "M.wilmanns"], "pmid": "21321225", "doi": "10.1073/PNAS.1015996108"}
-{"classification": "Unknown function", "pdb": "1SR0", "deposition_date": "2004-03-22", "title": "Crystal structure of signalling protein from sheep(sps-40) at 3.0a Resolution using crystal grown in the presence of polysaccharides", "Keywords": ["Ignalling protein", " involution", " unknown function"], "authors": ["D.b.srivastava", "A.s.ethayathulla", "N.singh", "J.kumar", "S.sharma", "T.p.singh"]}
-{"classification": "Dna binding protein", "pdb": "3RH2", "deposition_date": "2011-04-11", "title": "Crystal structure of a tetr-like transcriptional regulator (sama_0099) From shewanella amazonensis sb2b at 2.42 a resolution", "Keywords": ["Na/rna-binding 3-helical bundle", " structural genomics", " joint center", "For structural genomics", "Jcsg", "Protein structure initiative", "Psi-", "Biology", "Dna binding protein"], "authors": ["Joint center for structural genomics (jcsg)"]}
-{"classification": "Transferase", "pdb": "2WK5", "deposition_date": "2009-06-05", "title": "Structural features of native human thymidine phosphorylase And in complex with 5-iodouracil", "Keywords": ["Lycosyltransferase", " developmental protein", " angiogenesis", "", "5-iodouracil", "Growth factor", "Enzyme kinetics", "", "Differentiation", "Disease mutation", "Thymidine", "Phosphorylase", "Chemotaxis", "Transferase", "Mutagenesis", "", "Polymorphism"], "authors": ["E.mitsiki", "A.c.papageorgiou", "S.iyer", "N.thiyagarajan", "S.h.prior", "", "D.sleep", "C.finnis", "K.r.acharya"], "pmid": "19555658", "doi": "10.1016/J.BBRC.2009.06.104"}
-{"classification": "Hydrolase", "pdb": "3P9Y", "deposition_date": "2010-10-18", "title": "Crystal structure of the drosophila melanogaster ssu72-pctd complex", "Keywords": ["Hosphatase", " cis proline", " lmw ptp-like fold", " rna polymerase ii ctd", "", "Hydrolase"], "authors": ["J.w.werner-allen", "P.zhou"], "pmid": "21159777", "doi": "10.1074/JBC.M110.197129"}
-{"classification": "Recombination/dna", "pdb": "6OEO", "deposition_date": "2019-03-27", "title": "Cryo-em structure of mouse rag1/2 nfc complex (dna1)", "Keywords": ["(d)j recombination", " dna transposition", " rag", " scid", " recombination", "", "Recombination-dna complex"], "authors": ["X.chen", "Y.cui", "Z.h.zhou", "W.yang", "M.gellert"], "pmid": "32015552", "doi": "10.1038/S41594-019-0363-2"}
-{"classification": "Hydrolase", "pdb": "4ECA", "deposition_date": "1997-02-21", "title": "Asparaginase from e. coli, mutant t89v with covalently bound aspartate", "Keywords": ["Ydrolase", " acyl-enzyme intermediate", " threonine amidohydrolase"], "authors": ["G.j.palm", "J.lubkowski", "A.wlodawer"], "pmid": "8706862", "doi": "10.1016/0014-5793(96)00660-6"}
-{"classification": "Transcription/protein binding", "pdb": "3UVX", "deposition_date": "2011-11-30", "title": "Crystal structure of the first bromodomain of human brd4 in complex With a diacetylated histone 4 peptide (h4k12ack16ac)", "Keywords": ["Romodomain", " bromodomain containing protein 4", " cap", " hunk1", " mcap", "", "Mitotic chromosome associated protein", "Peptide complex", "Structural", "Genomics consortium", "Sgc", "Transcription-protein binding complex"], "authors": ["P.filippakopoulos", "S.picaud", "T.keates", "E.ugochukwu", "F.von delft", "", "C.h.arrowsmith", "A.m.edwards", "J.weigelt", "C.bountra", "S.knapp", "Structural", "Genomics consortium (sgc)"], "pmid": "22464331", "doi": "10.1016/J.CELL.2012.02.013"}
-{"classification": "Membrane protein", "pdb": "1TLZ", "deposition_date": "2004-06-10", "title": "Tsx structure complexed with uridine", "Keywords": ["Ucleoside transporter", " beta barrel", " uridine", " membrane", "Protein"], "authors": ["J.ye", "B.van den berg"], "pmid": "15272310", "doi": "10.1038/SJ.EMBOJ.7600330"}
-{"classification": "Dna binding protein", "pdb": "7AZD", "deposition_date": "2020-11-16", "title": "Dna polymerase sliding clamp from escherichia coli with peptide 20 Bound", "Keywords": ["Ntibacterial drug", " dna binding protein"], "authors": ["C.monsarrat", "G.compain", "C.andre", "I.martiel", "S.engilberge", "V.olieric", "", "P.wolff", "K.brillet", "M.landolfo", "C.silva da veiga", "J.wagner", "G.guichard", "", "D.y.burnouf"], "pmid": "34806883", "doi": "10.1021/ACS.JMEDCHEM.1C00918"}
-{"classification": "Transferase", "pdb": "5N3K", "deposition_date": "2017-02-08", "title": "Camp-dependent protein kinase a from cricetulus griseus in complex With fragment like molecule o-guanidino-l-homoserine", "Keywords": ["Ragment", " complex", " transferase", " serine threonine kinase", " camp", "", "Kinase", "Pka"], "authors": ["C.siefker", "A.heine", "G.klebe"]}
-{"classification": "Biosynthetic protein", "pdb": "8H52", "deposition_date": "2022-10-11", "title": "Crystal structure of helicobacter pylori carboxyspermidine Dehydrogenase in complex with nadp", "Keywords": ["Arboxyspermidine dehydrogenase", " biosynthetic protein"], "authors": ["K.y.ko", "S.c.park", "S.y.cho", "S.i.yoon"], "pmid": "36283333", "doi": "10.1016/J.BBRC.2022.10.049"}
-{"classification": "Metal binding protein", "pdb": "6DYC", "deposition_date": "2018-07-01", "title": "Co(ii)-bound structure of the engineered cyt cb562 variant, ch3", "Keywords": ["Esigned protein", " 4-helix bundle", " electron transport", " metal binding", "Protein"], "authors": ["F.a.tezcan", "J.rittle"], "pmid": "30778140", "doi": "10.1038/S41557-019-0218-9"}
-{"classification": "Protein fibril", "pdb": "6A6B", "deposition_date": "2018-06-27", "title": "Cryo-em structure of alpha-synuclein fiber", "Keywords": ["Lpha-syn fiber", " parkinson disease", " protein fibril"], "authors": ["Y.w.li", "C.y.zhao", "F.luo", "Z.liu", "X.gui", "Z.luo", "X.zhang", "D.li", "C.liu", "X.li"], "pmid": "30065316", "doi": "10.1038/S41422-018-0075-X"}
-{"classification": "Dna", "pdb": "7D5E", "deposition_date": "2020-09-25", "title": "Left-handed g-quadruplex containing two bulges", "Keywords": ["-quadruplex", " bulge", " dna", " left-handed"], "authors": ["P.das", "A.maity", "K.h.ngo", "F.r.winnerdy", "B.bakalar", "Y.mechulam", "E.schmitt", "", "A.t.phan"], "pmid": "33503265", "doi": "10.1093/NAR/GKAA1259"}
-{"classification": "Transferase", "pdb": "3RSY", "deposition_date": "2011-05-02", "title": "Cellobiose phosphorylase from cellulomonas uda in complex with sulfate And glycerol", "Keywords": ["H94", " alpha barrel", " cellobiose phosphorylase", " disaccharide", "Phosphorylase", "Transferase"], "authors": ["A.van hoorebeke", "J.stout", "W.soetaert", "J.van beeumen", "T.desmet", "S.savvides"]}
-{"classification": "Oxidoreductase", "pdb": "7MCI", "deposition_date": "2021-04-02", "title": "Mofe protein from azotobacter vinelandii with a sulfur-replenished Cofactor", "Keywords": ["Zotobacter vinelandii", " mofe-protein", " nitrogenase", " oxidoreductase"], "authors": ["W.kang", "C.lee", "Y.hu", "M.w.ribbe"], "doi": "10.1038/S41929-022-00782-7"}
-{"classification": "Dna", "pdb": "1XUW", "deposition_date": "2004-10-26", "title": "Structural rationalization of a large difference in rna affinity Despite a small difference in chemistry between two 2'-o-modified Nucleic acid analogs", "Keywords": ["Na mimetic methylcarbamate amide analog", " dna"], "authors": ["R.pattanayek", "L.sethaphong", "C.pan", "M.prhavc", "T.p.prakash", "M.manoharan", "", "M.egli"], "pmid": "15547979", "doi": "10.1021/JA044637K"}
-{"classification": "Lyase", "pdb": "7C0D", "deposition_date": "2020-05-01", "title": "Crystal structure of azospirillum brasilense l-2-keto-3-deoxyarabonate Dehydratase (hydroxypyruvate-bound form)", "Keywords": ["-2-keto-3-deoxyarabonate dehydratase", " lyase"], "authors": ["Y.watanabe", "S.watanabe"], "pmid": "32697085", "doi": "10.1021/ACS.BIOCHEM.0C00515"}
-{"classification": "Signaling protein", "pdb": "5LYK", "deposition_date": "2016-09-28", "title": "Crystal structure of intracellular b30.2 domain of btn3a1 bound to Citrate", "Keywords": ["30.2", " butyrophilin", " signaling protein"], "authors": ["F.mohammed", "A.t.baker", "M.salim", "B.e.willcox"], "pmid": "28862425", "doi": "10.1021/ACSCHEMBIO.7B00694"}
-{"classification": "Toxin", "pdb": "4IZL", "deposition_date": "2013-01-30", "title": "Structure of the n248a mutant of the panton-valentine leucocidin s Component from staphylococcus aureus", "Keywords": ["I-component leucotoxin", " staphylococcus aureus", " s component", "Leucocidin", "Beta-barrel pore forming toxin", "Toxin"], "authors": ["L.maveyraud", "B.j.laventie", "G.prevost", "L.mourey"], "pmid": "24643034", "doi": "10.1371/JOURNAL.PONE.0092094"}
-{"classification": "Dna", "pdb": "6F3C", "deposition_date": "2017-11-28", "title": "The cytotoxic [pt(h2bapbpy)] platinum complex interacting with the Cgtacg hexamer", "Keywords": ["Rug-dna complex", " four-way junction", " dna"], "authors": ["M.ferraroni", "C.bazzicalupi", "P.gratteri", "F.papi"], "pmid": "31046177", "doi": "10.1002/ANIE.201814532"}
-{"classification": "Signaling protein/inhibitor", "pdb": "4L5M", "deposition_date": "2013-06-11", "title": "Complexe of arno sec7 domain with the protein-protein interaction Inhibitor n-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at ph6.5", "Keywords": ["Ec-7domain", " signaling protein-inhibitor complex"], "authors": ["F.hoh", "J.rouhana"], "pmid": "24112024", "doi": "10.1021/JM4009357"}
-{"classification": "Signaling protein", "pdb": "5I6J", "deposition_date": "2016-02-16", "title": "Crystal structure of srgap2 f-barx", "Keywords": ["Rgap2", " f-bar", " fx", " signaling protein"], "authors": ["M.sporny", "J.guez-haddad", "M.n.isupov", "Y.opatowsky"], "pmid": "28333212", "doi": "10.1093/MOLBEV/MSX094"}
-{"classification": "Metal binding protein", "pdb": "1Q80", "deposition_date": "2003-08-20", "title": "Solution structure and dynamics of nereis sarcoplasmic calcium binding Protein", "Keywords": ["Ll-alpha", " metal binding protein"], "authors": ["G.rabah", "R.popescu", "J.a.cox", "Y.engelborghs", "C.t.craescu"], "pmid": "15819893", "doi": "10.1111/J.1742-4658.2005.04629.X"}
-{"classification": "Transferase", "pdb": "1TW1", "deposition_date": "2004-06-30", "title": "Beta-1,4-galactosyltransferase mutant met344his (m344h-gal-t1) complex With udp-galactose and magnesium", "Keywords": ["Et344his mutation; closed conformation; mn binding", " transferase"], "authors": ["B.ramakrishnan", "E.boeggeman", "P.k.qasba"], "pmid": "15449940", "doi": "10.1021/BI049007+"}
-{"classification": "Rna", "pdb": "2PN4", "deposition_date": "2007-04-23", "title": "Crystal structure of hepatitis c virus ires subdomain iia", "Keywords": ["Cv", " ires", " subdoamin iia", " rna", " strontium", " hepatitis"], "authors": ["Q.zhao", "Q.han", "C.r.kissinger", "P.a.thompson"], "pmid": "18391410", "doi": "10.1107/S0907444908002011"}
+{"pdb": "1CW0", "title": "crystal structure analysis of very short patch repair (vsr) endonuclease in complex with a duplex dna", "authors": ["S.E.Tsutakawa", "H.Jingami", "K.Morikawa"], "doi": "10.1016/S0092-8674(00)81550-0", "pmid": "10612397"}
+{"pdb": "2CWW", "title": "crystal structure of thermus thermophilus ttha1280, a putative sam- dependent rna methyltransferase, in complex with s-adenosyl-l- homocysteine", "authors": ["A.A.Pioszak", "K.Murayama", "N.Nakagawa", "A.Ebihara", "S.Kuramitsu", "M.Shirouzu", "S.Yokoyama", "Riken Structural Genomics/proteomics Initiative (Rsgi)"], "doi": "10.1107/S1744309105029842", "pmid": "16511182"}
+{"pdb": "6CWE", "title": "structure of alpha-gsa[8,6p] bound by cd1d and in complex with the va14vb8.2 tcr", "authors": ["J.Wang", "D.Zajonc"], "doi": null, "pmid": null}
+{"pdb": "5CWS", "title": "crystal structure of the intact chaetomium thermophilum nsp1-nup49- nup57 channel nucleoporin heterotrimer bound to its nic96 nuclear pore complex attachment site", "authors": ["C.J.Bley", "S.Petrovic", "M.Paduch", "V.Lu", "A.A.Kossiakoff", "A.Hoelz"], "doi": "10.1126/SCIENCE.AAC9176", "pmid": "26316600"}
+{"pdb": "5CWE", "title": "structure of cyp107l2 from streptomyces avermitilis with lauric acid", "authors": ["T.-V.Pham", "S.-H.Han", "J.-H.Kim", "D.-H.Kim", "L.-W.Kang"], "doi": null, "pmid": null}
+{"pdb": "7CW4", "title": "acetyl-coa acetyltransferase from bacillus cereus atcc 14579", "authors": ["J.Hong", "K.J.Kim"], "doi": "10.1016/J.BBRC.2020.09.048", "pmid": "32972748"}
+{"pdb": "2CWP", "title": "crystal structure of metrs related protein from pyrococcus horikoshii", "authors": ["K.Murayama", "M.Kato-Murayama", "M.Shirouzu", "S.Yokoyama", "Riken StructuralGenomics/proteomics Initiative (Rsgi)"], "doi": null, "pmid": null}
+{"pdb": "2CW7", "title": "crystal structure of intein homing endonuclease ii", "authors": ["H.Matsumura", "H.Takahashi", "T.Inoue", "H.Hashimoto", "M.Nishioka", "S.Fujiwara", "M.Takagi", "T.Imanaka", "Y.Kai"], "doi": "10.1002/PROT.20858", "pmid": "16493661"}
+{"pdb": "1CWU", "title": "brassica napus enoyl acp reductase a138g mutant complexed with nad+ and thienodiazaborine", "authors": ["A.Roujeinikova", "J.B.Rafferty", "D.W.Rice"], "doi": "10.1074/JBC.274.43.30811", "pmid": "10521472"}
+{"pdb": "3CWN", "title": "escherichia coli transaldolase b mutant f178y", "authors": ["T.Sandalova", "G.Schneider", "A.Samland"], "doi": "10.1074/JBC.M803184200", "pmid": "18687684"}
+{"pdb": "1CWL", "title": "human cyclophilin a complexed with 4 4-hydroxy-meleu cyclosporin", "authors": ["V.Mikol", "J.Kallen", "P.Taylor", "M.D.Walkinshaw"], "doi": "10.1006/JMBI.1998.2108", "pmid": "9769216"}
+{"pdb": "3CW2", "title": "crystal structure of the intact archaeal translation initiation factor 2 from sulfolobus solfataricus .", "authors": ["E.A.Stolboushkina", "S.V.Nikonov", "A.D.Nikulin", "U.Blaesi", "D.J.Manstein", "R.V.Fedorov", "M.B.Garber", "O.S.Nikonov"], "doi": "10.1016/J.JMB.2008.07.039", "pmid": "18675278"}
+{"pdb": "3CW9", "title": "4-chlorobenzoyl-coa ligase/synthetase in the thioester-forming conformation, bound to 4-chlorophenacyl-coa", "authors": ["A.S.Reger", "J.Cao", "R.Wu", "D.Dunaway-Mariano", "A.M.Gulick"], "doi": "10.1021/BI800696Y", "pmid": "18620418"}
+{"pdb": "3CWU", "title": "crystal structure of an alka host/guest complex 2'-fluoro-2'-deoxy-1, n6-ethenoadenine:thymine base pair", "authors": ["B.R.Bowman", "S.Lee", "S.Wang", "G.L.Verdine"], "doi": "10.1016/J.STR.2008.04.012", "pmid": "18682218"}
+{"pdb": "5CWF", "title": "crystal structure of de novo designed helical repeat protein dhr8", "authors": ["G.Bhabha", "D.C.Ekiert"], "doi": "10.1038/NATURE16162", "pmid": "26675729"}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump

