WIP: updated provision workflow to create a JSON based representation of the payload

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

@@ -0,0 +1,52 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.oa.provision;
+
+import java.io.StringReader;
+import java.io.StringWriter;
+
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.transform.stream.StreamSource;
+
+import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
+
+public abstract class AbstractSolrRecordTransformJob {
+
+	protected static String toIndexRecord(Transformer tr, final String xmlRecord) {
+		final StreamResult res = new StreamResult(new StringWriter());
+		try {
+			tr.transform(new StreamSource(new StringReader(xmlRecord)), res);
+			return res.getWriter().toString();
+		} catch (TransformerException e) {
+			throw new IllegalArgumentException("XPathException on record: \n" + xmlRecord, e);
+		}
+	}
+
+	/**
+	 * Creates the XSLT responsible for building the index xml records.
+	 *
+	 * @param format Metadata format name (DMF|TMF)
+	 * @param xslt xslt for building the index record transformer
+	 * @param fields the list of fields
+	 * @return the javax.xml.transform.Transformer
+	 * @throws TransformerException could happen
+	 */
+	protected static String getLayoutTransformer(String format, String fields, String xslt)
+		throws TransformerException {
+
+		final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt);
+		final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter());
+
+		layoutTransformer.setParameter("format", format);
+		layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt);
+
+		return layoutToXsltXslt.getWriter().toString();
+	}
+
+}

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

@@ -62,16 +62,8 @@ public class SolrAdminApplication implements Closeable {
 		final String collection = ProvisionConstants.getCollectionName(format);
 		log.info("collection: {}", collection);
 
-		final boolean shouldIndex = Optional
-			.ofNullable(parser.get("shouldIndex"))
-			.map(Boolean::valueOf)
-			.orElse(false);
-		log.info("shouldIndex: {}", shouldIndex);
-
-		if (shouldIndex) {
-			try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) {
-				app.execute(action, collection, query, commit);
-			}
+		try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) {
+			app.execute(action, collection, query, commit);
 		}
 	}
 

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

@@ -0,0 +1,144 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.util.Optional;
+
+import javax.xml.transform.TransformerException;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.solr.common.SolrInputDocument;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoder;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+
+public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
+
+	private static final Logger log = LoggerFactory.getLogger(SolrRecordDumpJob.class);
+
+	private static final Integer DEFAULT_BATCH_SIZE = 1000;
+
+	private final String inputPath;
+
+	private final String format;
+
+	private final String outputPath;
+
+	private final SparkSession spark;
+
+	public static void main(String[] args) throws Exception {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SolrRecordDumpJob.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json")));
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath: {}", inputPath);
+
+		final String format = parser.get("format");
+		log.info("format: {}", format);
+
+		final String outputPath = Optional
+			.ofNullable(parser.get("outputPath"))
+			.map(StringUtils::trim)
+			.orElse(null);
+		log.info("outputPath: {}", outputPath);
+
+		final Integer batchSize = Optional
+			.ofNullable(parser.get("batchSize"))
+			.map(Integer::valueOf)
+			.orElse(DEFAULT_BATCH_SIZE);
+		log.info("batchSize: {}", batchSize);
+
+		final boolean shouldIndex = Optional
+			.ofNullable(parser.get("shouldIndex"))
+			.map(Boolean::valueOf)
+			.orElse(false);
+		log.info("shouldIndex: {}", shouldIndex);
+
+		final SparkConf conf = new SparkConf();
+
+		conf.registerKryoClasses(new Class[] {
+			SerializableSolrInputDocument.class
+		});
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				final String isLookupUrl = parser.get("isLookupUrl");
+				log.info("isLookupUrl: {}", isLookupUrl);
+				final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
+				new SolrRecordDumpJob(spark, inputPath, format, outputPath).run(isLookup);
+			});
+	}
+
+	public SolrRecordDumpJob(SparkSession spark, String inputPath, String format, String outputPath) {
+		this.spark = spark;
+		this.inputPath = inputPath;
+		this.format = format;
+		this.outputPath = outputPath;
+	}
+
+	public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
+		final String fields = isLookup.getLayoutSource(format);
+		log.info("fields: {}", fields);
+
+		final String xslt = isLookup.getLayoutTransformer();
+
+		final String dsId = isLookup.getDsId(format);
+		log.info("dsId: {}", dsId);
+
+		final String indexRecordXslt = getLayoutTransformer(format, fields, xslt);
+		log.info("indexRecordTransformer {}", indexRecordXslt);
+
+		final Encoder<TupleWrapper> encoder = Encoders.bean(TupleWrapper.class);
+		spark
+			.read()
+			.schema(encoder.schema())
+			.json(inputPath)
+			.as(encoder)
+			.map(
+				(MapFunction<TupleWrapper, TupleWrapper>) t -> new TupleWrapper(
+					toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()),
+					t.getJson()),
+				Encoders.bean(TupleWrapper.class))
+			.map(
+				(MapFunction<TupleWrapper, SerializableSolrInputDocument>) t -> {
+					SolrInputDocument s = new StreamingInputDocumentFactory()
+						.parseDocument(t.getXml(), t.getJson());
+					return new SerializableSolrInputDocument(s);
+				},
+				Encoders.kryo(SerializableSolrInputDocument.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.parquet(outputPath);
+	}
+
+}

