more logging on the MDStore mongodb client. Forcing UTF_8 encoding on the content

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

@@ -21,17 +21,19 @@ import com.mongodb.MongoClientURI;
 import com.mongodb.QueryBuilder;
 import com.mongodb.client.MongoCollection;
 import com.mongodb.client.MongoDatabase;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class MdstoreClient implements Closeable {
 
+	private static final Logger log = LoggerFactory.getLogger(MdstoreClient.class);
+
 	private final MongoClient client;
 	private final MongoDatabase db;
 
 	private static final String COLL_METADATA = "metadata";
 	private static final String COLL_METADATA_MANAGER = "metadataManager";
 
-	private static final Log log = LogFactory.getLog(MdstoreClient.class);
-
 	public MdstoreClient(final String baseUrl, final String dbName) {
 		this.client = new MongoClient(new MongoClientURI(baseUrl));
 		this.db = getDb(client, dbName);
@@ -40,11 +42,16 @@ public class MdstoreClient implements Closeable {
 	public MongoCollection<Document> mdStore(final String mdId) {
 		BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
 
+		log.info("querying current mdId: {}", query.toJson());
+
 		final String currentId = Optional
 			.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
 			.map(r -> r.first())
 			.map(d -> d.getString("currentId"))
 			.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
+
+		log.info("currentId: {}", currentId);
+
 		return getColl(db, currentId, true);
 	}
 

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

@@ -8,6 +8,8 @@ import java.util.stream.Stream;
 import java.util.stream.StreamSupport;
 
 import org.bson.Document;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import com.mongodb.client.MongoCollection;
 
@@ -19,6 +21,8 @@ import eu.dnetlib.dhp.common.MdstoreClient;
 
 public class MDStoreCollectorPlugin implements CollectorPlugin {
 
+	private static final Logger log = LoggerFactory.getLogger(MDStoreCollectorPlugin.class);
+
 	public static final String MONGODB_DBNAME = "mongodb_dbname";
 	public static final String MDSTORE_ID = "mdstore_id";
 
@@ -30,14 +34,17 @@ public class MDStoreCollectorPlugin implements CollectorPlugin {
 			.orElseThrow(
 				() -> new CollectorException(
 					"missing mongodb baseUrl, expected in eu.dnetlib.dhp.collection.ApiDescriptor.baseUrl"));
+		log.info("mongoBaseUrl: {}", mongoBaseUrl);
 
 		final String dbName = Optional
 			.ofNullable(api.getParams().get(MONGODB_DBNAME))
 			.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MONGODB_DBNAME)));
+		log.info("dbName: {}", dbName);
 
 		final String mdId = Optional
 			.ofNullable(api.getParams().get(MDSTORE_ID))
 			.orElseThrow(() -> new CollectorException(String.format("missing parameter '%s'", MDSTORE_ID)));
+		log.info("mdId: {}", mdId);
 
 		final MdstoreClient client = new MdstoreClient(mongoBaseUrl, dbName);
 		final MongoCollection<Document> mdstore = client.mdStore(mdId);

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

@@ -3,9 +3,11 @@ package eu.dnetlib.dhp.transformation.xslt;
 
 import java.io.ByteArrayInputStream;
 import java.io.StringWriter;
+import java.nio.charset.StandardCharsets;
 
 import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.spark.api.java.function.MapFunction;
 
 import eu.dnetlib.dhp.aggregation.common.AggregationCounter;
@@ -44,18 +46,20 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
 			Processor processor = new Processor(false);
 			processor.registerExtensionFunction(cleanFunction);
 			processor.registerExtensionFunction(new DateCleaner());
+
 			final XsltCompiler comp = processor.newXsltCompiler();
 			XsltExecutable xslt = comp
-				.compile(new StreamSource(new ByteArrayInputStream(transformationRule.getBytes())));
+				.compile(new StreamSource(IOUtils.toInputStream(transformationRule, StandardCharsets.UTF_8)));
 			XdmNode source = processor
 				.newDocumentBuilder()
-				.build(new StreamSource(new ByteArrayInputStream(value.getBody().getBytes())));
+				.build(new StreamSource(IOUtils.toInputStream(value.getBody(), StandardCharsets.UTF_8)));
 			XsltTransformer trans = xslt.load();
 			trans.setInitialContextNode(source);
 			final StringWriter output = new StringWriter();
 			Serializer out = processor.newSerializer(output);
 			out.setOutputProperty(Serializer.Property.METHOD, "xml");
 			out.setOutputProperty(Serializer.Property.INDENT, "yes");
+
 			trans.setDestination(out);
 			trans.transform();
 			final String xml = output.toString();