@@ -1,36 +1,6 @@
-{"pid": " Q6GZX4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 43"}], "title": "Putative transcription factor 001R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZX3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 45"}], "title": "Uncharacterized protein 002L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197F8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 29"}], "title": "Uncharacterized protein 002R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q197F7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 23"}], "title": "Uncharacterized protein 003L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZX2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 3R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZX1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 38"}], "title": "Uncharacterized protein 004R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197F5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 005L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZX0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 47"}], "title": "Uncharacterized protein 005R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q91G88", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-06-28", "date_info": "entry version 53"}], "title": "Putative KilA-N domain-containing protein 006L", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
-{"pid": " Q6GZW9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 34"}], "title": "Uncharacterized protein 006R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZW8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 32"}], "title": "Uncharacterized protein 007R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197F3", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 007R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q197F2", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 22"}], "title": "Uncharacterized protein 008L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZW6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 67"}], "title": "Putative helicase 009L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q91G85", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 38"}], "title": "Uncharacterized protein 009R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
-{"pid": " Q6GZW5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 010R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197E9", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 011L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZW4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 011R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZW3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 012L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197E7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 37"}], "title": "Uncharacterized protein IIV3-013L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZW2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 30"}], "title": "Uncharacterized protein 013R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZW1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 014R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZW0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 50"}], "title": "Uncharacterized protein 015R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZV8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 017L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZV7", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 018L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZV6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 87"}], "title": "Putative serine/threonine-protein kinase 019R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZV5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 40"}], "title": "Uncharacterized protein 020R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZV4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 021L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197D8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-12-14", "date_info": "entry version 35"}], "title": "Transmembrane protein 022L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZV2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 023R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197D7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 25"}], "title": "Uncharacterized protein 023R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q6GZV1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 024R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q197D5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 24"}], "title": "Uncharacterized protein 025R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]}
-{"pid": " Q91G70", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 026R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]}
-{"pid": " Q6GZU9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 49"}], "title": "Uncharacterized protein 027R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
-{"pid": " Q6GZU8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 55"}], "title": "Uncharacterized protein 028R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]}
+{"pid": "Q6GZX4", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 41."}], "title": "Putative transcription factor 001R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
+{"pid": "Q6GZX3", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 42."}], "title": "Uncharacterized protein 002L;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
+{"pid": "Q197F8", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 27."}], "title": "Uncharacterized protein 002R;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]}
+{"pid": "Q197F7", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 23."}], "title": "Uncharacterized protein 003L;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]}
+{"pid": "Q6GZX2", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 36."}], "title": "Uncharacterized protein 3R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}
+{"pid": "Q6GZX1", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 34."}], "title": "Uncharacterized protein 004R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]}