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

@@ -3,26 +3,18 @@ package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.text.SimpleDateFormat;
-import java.util.Date;
 import java.util.Optional;
 
-import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerException;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.hadoop.io.Text;
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.*;
+import org.apache.spark.sql.Encoder;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,32 +28,19 @@ import eu.dnetlib.dhp.oa.provision.utils.StreamingInputDocumentFactory;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import scala.Tuple2;
 
-public class XmlIndexingJob {
+public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 
 	private static final Logger log = LoggerFactory.getLogger(XmlIndexingJob.class);
 
-	public enum OutputFormat {
-		SOLR, HDFS
-	}
-
 	private static final Integer DEFAULT_BATCH_SIZE = 1000;
 
-	protected static final String DATE_FORMAT = "yyyy-MM-dd'T'hh:mm:ss'Z'";
-
 	private final String inputPath;
 
 	private final String format;
 
 	private final int batchSize;
 
-	private final OutputFormat outputFormat;
-
-	private final String outputPath;
-
-	private boolean shouldIndex;
-
 	private final SparkSession spark;
 
 	public static void main(String[] args) throws Exception {
@@ -86,30 +65,12 @@ public class XmlIndexingJob {
 		final String format = parser.get("format");
 		log.info("format: {}", format);
 
-		final String outputPath = Optional
-			.ofNullable(parser.get("outputPath"))
-			.map(StringUtils::trim)
-			.orElse(null);
-		log.info("outputPath: {}", outputPath);
-
 		final Integer batchSize = Optional
 			.ofNullable(parser.get("batchSize"))
 			.map(Integer::valueOf)
 			.orElse(DEFAULT_BATCH_SIZE);
 		log.info("batchSize: {}", batchSize);
 
-		final OutputFormat outputFormat = Optional
-			.ofNullable(parser.get("outputFormat"))
-			.map(OutputFormat::valueOf)
-			.orElse(OutputFormat.SOLR);
-		log.info("outputFormat: {}", outputFormat);
-
-		final boolean shouldIndex = Optional
-			.ofNullable(parser.get("shouldIndex"))
-			.map(Boolean::valueOf)
-			.orElse(false);
-		log.info("shouldIndex: {}", shouldIndex);
-
 		final SparkConf conf = new SparkConf();
 
 		conf.registerKryoClasses(new Class[] {
@@ -123,20 +84,16 @@ public class XmlIndexingJob {
 				final String isLookupUrl = parser.get("isLookupUrl");
 				log.info("isLookupUrl: {}", isLookupUrl);
 				final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
-				new XmlIndexingJob(spark, inputPath, format, batchSize, outputFormat, shouldIndex, outputPath)
+				new XmlIndexingJob(spark, inputPath, format, batchSize)
 					.run(isLookup);
 			});
 	}
 
-	public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize,
-		OutputFormat outputFormat, boolean shouldIndex, String outputPath) {
+	public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize) {
 		this.spark = spark;
 		this.inputPath = inputPath;
 		this.format = format;
 		this.batchSize = batchSize;
-		this.outputFormat = outputFormat;
-		this.shouldIndex = shouldIndex;
-		this.outputPath = outputPath;
 	}
 
 	public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
@@ -148,6 +105,9 @@ public class XmlIndexingJob {
 		final String dsId = isLookup.getDsId(format);
 		log.info("dsId: {}", dsId);
 
+		final String collection = ProvisionConstants.getCollectionName(format);
+		log.info("collection: {}", collection);
+
 		final String zkHost = isLookup.getZkHost();
 		log.info("zkHost: {}", zkHost);
 
@@ -155,7 +115,8 @@ public class XmlIndexingJob {
 		log.info("indexRecordTransformer {}", indexRecordXslt);
 
 		final Encoder<TupleWrapper> encoder = Encoders.bean(TupleWrapper.class);
-		final Dataset<TupleWrapper> records = spark
+
+		JavaRDD<SolrInputDocument> docs = spark
 			.read()
 			.schema(encoder.schema())
 			.json(inputPath)
@@ -164,80 +125,11 @@ public class XmlIndexingJob {
 				(MapFunction<TupleWrapper, TupleWrapper>) t -> new TupleWrapper(
 					toIndexRecord(SaxonTransformerFactory.newInstance(indexRecordXslt), t.getXml()),
 					t.getJson()),
-				Encoders.bean(TupleWrapper.class));
-
-		switch (outputFormat) {
-			case SOLR:
-				if (shouldIndex) {
-					final String collection = ProvisionConstants.getCollectionName(format);
-
-					// SparkSolr >= 4
-					// com.lucidworks.spark.BatchSizeType bt = com.lucidworks.spark.BatchSizeType.NUM_DOCS;
-					// SolrSupport.indexDocs(zkHost, collection, batchSize, bt, docs.rdd());
-					// SparkSolr < 4
-					JavaRDD<SolrInputDocument> docs = records
-						.javaRDD()
-						.map(
-							t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
-					SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
-				}
-				break;
-			case HDFS:
-				records
-					.map(
-						(MapFunction<TupleWrapper, SerializableSolrInputDocument>) t -> {
-							SolrInputDocument s = new StreamingInputDocumentFactory()
-								.parseDocument(t.getXml(), t.getJson());
-							return new SerializableSolrInputDocument(s);
-						},
-						Encoders.kryo(SerializableSolrInputDocument.class))
-					.write()
-					.mode(SaveMode.Overwrite)
-					.parquet(outputPath);
-				break;
-			default:
-				throw new IllegalArgumentException("invalid outputFormat: " + outputFormat);
-		}
-	}
-
-	protected static String toIndexRecord(Transformer tr, final String xmlRecord) {
-		final StreamResult res = new StreamResult(new StringWriter());
-		try {
-			tr.transform(new StreamSource(new StringReader(xmlRecord)), res);
-			return res.getWriter().toString();
-		} catch (TransformerException e) {
-			throw new IllegalArgumentException("XPathException on record: \n" + xmlRecord, e);
-		}
-	}
-
-	/**
-	 * Creates the XSLT responsible for building the index xml records.
-	 *
-	 * @param format Metadata format name (DMF|TMF)
-	 * @param xslt xslt for building the index record transformer
-	 * @param fields the list of fields
-	 * @return the javax.xml.transform.Transformer
-	 * @throws TransformerException could happen
-	 */
-	protected static String getLayoutTransformer(String format, String fields, String xslt)
-		throws TransformerException {
-
-		final Transformer layoutTransformer = SaxonTransformerFactory.newInstance(xslt);
-		final StreamResult layoutToXsltXslt = new StreamResult(new StringWriter());
-
-		layoutTransformer.setParameter("format", format);
-		layoutTransformer.transform(new StreamSource(new StringReader(fields)), layoutToXsltXslt);
-
-		return layoutToXsltXslt.getWriter().toString();
-	}
-
-	/**
-	 * method return a solr-compatible string representation of a date, used to mark all records as indexed today
-	 *
-	 * @return the parsed date
-	 */
-	public static String getRecordDatestamp() {
-		return new SimpleDateFormat(DATE_FORMAT).format(new Date());
+				Encoders.bean(TupleWrapper.class))
+			.javaRDD()
+			.map(
+				t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
+		SolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
 	}
 