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala

@@ -2,7 +2,9 @@ package eu.dnetlib.dhp.collection.crossref
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
-import org.junit.jupiter.api.BeforeEach
+import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType
+import org.apache.commons.io.IOUtils
+import org.junit.jupiter.api.{BeforeEach, Test}
 import org.junit.jupiter.api.extension.ExtendWith
 import org.mockito.junit.jupiter.MockitoExtension
 import org.slf4j.{Logger, LoggerFactory}
@@ -18,4 +20,13 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     super.setUpVocabulary()
   }
 
+  @Test
+  def mappingRecord(): Unit = {
+    val input =
+      IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
+
+    println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All))
+
+  }
+
 }

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala

@@ -16,6 +16,7 @@ import org.mockito.junit.jupiter.MockitoExtension
 
 import java.io.{BufferedReader, InputStream, InputStreamReader}
 import java.util.zip.GZIPInputStream
+import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
@@ -49,10 +50,8 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testEBIData() = {
-    val inputXML = Source
-      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-      .mkString
-    val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
     new PMParser(xml).foreach(s => println(mapper.writeValueAsString(s)))
   }
 
@@ -91,9 +90,10 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testParsingPubmedXML(): Unit = {
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     parser.foreach(checkPMArticle)
   }
@@ -156,9 +156,9 @@ class BioScholixTest extends AbstractVocabularyTest {
   @Test
   def testPubmedMapping(): Unit = {
 
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     val results = ListBuffer[Oaf]()
     parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies))

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java

@@ -26,15 +26,15 @@ import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.Software;
 
-public class PrepareSimpleEntitiesJob {
+public class PrepareSimpleEntititiesJob {
 
-	private static final Logger log = LoggerFactory.getLogger(PrepareSimpleEntitiesJob.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareSimpleEntititiesJob.class);
 
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
-					PrepareSimpleEntitiesJob.class
+					PrepareSimpleEntititiesJob.class
 						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
 		parser.parseArgument(args);
 

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java

@@ -160,7 +160,8 @@ public class ConversionUtils {
 			.stream()
 			.filter(Objects::nonNull)
 			.filter(pid -> pid.getQualifier() != null)
-			.filter(pid -> StringUtils.startsWithIgnoreCase(pid.getQualifier().getClassid(), ModelConstants.ORCID))
+			.filter(pid -> pid.getQualifier().getClassid() != null)
+			.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID))
 			.map(StructuredProperty::getValue)
 			.map(ConversionUtils::cleanOrcid)
 			.filter(StringUtils::isNotBlank)

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml

@@ -7,7 +7,7 @@
         </property>
         <property>
             <name>outputDir</name>
-            <description>the path where the generated data will be stored</description>
+            <description>the path where the the generated data will be stored</description>
         </property>
 		<property>
             <name>datasourceIdWhitelist</name>
@@ -179,18 +179,17 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>PrepareSimpleEntititiesJob</name>
-            <class>eu.dnetlib.dhp.broker.oa.PrepareSimpleEntitiesJob</class>
+            <class>eu.dnetlib.dhp.broker.oa.PrepareSimpleEntititiesJob</class>
             <jar>dhp-broker-events-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -210,12 +209,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -236,12 +234,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -261,12 +258,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -286,12 +282,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=10000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -311,12 +306,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=2000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -338,12 +332,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -363,12 +356,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -388,12 +380,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -413,12 +404,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -438,12 +428,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -463,12 +452,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -488,12 +476,11 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=8000
+                --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
             <arg>--outputDir</arg><arg>${outputDir}</arg>
@@ -516,7 +503,6 @@
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} 
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -549,7 +535,6 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -577,7 +562,6 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -601,7 +585,6 @@
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} 
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java

@@ -1,64 +0,0 @@
-package eu.dnetlib.dhp.broker.oa.matchers.simple;
-
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
-
-import java.util.List;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-import eu.dnetlib.broker.objects.OaBrokerAuthor;
-import eu.dnetlib.broker.objects.OaBrokerMainEntity;
-
-class EnrichMissingAuthorOrcidTest {
-
-	final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
-
-	@BeforeEach
-	void setUp() throws Exception {}
-
-	@Test
-	void testFindDifferences_1() {
-		final OaBrokerMainEntity source = new OaBrokerMainEntity();
-		final OaBrokerMainEntity target = new OaBrokerMainEntity();
-		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
-		assertTrue(list.isEmpty());
-	}
-
-	@Test
-	void testFindDifferences_2() {
-		final OaBrokerMainEntity source = new OaBrokerMainEntity();
-		final OaBrokerMainEntity target = new OaBrokerMainEntity();
-
-		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
-		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
-
-		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
-		assertEquals(1, list.size());
-	}
-
-	@Test
-	void testFindDifferences_3() {
-		final OaBrokerMainEntity source = new OaBrokerMainEntity();
-		final OaBrokerMainEntity target = new OaBrokerMainEntity();
-
-		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
-		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
-
-		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
-		assertTrue(list.isEmpty());
-	}
-
-	@Test
-	void testFindDifferences_4() {
-		final OaBrokerMainEntity source = new OaBrokerMainEntity();
-		final OaBrokerMainEntity target = new OaBrokerMainEntity();
-		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
-		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
-
-		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
-		assertTrue(list.isEmpty());
-	}
-
-}

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java

@@ -2,31 +2,27 @@
 package eu.dnetlib.dhp.broker.oa.util;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNull;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
-import eu.dnetlib.broker.objects.OaBrokerMainEntity;
 import eu.dnetlib.broker.objects.OaBrokerTypedValue;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Author;
 import eu.dnetlib.dhp.schema.oaf.Instance;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
-public class ConversionUtilsTest {
+class ConversionUtilsTest {
 
 	@BeforeEach
-	public void setUp() throws Exception {}
+	void setUp() throws Exception {
+	}
 
 	@Test
-	public void testAllResultPids() {
+	void testAllResultPids() {
 		final Qualifier qf = new Qualifier();
 		qf.setClassid("test");
 		qf.setClassname("test");
@@ -95,42 +91,4 @@ public class ConversionUtilsTest {
 		assertEquals(6, list.size());
 	}
 
-	public void testOafResultToBrokerResult() {
-
-		final Author a1 = createAuthor("Michele Artini", "0000-0002-4406-428X");
-		final Author a2 = createAuthor("Claudio Atzori", "http://orcid.org/0000-0001-9613-6639");
-		final Author a3 = createAuthor("Alessia Bardi", null);
-
-		final Result r = new Result();
-		r.setAuthor(Arrays.asList(a1, a2, a3));
-
-		final OaBrokerMainEntity br = ConversionUtils.oafResultToBrokerResult(r);
-
-		assertEquals(3, br.getCreators().size());
-		assertEquals("0000-0002-4406-428X", br.getCreators().get(0).getOrcid());
-		assertEquals("0000-0001-9613-6639", br.getCreators().get(1).getOrcid());
-		assertNull(br.getCreators().get(2).getOrcid());
-	}
-
-	private Author createAuthor(final String name, final String orcid) {
-
-		final Author a = new Author();
-		a.setFullname("Michele Artini");
-
-		if (orcid != null) {
-			final Qualifier q = new Qualifier();
-			q.setClassid(ModelConstants.ORCID);
-			q.setClassname(ModelConstants.ORCID);
-			q.setSchemeid("dnet:pids");
-			q.setSchemename("dnet:pids");
-
-			final StructuredProperty pid = new StructuredProperty();
-			pid.setQualifier(q);
-			pid.setValue(orcid);
-
-			a.setPid(Arrays.asList(pid));
-		}
-		return a;
-	}
-
 }

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

@@ -53,24 +53,10 @@
             <artifactId>dhp-pace-core</artifactId>
             <version>${project.version}</version>
         </dependency>
-
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
         </dependency>
-
-        <dependency>
-            <groupId>org.scala-lang.modules</groupId>
-            <artifactId>scala-java8-compat_${scala.binary.version}</artifactId>
-            <version>1.0.2</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.scala-lang.modules</groupId>
-            <artifactId>scala-collection-compat_${scala.binary.version}</artifactId>
-            <version>2.11.0</version>
-        </dependency>
-
         <dependency>
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-core_${scala.binary.version}</artifactId>
@@ -79,16 +65,10 @@
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-sql_${scala.binary.version}</artifactId>
         </dependency>
-
         <dependency>
             <groupId>org.apache.spark</groupId>
             <artifactId>spark-graphx_${scala.binary.version}</artifactId>
         </dependency>
-
-        <dependency>
-            <groupId>com.arakelian</groupId>
-            <artifactId>java-jq</artifactId>
-        </dependency>
         <dependency>
             <groupId>dom4j</groupId>
             <artifactId>dom4j</artifactId>
@@ -101,10 +81,6 @@
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
         </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>

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

@@ -42,6 +42,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import eu.dnetlib.pace.config.DedupConfig;
+import eu.dnetlib.pace.util.SparkCompatUtils;
 import scala.Tuple3;
 import scala.collection.JavaConversions;
 
@@ -148,8 +149,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			Dataset<Row> pivotHistory = spark
 				.createDataset(
 					Collections.emptyList(),
-					RowEncoder
-						.apply(StructType.fromDDL("id STRING, lastUsage STRING")));
+					SparkCompatUtils.encoderFor(StructType.fromDDL("id STRING, lastUsage STRING")));
 
 			if (StringUtils.isNotBlank(pivotHistoryDatabase)) {
 				pivotHistory = spark

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

@@ -8,7 +8,6 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
-import org.apache.spark.sql.catalyst.encoders.RowEncoder;
 import org.apache.spark.sql.types.StructType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -23,6 +22,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import eu.dnetlib.pace.util.SparkCompatUtils;
 import scala.Tuple2;
 import scala.Tuple3;
 