 }

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

@@ -63,27 +63,32 @@ public class ProvisionModelSupport {
 	}
 
 	public static SolrRecord transform(JoinedEntity je, ContextMapper contextMapper, VocabularyGroup vocs) {
-		SolrRecord s = new SolrRecord();
+		SolrRecord record = new SolrRecord();
 		final OafEntity e = je.getEntity();
-		s
+		final RecordType type = RecordType.valueOf(e.getClass().getSimpleName().toLowerCase());
+		final Boolean deletedbyinference = Optional
+			.ofNullable(e.getDataInfo())
+			.map(DataInfo::getDeletedbyinference)
+			.orElse(null);
+		record
 			.setHeader(
 				SolrRecordHeader
 					.newInstance(
-						e.getId(), e.getOriginalId(), RecordType.valueOf(e.getClass().getSimpleName().toLowerCase())));
-		s.setCollectedfrom(asProvenance(e.getCollectedfrom()));
-		s.setContext(asContext(e.getContext(), contextMapper));
-		s.setPid(asPid(e.getPid()));
+						e.getId(), e.getOriginalId(), type, deletedbyinference));
+		record.setCollectedfrom(asProvenance(e.getCollectedfrom()));
+		record.setContext(asContext(e.getContext(), contextMapper));
+		record.setPid(asPid(e.getPid()));
 
 		if (e instanceof eu.dnetlib.dhp.schema.oaf.Result) {
-			s.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e));
+			record.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e));
 		} else if (e instanceof eu.dnetlib.dhp.schema.oaf.Datasource) {
-			s.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e));
+			record.setDatasource(mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) e));
 		} else if (e instanceof eu.dnetlib.dhp.schema.oaf.Organization) {
-			s.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e));
+			record.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e));
 		} else if (e instanceof eu.dnetlib.dhp.schema.oaf.Project) {
-			s.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs));
+			record.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs));
 		}
-		s
+		record
 			.setLinks(
 				Optional
 					.ofNullable(je.getLinks())
@@ -94,7 +99,7 @@ public class ProvisionModelSupport {
 							.collect(Collectors.toList()))
 					.orElse(null));
 
-		return s;
+		return record;
 	}
 
 	private static RelatedRecord mapRelatedRecord(RelatedEntityWrapper rew, VocabularyGroup vocs) {

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

@@ -10,6 +10,7 @@ import java.io.Serializable;
 
 public class TupleWrapper implements Serializable {
 
+	private static final long serialVersionUID = -1418439827125577822L;
 	private String xml;
 
 	private String json;

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json

@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "is",
+    "paramLongName": "isLookupUrl",
+    "paramDescription": "URL of the isLookUp Service",
+    "paramRequired": true
+  },
+  {
+    "paramName": "i",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path of the sequence file to read the XML records",
+    "paramRequired": true
+  },
+  {
+    "paramName": "f",
+    "paramLongName": "format",
+    "paramDescription": "MDFormat name found in the IS profile",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "path on hdfs activating an alternative output for the SolrInputDocuments",
+    "paramRequired": false
+  }
+]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json

@@ -22,23 +22,5 @@
     "paramLongName": "batchSize",
     "paramDescription": "size of the batch of documents sent to solr",
     "paramRequired": false
-  },
-  {
-    "paramName": "of",
-    "paramLongName": "outputFormat",
-    "paramDescription": "decides the job output format, SOLR | HDFS",
-    "paramRequired": false
-  },
-  {
-    "paramName": "si",
-    "paramLongName": "shouldIndex",
-    "paramDescription": "should the action actually index the records?",
-    "paramRequired": true
-  },
-  {
-    "paramName": "op",
-    "paramLongName": "outputPath",
-    "paramDescription": "path on hdfs activating an alternative output for the SolrInputDocuments",
-    "paramRequired": false
   }
 ]

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json

@@ -28,11 +28,5 @@
     "paramLongName": "commit",
     "paramDescription": "should the action be followed by a commit?",
     "paramRequired": false
-  },
-  {
-    "paramName": "i",
-    "paramLongName": "shouldIndex",
-    "paramDescription": "should the action actually index the records?",
-    "paramRequired": true
   }
 ]