@@ -145,7 +145,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		StructType idsSchema = StructType
 			.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
 
-		Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
+		Dataset<Row> allIds = spark.emptyDataset(SparkCompatUtils.encoderFor(idsSchema));
 
 		for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
 			String entityPath = graphBasePath + '/' + entityType.name();

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

@@ -15,12 +15,4 @@
         <name>oozie.action.sharelib.for.spark</name>
         <value>spark2</value>
     </property>
-    <property>
-        <name>hiveMetastoreUris</name>
-        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
-    </property>
-    <property>
-        <name>pivotHistoryDatabase</name>
-        <value>&#x200B;</value>
-    </property>
 </configuration>

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

@@ -198,8 +198,6 @@
             <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
             <arg>--actionSetId</arg><arg>${actionSetId}</arg>
             <arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
-            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--pivotHistoryDatabase</arg><arg>${pivotHistoryDatabase}</arg>
         </spark>
         <ok to="PrepareOrgRels"/>
         <error to="Kill"/>

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json

@@ -49,7 +49,7 @@
           },
           {
             "field": "country",
-            "comparator": "countryMatch",
+            "comparator": "exactMatch",
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json

@@ -73,6 +73,12 @@
     "name": "Irish Nephrology Society",
     "synonym": []
   },
+  {
+    "id": "100011062",
+    "uri": "http://dx.doi.org/10.13039/100011062",
+    "name": "Asian Spinal Cord Network",
+    "synonym": []
+  },
   {
     "id": "100011096",
     "uri": "http://dx.doi.org/10.13039/100011096",
@@ -217,6 +223,12 @@
     "name": "Global Brain Health Institute",
     "synonym": []
   },
+  {
+    "id": "100015776",
+    "uri": "http://dx.doi.org/10.13039/100015776",
+    "name": "Health and Social Care Board",
+    "synonym": []
+  },
   {
     "id": "100015992",
     "uri": "http://dx.doi.org/10.13039/100015992",
@@ -391,6 +403,18 @@
     "name": "Irish Hospice Foundation",
     "synonym": []
   },
+  {
+    "id": "501100001596",
+    "uri": "http://dx.doi.org/10.13039/501100001596",
+    "name": "Irish Research Council for Science, Engineering and Technology",
+    "synonym": []
+  },
+  {
+    "id": "501100001597",
+    "uri": "http://dx.doi.org/10.13039/501100001597",
+    "name": "Irish Research Council for the Humanities and Social Sciences",
+    "synonym": []
+  },
   {
     "id": "501100001598",
     "uri": "http://dx.doi.org/10.13039/501100001598",
@@ -491,7 +515,7 @@
     "id": "501100002081",
     "uri": "http://dx.doi.org/10.13039/501100002081",
     "name": "Irish Research Council",
-    "synonym": ["501100001596", "501100001597"]
+    "synonym": []
   },
   {
     "id": "501100002736",

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

@@ -560,15 +560,7 @@ case object Crossref2Oaf {
                 "10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
                 "10.13039/501100013589" | "10.13039/501100000271" =>
               generateSimpleRelationFromAward(funder, "ukri________", a => a)
-            //HFRI
-            case "10.13039/501100013209" =>
-              generateSimpleRelationFromAward(funder, "hfri________", a => a)
-              val targetId = getProjectId("hfri________", "1e5e62235d094afd01cd56e65112fc63")
-              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
-              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
-            //ERASMUS+
-            case "10.13039/501100010790" =>
-              generateSimpleRelationFromAward(funder, "erasmusplus_", a => a)
+
             case _ => logger.debug("no match for " + funder.DOI.get)
 
           }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java

@@ -53,8 +53,6 @@ public class Constraints implements Serializable {
 
 		for (Constraint sc : constraint) {
 			boolean verified = false;
-			if (!param.containsKey(sc.getField()))
-				return false;
 			for (String value : param.get(sc.getField())) {
 				if (sc.verifyCriteria(value.trim())) {
 					verified = true;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java

@@ -14,7 +14,6 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
@@ -85,12 +84,11 @@ public class SparkCountryPropagationJob {
 		Dataset<R> res = readPath(spark, sourcePath, resultClazz);
 
 		log.info("Reading prepared info: {}", preparedInfoPath);
-		final Dataset<Row> preparedInfoRaw = spark
+		Dataset<ResultCountrySet> prepared = spark
 			.read()
-			.json(preparedInfoPath);
+			.json(preparedInfoPath)
+			.as(Encoders.bean(ResultCountrySet.class));
 
-		if (!preparedInfoRaw.isEmpty()) {
-			final Dataset<ResultCountrySet> prepared = preparedInfoRaw.as(Encoders.bean(ResultCountrySet.class));
 		res
 			.joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer")
 			.map(getCountryMergeFn(), Encoders.bean(resultClazz))
@@ -98,13 +96,7 @@ public class SparkCountryPropagationJob {
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
 			.json(outputPath);
-		} else {
-			res
-				.write()
-				.option("compression", "gzip")
-				.mode(SaveMode.Overwrite)
-				.json(outputPath);
-		}
+
 	}
 
 	private static <R extends Result> MapFunction<Tuple2<R, ResultCountrySet>, R> getCountryMergeFn() {

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

@@ -147,7 +147,6 @@ public class CleanGraphSparkJob {
 			.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
 			.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
-			.map((MapFunction<T, T>) GraphCleaningFunctions::dedicatedUglyHacks, Encoders.bean(clazz))
 			.filter((FilterFunction<T>) GraphCleaningFunctions::filter);
 
 		// read the master-duplicate tuples

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

@@ -223,13 +223,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
-                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
@@ -255,13 +253,11 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
-                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--outputPath</arg><arg>${outputPath}/publication</arg>
             <arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
@@ -282,7 +278,6 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql

@@ -25,8 +25,7 @@ SELECT
 		o.country || '@@@dnet:countries'                          AS country,
 		array[]::text[]                                           AS alternativenames,
 		'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction,
-		 array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid,
-        'Unknown'                                                 AS typology
+		 array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid
 FROM dsm_organizations o
 	LEFT OUTER JOIN dsm_services d ON (d.id = o.collectedfrom)
 	LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id)

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/create_scholix_dump_params.json

@@ -0,0 +1,5 @@
+[
+  {"paramName":"mt",  "paramLongName":"master",     "paramDescription": "should be local or yarn",  "paramRequired": false},
+  {"paramName":"s",   "paramLongName":"sourcePath", "paramDescription": "the source Path",           "paramRequired": true},
+  {"paramName":"t",   "paramLongName":"targetPath", "paramDescription": "the path of the scholix dump", "paramRequired": true}
+]