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

@@ -591,18 +591,23 @@
                 --conf spark.sql.shuffle.partitions=3840
                 --conf spark.network.timeout=${sparkNetworkTimeout}
             </spark-opts>
-            <!--<arg>- -inputPath</arg><arg>${workingDir}/join_entities</arg>-->
-            <arg>--inputPath</arg><arg>/user/claudio.atzori/data/provision/join_entities</arg>
-
-            <!--<arg>- -outputPath</arg><arg>${workingDir}/xml_json</arg>-->
-            <arg>--outputPath</arg><arg>/user/claudio.atzori/data/provision/xml_json_test</arg>
+            <arg>--inputPath</arg><arg>${workingDir}/join_entities</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/xml_json</arg>
             <arg>--contextApiBaseUrl</arg><arg>${contextApiBaseUrl}</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>
-        <ok to="drop_solr_collection"/>
+        <ok to="should_index"/>
         <error to="Kill"/>
     </action>
 
+    <decision name="should_index">
+        <switch>
+            <case to="drop_solr_collection">${wf:conf('shouldIndex') eq 'true'}</case>
+            <case to="dump_solr_records_hdfs">${wf:conf('shouldIndex') eq 'false'}</case>
+            <default to="dump_solr_records_hdfs"/>
+        </switch>
+    </decision>
+
     <action name="drop_solr_collection">
         <java>
             <configuration>
@@ -617,7 +622,6 @@
             <arg>--action</arg><arg>DELETE_BY_QUERY</arg>
             <arg>--query</arg><arg>${solrDeletionQuery}</arg>
             <arg>--commit</arg><arg>true</arg>
-            <arg>--shouldIndex</arg><arg>${shouldIndex}</arg>
         </java>
         <ok to="to_solr_index"/>
         <error to="Kill"/>
@@ -643,17 +647,10 @@
                 --conf spark.hadoop.mapreduce.map.speculative=false
                 --conf spark.hadoop.mapreduce.reduce.speculative=false
             </spark-opts>
-            <!--<arg>- -inputPath</arg><arg>${workingDir}/xml_json</arg>-->
-            <arg>--inputPath</arg><arg>/user/claudio.atzori/data/provision/xml_json_test</arg>
+            <arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--format</arg><arg>${format}</arg>
             <arg>--batchSize</arg><arg>${batchSize}</arg>
-            <arg>--outputFormat</arg><arg>${outputFormat}</arg>
-
-            <!--<arg>- -outputPath</arg><arg>${workingDir}/solr_documents</arg>-->
-            <arg>--outputPath</arg><arg>/user/claudio.atzori/data/provision/solr_documents</arg>
-
-            <arg>--shouldIndex</arg><arg>${shouldIndex}</arg>
         </spark>
         <ok to="commit_solr_collection"/>
         <error to="Kill"/>
@@ -671,11 +668,35 @@
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--format</arg><arg>${format}</arg>
             <arg>--action</arg><arg>COMMIT</arg>
-            <arg>--shouldIndex</arg><arg>${shouldIndex}</arg>
         </java>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
 
+    <action name="dump_solr_records_hdfs">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>dump_solr_records_hdfs</name>
+            <class>eu.dnetlib.dhp.oa.provision.SolrRecordDumpJob</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--format</arg><arg>${format}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/solr_documents</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
     <end name="End"/>
 </workflow-app>

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

@@ -86,8 +86,7 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null)
-			.run(isLookupClient);
+		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
 		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
 
 		String[] queryStrings = {

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

@@ -95,7 +95,7 @@ public class SolrConfigTest extends SolrTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, false, null)
+		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize)
 			.run(isLookupClient);
 		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
 

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

@@ -0,0 +1,170 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.oa.provision;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import java.io.IOException;
+import java.io.StringReader;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.solr.common.SolrInputField;
+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.SparkSession;
+import org.dom4j.io.SAXReader;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+
+@ExtendWith(MockitoExtension.class)
+class SolrRecordDumpJobTest {
+
+	protected static final Logger log = LoggerFactory.getLogger(SolrRecordDumpJobTest.class);
+
+	protected static SparkSession spark;
+
+	protected static final String FORMAT = "test";
+
+	@Mock
+	private ISLookUpService isLookUpService;
+
+	@Mock
+	private ISLookupClient isLookupClient;
+
+	@TempDir
+	public static Path workingDir;
+
+	@BeforeAll
+	public static void before() {
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(SolrRecordDumpJobTest.class.getSimpleName());
+
+		conf.registerKryoClasses(new Class[] {
+			SerializableSolrInputDocument.class
+		});
+
+		conf.setMaster("local[1]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(SolrRecordDumpJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void shutDown() throws Exception {
+		spark.stop();
+		FileUtils.deleteDirectory(workingDir.toFile());
+	}
+
+	@BeforeEach
+	public void prepareMocks() throws ISLookUpException, IOException {
+		isLookupClient.setIsLookup(isLookUpService);
+
+		Mockito
+			.when(isLookupClient.getDsId(Mockito.anyString()))
+			.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
+		Mockito
+			.when(isLookupClient.getLayoutSource(Mockito.anyString()))
+			.thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml")));
+		Mockito
+			.when(isLookupClient.getLayoutTransformer())
+			.thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl")));
+	}
+
+	@Test
+	void testXmlIndexingJob_saveOnHDFS() throws Exception {
+		final String ID_XPATH = "//*[local-name()='header']/*[local-name()='objIdentifier']";
+
+		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
+		// String inputPath = "/Users/claudio/workspace/data/index";
+
+		Dataset<TupleWrapper> records = spark
+			.read()
+			.schema(Encoders.bean(TupleWrapper.class).schema())
+			.json(inputPath)
+			.as(Encoders.bean(TupleWrapper.class));
+
+		records.printSchema();
+
+		long nRecord = records.count();
+		log.info("found {} records", nRecord);
+
+		final Dataset<String> ids = records
+			.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
+			.map(
+				(MapFunction<String, String>) s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH),
+				Encoders.STRING());
+
+		log.info("found {} ids", ids.count());
+
+		long xmlIdUnique = ids
+			.distinct()
+			.count();
+
+		log.info("found {} unique ids", xmlIdUnique);
+
+		assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records");
+
+		final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString();
+		new SolrRecordDumpJob(spark, inputPath, FORMAT, outputPath).run(isLookupClient);
+
+		final Dataset<SerializableSolrInputDocument> solrDocs = spark
+			.read()
+			.load(outputPath)
+			.as(Encoders.kryo(SerializableSolrInputDocument.class));
+
+		solrDocs.foreach(doc -> {
+			assertNotNull(doc.get("__result"));
+			assertNotNull(doc.get("__json"));
+		});
+
+		long docIdUnique = solrDocs.map((MapFunction<SerializableSolrInputDocument, String>) doc -> {
+			final SolrInputField id = doc.getField("__indexrecordidentifier");
+			return id.getFirstValue().toString();
+		}, Encoders.STRING())
+			.distinct()
+			.count();
+		assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output XML records");
+
+		long jsonUnique = solrDocs
+			.map(
+				(MapFunction<SerializableSolrInputDocument, String>) je -> (String) je.getField("__json").getValue(),
+				Encoders.STRING())
+			.distinct()
+			.count();
+
+		assertEquals(jsonUnique, docIdUnique, "IDs should be unique among the output JSON records");
+
+	}
+}

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

@@ -92,7 +92,7 @@ public abstract class SolrTest {
 		FileUtils.deleteDirectory(workingDir.toFile());
 	}
 
-	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
+	public static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
 		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());

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

@@ -1,24 +1,21 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.net.URI;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.response.QueryResponse;
-import org.apache.solr.common.SolrInputField;
 import org.apache.solr.common.params.CommonParams;
 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.SparkSession;
-import org.dom4j.io.SAXReader;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.BeforeEach;
@@ -106,8 +103,7 @@ public class XmlIndexingJobTest extends SolrTest {
 
 		long nRecord = records.count();
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, true, null)
-			.run(isLookupClient);
+		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
 