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/relation/relations.json

@@ -0,0 +1,166 @@
+{
+  "cites":{
+    "original":"Cites",
+    "inverse":"IsCitedBy"
+  },
+  "compiles":{
+    "original":"Compiles",
+    "inverse":"IsCompiledBy"
+  },
+  "continues":{
+    "original":"Continues",
+    "inverse":"IsContinuedBy"
+  },
+  "derives":{
+    "original":"IsSourceOf",
+    "inverse":"IsDerivedFrom"
+  },
+  "describes":{
+    "original":"Describes",
+    "inverse":"IsDescribedBy"
+  },
+  "documents":{
+    "original":"Documents",
+    "inverse":"IsDocumentedBy"
+  },
+  "hasmetadata":{
+    "original":"HasMetadata",
+    "inverse":"IsMetadataOf"
+  },
+  "hasassociationwith":{
+    "original":"HasAssociationWith",
+    "inverse":"HasAssociationWith"
+  },
+  "haspart":{
+    "original":"HasPart",
+    "inverse":"IsPartOf"
+  },
+  "hasversion":{
+    "original":"HasVersion",
+    "inverse":"IsVersionOf"
+  },
+  "iscitedby":{
+    "original":"IsCitedBy",
+    "inverse":"Cites"
+  },
+  "iscompiledby":{
+    "original":"IsCompiledBy",
+    "inverse":"Compiles"
+  },
+  "iscontinuedby":{
+    "original":"IsContinuedBy",
+    "inverse":"Continues"
+  },
+  "isderivedfrom":{
+    "original":"IsDerivedFrom",
+    "inverse":"IsSourceOf"
+  },
+  "isdescribedby":{
+    "original":"IsDescribedBy",
+    "inverse":"Describes"
+  },
+  "isdocumentedby":{
+    "original":"IsDocumentedBy",
+    "inverse":"Documents"
+  },
+  "isidenticalto":{
+    "original":"IsIdenticalTo",
+    "inverse":"IsIdenticalTo"
+  },
+  "ismetadatafor":{
+    "original":"IsMetadataFor",
+    "inverse":"IsMetadataOf"
+  },
+  "ismetadataof":{
+    "original":"IsMetadataOf",
+    "inverse":"IsMetadataFor"
+  },
+  "isnewversionof":{
+    "original":"IsNewVersionOf",
+    "inverse":"IsPreviousVersionOf"
+  },
+  "isobsoletedby":{
+    "original":"IsObsoletedBy",
+    "inverse":"Obsoletes"
+  },
+  "isoriginalformof":{
+    "original":"IsOriginalFormOf",
+    "inverse":"IsVariantFormOf"
+  },
+  "ispartof":{
+    "original":"IsPartOf",
+    "inverse":"HasPart"
+  },
+  "ispreviousversionof":{
+    "original":"IsPreviousVersionOf",
+    "inverse":"IsNewVersionOf"
+  },
+  "isreferencedby":{
+    "original":"IsReferencedBy",
+    "inverse":"References"
+  },
+  "isrelatedto":{
+    "original":"IsRelatedTo",
+    "inverse":"IsRelatedTo"
+  },
+  "isrequiredby":{
+    "original":"IsRequiredBy",
+    "inverse":"Requires"
+  },
+  "isreviewedby":{
+    "original":"IsReviewedBy",
+    "inverse":"Reviews"
+  },
+  "issourceof":{
+    "original":"IsSourceOf",
+    "inverse":"IsDerivedFrom"
+  },
+  "issupplementedby":{
+    "original":"IsSupplementedBy",
+    "inverse":"IsSupplementTo"
+  },
+  "issupplementto":{
+    "original":"IsSupplementTo",
+    "inverse":"IsSupplementedBy"
+  },
+  "isvariantformof":{
+    "original":"IsVariantFormOf",
+    "inverse":"IsOriginalFormOf"
+  },
+  "isversionof":{
+    "original":"IsVersionOf",
+    "inverse":"HasVersion"
+  },
+  "obsoletes":{
+    "original":"Obsoletes",
+    "inverse":"IsObsoletedBy"
+  },
+  "references":{
+    "original":"References",
+    "inverse":"IsReferencedBy"
+  },
+  "requires":{
+    "original":"Requires",
+    "inverse":"IsRequiredBy"
+  },
+  "related":{
+    "original":"IsRelatedTo",
+    "inverse":"IsRelatedTo"
+  },
+  "reviews":{
+    "original":"Reviews",
+    "inverse":"IsReviewedBy"
+  },
+  "unknown":{
+    "original":"Unknown",
+    "inverse":"Unknown"
+  },
+  "isamongtopnsimilardocuments": {
+    "original": "IsAmongTopNSimilarDocuments",
+    "inverse": "HasAmongTopNSimilarDocuments"
+  },
+  "hasamongtopnsimilardocuments": {
+    "original": "HasAmongTopNSimilarDocuments",
+    "inverse": "IsAmongTopNSimilarDocuments"
+  }
+}