 		assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
 
@@ -164,71 +160,4 @@ public class XmlIndexingJobTest extends SolrTest {
 
 	}
 
-	@Test
-	void testXmlIndexingJob_saveOnHDFS() throws Exception {
-		final String ID_XPATH = "//*[local-name()='header']/*[local-name()='objIdentifier']";
-
-		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
-		// String inputPath = "/Users/claudio/workspace/data/index";
-
-		Dataset<TupleWrapper> records = spark
-			.read()
-			.schema(Encoders.bean(TupleWrapper.class).schema())
-			.json(inputPath)
-			.as(Encoders.bean(TupleWrapper.class));
-
-		records.printSchema();
-
-		long nRecord = records.count();
-		log.info("found {} records", nRecord);
-
-		final Dataset<String> ids = records
-			.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
-			.map(
-				(MapFunction<String, String>) s -> new SAXReader().read(new StringReader(s)).valueOf(ID_XPATH),
-				Encoders.STRING());
-
-		log.info("found {} ids", ids.count());
-
-		long xmlIdUnique = ids
-			.distinct()
-			.count();
-
-		log.info("found {} unique ids", xmlIdUnique);
-
-		assertEquals(nRecord, xmlIdUnique, "IDs should be unique among input records");
-
-		final String outputPath = workingDir.resolve("outputPath").toAbsolutePath().toString();
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.HDFS, false, outputPath)
-			.run(isLookupClient);
-
-		final Dataset<SerializableSolrInputDocument> solrDocs = spark
-			.read()
-			.load(outputPath)
-			.as(Encoders.kryo(SerializableSolrInputDocument.class));
-
-		solrDocs.foreach(doc -> {
-			assertNotNull(doc.get("__result"));
-			assertNotNull(doc.get("__json"));
-		});
-
-		long docIdUnique = solrDocs.map((MapFunction<SerializableSolrInputDocument, String>) doc -> {
-			final SolrInputField id = doc.getField("__indexrecordidentifier");
-			return id.getFirstValue().toString();
-		}, Encoders.STRING())
-			.distinct()
-			.count();
-		assertEquals(xmlIdUnique, docIdUnique, "IDs should be unique among the output XML records");
-
-		long jsonUnique = solrDocs
-			.map(
-				(MapFunction<SerializableSolrInputDocument, String>) je -> (String) je.getField("__json").getValue(),
-				Encoders.STRING())
-			.distinct()
-			.count();
-
-		assertEquals(jsonUnique, docIdUnique, "IDs should be unique among the output JSON records");
-
-	}
-
 }

dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema

@@ -202,6 +202,7 @@
   <field name="__dsversion" type="pdate" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="true"/>
   <field name="__indexrecordidentifier" type="string" multiValued="false" indexed="true" required="true" stored="true"/>
   <field name="__result" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
+  <field name="__json" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
   <field name="_root_" type="string" docValues="false" indexed="true" stored="false"/>
   <field name="_version_" type="long" multiValued="false" indexed="true" stored="true"/>
   <field name="authorid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
@@ -223,17 +224,22 @@
   <field name="datasourcecompatibilityid" type="string" multiValued="false" indexed="true" stored="false"/>
   <field name="datasourcecompatibilityname" type="string" multiValued="false" indexed="true" stored="false"/>
   <field name="datasourceenglishname" type="text_common" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourcejurisdiction" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourceodcontenttypes" type="string" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourceoddescription" type="text_common" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourceodlanguages" type="string" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourceodsubjects" type="string" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourceofficialname" type="text_common" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourcesubject" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourcethematic" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourcetypename" type="string" multiValued="false" indexed="true" stored="false"/>
   <field name="datasourcetypeuiid" type="string" multiValued="false" indexed="true" stored="false"/>
   <field name="datasourcetypeuiname" type="string" multiValued="false" indexed="true" stored="false"/>
   <field name="dateofcollection" type="pdate" multiValued="false" indexed="true" stored="false"/>
   <field name="deletedbyinference" type="string" multiValued="true" indexed="true" stored="false"/>
+  <field name="eoscdatasourcetype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="eoscifguidelines" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="eosctype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="externalrefclass" type="string" multiValued="true" indexed="true" stored="false"/>
   <field name="externalrefid" type="string" multiValued="true" indexed="true" stored="false"/>
   <field name="externalreflabel" type="text_common" multiValued="true" indexed="true" stored="false"/>