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/ScholexplorerUtils.scala

@@ -0,0 +1,258 @@
+package eu.dnetlib.dhp.sx.graph
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import eu.dnetlib.dhp.schema.oaf.{KeyValue, Result, StructuredProperty}
+import eu.dnetlib.dhp.schema.sx.scholix.{
+  Scholix,
+  ScholixCollectedFrom,
+  ScholixEntityId,
+  ScholixIdentifier,
+  ScholixRelationship,
+  ScholixResource
+}
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.jackson.JsonMethods.parse
+
+import scala.collection.JavaConverters._
+import scala.io.Source
+
+case class RelationInfo(
+  source: String,
+  target: String,
+  relclass: String,
+  id: String,
+  collectedfrom: Seq[RelKeyValue]
+) {}
+case class RelKeyValue(key: String, value: String) {}
+
+object ScholexplorerUtils {
+
+  val OPENAIRE_IDENTIFIER_SCHEMA: String = "OpenAIRE Identifier"
+  val mapper = new ObjectMapper()
+
+  case class RelationVocabulary(original: String, inverse: String) {}
+
+  val relations: Map[String, RelationVocabulary] = {
+    val input = Source
+      .fromInputStream(
+        getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/relation/relations.json")
+      )
+      .mkString
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+
+    lazy val json: json4s.JValue = parse(input)
+
+    json.extract[Map[String, RelationVocabulary]]
+  }
+
+  def invRel(rel: String): String = {
+    val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
+    if (semanticRelation != null)
+      semanticRelation.inverse
+    else
+      null
+  }
+
+  def generateDatasourceOpenAIREURLS(id: String): String = {
+    if (id != null && id.length > 12)
+      s"https://explore.openaire.eu/search/dataprovider?datasourceId=${id.substring(3)}"
+    else
+      null
+  }
+
+  def findURLForPID(
+    pidValue: List[StructuredProperty],
+    urls: List[String]
+  ): List[(StructuredProperty, String)] = {
+    pidValue.map { p =>
+      val pv = p.getValue
+
+      val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
+      (p, r.orNull)
+    }
+  }
+
+  def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
+    if (r.getInstance() == null || r.getInstance().isEmpty)
+      return List()
+    r.getInstance()
+      .asScala
+      .filter(i => i.getUrl != null && !i.getUrl.isEmpty)
+      .filter(i => i.getPid != null && i.getUrl != null)
+      .flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
+      .map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2))
+      .distinct
+      .toList
+  }
+
+  def generateScholixResourceFromResult(result: Result): ScholixResource = {
+
+    if (result.getInstance() == null || result.getInstance().size() == 0)
+      return null
+
+    if (result.getPid == null || result.getPid.isEmpty)
+      return null
+
+    val r = new ScholixResource
+    r.setDnetIdentifier(result.getId)
+
+    val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(result)
+    if (persistentIdentifiers.isEmpty)
+      return null
+
+    r.setIdentifier(persistentIdentifiers.asJava)
+
+    r.setObjectType(result.getResulttype.getClassid)
+
+    r.setObjectSubType(
+      result
+        .getInstance()
+        .asScala
+        .filter(i => i != null && i.getInstancetype != null)
+        .map(i => i.getInstancetype.getClassname)
+        .distinct
+        .head
+    )
+
+    if (result.getTitle != null && result.getTitle.asScala.nonEmpty) {
+      val titles: List[String] = result.getTitle.asScala.map(t => t.getValue).toList
+      if (titles.nonEmpty)
+        r.setTitle(titles.head)
+      else
+        return null
+    }
+    if (result.getAuthor != null && !result.getAuthor.isEmpty) {
+      val authors: List[ScholixEntityId] =
+        result.getAuthor.asScala
+          .map(a => {
+            val entity = new ScholixEntityId()
+            entity.setName(a.getFullname)
+            if (a.getPid != null && a.getPid.size() > 0)
+              entity.setIdentifiers(
+                a.getPid.asScala
+                  .map(sp => {
+                    val id = new ScholixIdentifier()
+                    id.setIdentifier(sp.getValue)
+                    id.setSchema(sp.getQualifier.getClassid)
+                    id
+                  })
+                  .take(3)
+                  .toList
+                  .asJava
+              )
+            entity
+          })
+          .toList
+      if (authors.nonEmpty)
+        r.setCreator(authors.asJava)
+
+    }
+
+    val dt: List[String] = result
+      .getInstance()
+      .asScala
+      .filter(i => i.getDateofacceptance != null)
+      .map(i => i.getDateofacceptance.getValue)
+      .toList
+    if (dt.nonEmpty)
+      r.setPublicationDate(dt.distinct.head)
+
+    r.setPublisher(
+      result
+        .getInstance()
+        .asScala
+        .map(i => i.getHostedby)
+        .filter(h => !"unknown".equalsIgnoreCase(h.getValue))
+        .map(h => {
+          val eid = new ScholixEntityId()
+          eid.setName(h.getValue)
+          val id = new ScholixIdentifier()
+          id.setIdentifier(h.getKey)
+          id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+          id.setUrl(generateDatasourceOpenAIREURLS(h.getKey))
+          eid.setIdentifiers(List(id).asJava)
+          eid
+        })
+        .distinct
+        .asJava
+    )
+
+    r.setCollectedFrom(
+      result.getCollectedfrom.asScala
+        .map(cf => {
+          val scf = new ScholixCollectedFrom()
+          scf.setProvisionMode("collected")
+          scf.setCompletionStatus("complete")
+          val eid = new ScholixEntityId()
+          eid.setName(cf.getValue)
+          val id = new ScholixIdentifier()
+          id.setIdentifier(cf.getKey)
+          id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+          id.setUrl(generateDatasourceOpenAIREURLS(cf.getKey))
+          eid.setIdentifiers(List(id).asJava)
+          scf.setProvider(eid)
+          scf
+        })
+        .asJava
+    )
+
+    r
+  }
+
+  def generateScholix(relation: RelationInfo, source: ScholixResource): Scholix = {
+    val s: Scholix = new Scholix
+    s.setSource(source)
+    if (relation.collectedfrom != null && relation.collectedfrom.nonEmpty)
+      s.setLinkprovider(
+        relation.collectedfrom
+          .map(cf => {
+            val eid = new ScholixEntityId()
+            eid.setName(cf.value)
+            val id = new ScholixIdentifier()
+            id.setIdentifier(cf.key)
+            id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+            id.setUrl(generateDatasourceOpenAIREURLS(cf.key))
+            eid.setIdentifiers(List(id).asJava)
+            eid
+          })
+          .toList
+          .asJava
+      )
+    else {
+      val eid = new ScholixEntityId()
+      eid.setName("OpenAIRE")
+      val id = new ScholixIdentifier()
+      id.setIdentifier("10|infrastruct_::f66f1bd369679b5b077dcdf006089556")
+      id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
+      id.setUrl(generateDatasourceOpenAIREURLS(id.getIdentifier))
+      eid.setIdentifiers(List(id).asJava)
+      s.setLinkprovider(List(eid).asJava)
+    }
+    s.setIdentifier(relation.id)
+    val semanticRelation = relations.getOrElse(relation.relclass.toLowerCase, null)
+    if (semanticRelation == null)
+      return null
+    s.setRelationship(
+      new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
+    )
+    s.setPublicationDate(source.getPublicationDate)
+    s.setPublisher(source.getPublisher)
+    val mockTarget = new ScholixResource
+    mockTarget.setDnetIdentifier(relation.target)
+    s.setTarget(mockTarget)
+    s
+  }
+
+  def updateTarget(s: Scholix, t: ScholixResource): String = {
+
+    s.setTarget(t)
+    val spublishers: Seq[ScholixEntityId] =
+      if (s.getPublisher != null && !s.getPublisher.isEmpty) s.getPublisher.asScala else List()
+    val tpublishers: Seq[ScholixEntityId] =
+      if (t.getPublisher != null && !t.getPublisher.isEmpty) t.getPublisher.asScala else List()
+    val mergedPublishers = spublishers.union(tpublishers).distinct.take(10).toList
+    s.setPublisher(mergedPublishers.asJava)
+    mapper.writeValueAsString(s)
+  }
+}

dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateScholexplorerDump.scala

@@ -0,0 +1,141 @@
+package eu.dnetlib.dhp.sx.graph
+
+import eu.dnetlib.dhp.application.AbstractScalaApplication
+import eu.dnetlib.dhp.schema.oaf.{
+  KeyValue,
+  OtherResearchProduct,
+  Publication,
+  Relation,
+  Result,
+  Software,
+  Dataset => OafDataset
+}
+import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
+import org.apache.spark.sql.functions.{col, concat, expr, first, md5}
+import org.apache.spark.sql.types.StructType
+import org.apache.spark.sql._
+import org.slf4j.{Logger, LoggerFactory}
+
+class SparkCreateScholexplorerDump(propertyPath: String, args: Array[String], log: Logger)
+    extends AbstractScalaApplication(propertyPath, args, log: Logger) {
+
+  /** Here all the spark applications runs this method
+    * where the whole logic of the spark node is defined
+    */
+  override def run(): Unit = {
+    val sourcePath = parser.get("sourcePath")
+    log.info("sourcePath: {}", sourcePath)
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
+    generateBidirectionalRelations(sourcePath, targetPath, spark)
+    generateScholixResource(sourcePath, targetPath, spark)
+    generateScholix(targetPath, spark)
+  }
+
+  def generateScholixResource(inputPath: String, outputPath: String, spark: SparkSession): Unit = {
+    val entityMap: Map[String, StructType] = Map(
+      "publication"          -> Encoders.bean(classOf[Publication]).schema,
+      "dataset"              -> Encoders.bean(classOf[OafDataset]).schema,
+      "software"             -> Encoders.bean(classOf[Software]).schema,
+      "otherresearchproduct" -> Encoders.bean(classOf[OtherResearchProduct]).schema
+    )
+
+    implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
+    implicit val resultEncoder: Encoder[Result] = Encoders.bean(classOf[Result])
+
+    val resDs = spark.emptyDataset[ScholixResource]
+    val scholixResourceDS = entityMap.foldLeft[Dataset[ScholixResource]](resDs)((res, item) => {
+      println(s"adding ${item._1}")
+      res.union(
+        spark.read
+          .schema(item._2)
+          .json(s"$inputPath/${item._1}")
+          .as[Result]
+          .map(r => ScholexplorerUtils.generateScholixResourceFromResult(r))
+          .filter(s => s != null)
+      )
+    })
+    scholixResourceDS.write.mode(SaveMode.Overwrite).save(s"$outputPath/resource")
+  }
+
+  def generateBidirectionalRelations(inputPath: String, otuputPath: String, spark: SparkSession): Unit = {
+    val relSchema = Encoders.bean(classOf[Relation]).schema
+
+    val relDF = spark.read
+      .schema(relSchema)
+      .json(s"$inputPath/relation")
+      .where(
+        "datainfo.deletedbyinference is false and source like '50%' and target like '50%' " +
+        "and relClass <> 'merges' and relClass <> 'isMergedIn'"
+      )
+      .select("source", "target", "collectedfrom", "relClass")
+
+    def invRel: String => String = { s =>
+      ScholexplorerUtils.invRel(s)
+    }
+
+    import org.apache.spark.sql.functions.udf
+    val inverseRelationUDF = udf(invRel)
+    val inverseRelation = relDF.select(
+      col("target").alias("source"),
+      col("source").alias("target"),
+      col("collectedfrom"),
+      inverseRelationUDF(col("relClass")).alias("relClass")
+    )
+
+    val bidRel = inverseRelation
+      .union(relDF)
+      .withColumn("id", md5(concat(col("source"), col("relClass"), col("target"))))
+      .withColumn("cf", expr("transform(collectedfrom, x -> struct(x.key, x.value))"))
+      .drop("collectedfrom")
+      .withColumnRenamed("cf", "collectedfrom")
+      .groupBy(col("id"))
+      .agg(
+        first("source").alias("source"),
+        first("target").alias("target"),
+        first("relClass").alias("relClass"),
+        first("collectedfrom").alias("collectedfrom")
+      )
+
+    bidRel.write.mode(SaveMode.Overwrite).save(s"$otuputPath/relation")
+
+  }
+
+  def generateScholix(outputPath: String, spark: SparkSession): Unit = {
+    implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
+    implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo(classOf[Scholix])
+
+    import spark.implicits._
+    val relations = spark.read.load(s"$outputPath/relation").as[RelationInfo]
+    val resource = spark.read.load(s"$outputPath/resource").as[ScholixResource]
+
+    val scholix_one_verse = relations
+      .joinWith(resource, relations("source") === resource("dnetIdentifier"), "inner")
+      .map(res => ScholexplorerUtils.generateScholix(res._1, res._2))
+      .map(s => (s.getIdentifier, s))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[Scholix])))
+
+    val resourceTarget = relations
+      .joinWith(resource, relations("target") === resource("dnetIdentifier"), "inner")
+      .map(res => (res._1.id, res._2))(Encoders.tuple(Encoders.STRING, Encoders.kryo(classOf[ScholixResource])))
+
+    scholix_one_verse
+      .joinWith(resourceTarget, scholix_one_verse("_1") === resourceTarget("_1"), "inner")
+      .map(k => ScholexplorerUtils.updateTarget(k._1._2, k._2._2))
+      .write
+      .mode(SaveMode.Overwrite)
+      .option("compression", "gzip")
+      .text(s"$outputPath/scholix")
+  }
+}
+
+object SparkCreateScholexplorerDump {
+  val logger: Logger = LoggerFactory.getLogger(SparkCreateScholexplorerDump.getClass)
+
+  def main(args: Array[String]): Unit = {
+    new SparkCreateScholexplorerDump(
+      log = logger,
+      args = args,
+      propertyPath = "/eu/dnetlib/dhp/sx/create_scholix_dump_params.json"
+    ).initialize().run()
+  }
+}

dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala

@@ -0,0 +1,26 @@
+package eu.dnetlib.dhp.sx.graph.scholix
+
+import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource
+import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
+import org.junit.jupiter.api.Test
+import org.objenesis.strategy.StdInstantiatorStrategy
+
+class ScholixGenerationTest {
+
+  @Test
+  def generateScholix(): Unit = {
+
+    val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()
+    val app = new SparkCreateScholexplorerDump(null, null, null)
+//   app.generateScholixResource("/home/sandro/Downloads/scholix_sample/", "/home/sandro/Downloads/scholix/", spark)
+//    app.generateBidirectionalRelations(
+//      "/home/sandro/Downloads/scholix_sample/",
+//      "/home/sandro/Downloads/scholix/",
+//      spark
+//    )
+    app.generateScholix("/home/sandro/Downloads/scholix/", spark)
+
+  }
+}

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

@@ -128,14 +128,12 @@ public class SolrAdminApplication implements Closeable {
 
 	public SolrResponse deleteAlias(String aliasName) throws SolrServerException, IOException {
 		CollectionAdminRequest.DeleteAlias deleteAliasRequest = CollectionAdminRequest.deleteAlias(aliasName);
-		log.info("deleting alias: {}", aliasName);
 		return deleteAliasRequest.process(solrClient);
 	}
 
 	public SolrResponse createAlias(String aliasName, String collection) throws IOException, SolrServerException {
 		CollectionAdminRequest.CreateAlias createAliasRequest = CollectionAdminRequest
 			.createAlias(aliasName, collection);
-		log.info("creating alias: {} for collection: {}", aliasName, collection);
 		return createAliasRequest.process(solrClient);
 	}
 

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

@@ -30,6 +30,7 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -375,7 +376,7 @@ public class ProvisionModelSupport {
 		rs.setIsInDiamondJournal(r.getIsInDiamondJournal());
 		rs.setPubliclyFunded(r.getPubliclyFunded());
 		rs.setTransformativeAgreement(r.getTransformativeAgreement());
-
+		rs.setExternalReference(mapExternalReference(r.getExternalReference()));
 		rs.setInstance(mapInstances(r.getInstance()));
 
 		if (r instanceof Publication) {
@@ -561,6 +562,27 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
+	private static List<ExternalReference> mapExternalReference(
+		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional
+			.ofNullable(externalReference)
+			.map(
+				ext -> ext
+					.stream()
+					.map(
+						e -> ExternalReference
+							.newInstance(
+								e.getSitename(),
+								e.getLabel(),
+								e.getAlternateLabel(),
+								e.getUrl(),
+								mapCodeLabel(e.getQualifier()),
+								e.getRefidentifier(),
+								e.getQuery()))
+					.collect(Collectors.toList()))
+			.orElse(Lists.newArrayList());
+	}
+
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
 		ContextMapper contextMapper) {
 
@@ -579,7 +601,7 @@ public class ProvisionModelSupport {
 		}
 
 		return Optional
-			.ofNullable(contexts)
+			.of(contexts)
 			.map(
 				ctx -> ctx
 					.stream()

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

@@ -213,7 +213,7 @@ public class StreamingInputDocumentFactory implements Serializable {
 			}
 			writer.close();
 			indexDocument.addField(INDEX_RESULT, results.toString());
-			// indexDocument.addField(INDEX_JSON_RESULT, json);
+			indexDocument.addField(INDEX_JSON_RESULT, json);
 		} finally {
 			outputFactory.remove();
 			eventFactory.remove();

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

@@ -69,7 +69,7 @@
         </configuration>
     </global>
 
-    <start to="irish_oaiphm_provision"/>
+    <start to="oaiphm_provision"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>

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

@@ -67,7 +67,7 @@ public class PrepareRelationsJobTest {
 	@Test
 	void testRunPrepareRelationsJob(@TempDir Path testPath) throws Exception {
 
-		final int maxRelations = 5;
+		final int maxRelations = 20;
 		PrepareRelationsJob
 			.main(
 				new String[] {
@@ -86,7 +86,7 @@ public class PrepareRelationsJobTest {
 			.as(Encoders.bean(Relation.class))
 			.cache();
 
-		assertEquals(44, out.count());
+		assertEquals(maxRelations, out.count());
 
 		Dataset<Row> freq = out
 			.toDF()
@@ -101,8 +101,12 @@ public class PrepareRelationsJobTest {
 		long affiliation = getRows(freq, AFFILIATION).get(0).getAs("count");
 
 		assertEquals(outcome, participation);
-		assertEquals(outcome, affiliation);
-		assertEquals(4, affiliation);
+		assertTrue(outcome > affiliation);
+		assertTrue(participation > affiliation);
+
+		assertEquals(7, outcome);
+		assertEquals(7, participation);
+		assertEquals(6, affiliation);
 	}
 
 	protected List<Row> getRows(Dataset<Row> freq, String col) {