bug fixing

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMigrationExecutor.java

@@ -111,6 +111,10 @@ public class AbstractMigrationExecutor implements Closeable {
 		return Arrays.stream(values).map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList());
 	}
 
+	public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
+		return values.stream().map(v -> field(v, info)).filter(Objects::nonNull).collect(Collectors.toList());
+	}
+
 	public static Qualifier qualifier(final String classid, final String classname, final String schemeid, final String schemename) {
 		final Qualifier q = new Qualifier();
 		q.setClassid(classid);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/AbstractMongoExecutor.java

@@ -385,6 +385,8 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
 	protected OAIProvenance prepareOAIprovenance(final Document doc) {
 		final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
 
+		if (n == null) { return null; }
+
 		final String identifier = n.valueOf("./*[local-name()='identifier']");
 		final String baseURL = n.valueOf("./*[local-name()='baseURL']");;
 		final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");;
@@ -393,6 +395,7 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
 		final String harvestDate = n.valueOf("@harvestDate");;
 
 		return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
+
 	}
 
 	protected DataInfo prepareDataInfo(final Document doc) {
@@ -416,7 +419,7 @@ public abstract class AbstractMongoExecutor extends AbstractMigrationExecutor {
 	}
 
 	protected List<Field<String>> prepareListFields(final Node node, final String xpath, final DataInfo info) {
-		return listFields(info, (String[]) prepareListString(node, xpath).toArray());
+		return listFields(info, prepareListString(node, xpath));
 	}
 
 	protected List<String> prepareListString(final Node node, final String xpath) {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/MdstoreClient.java

@@ -2,6 +2,7 @@ package eu.dnetlib.dhp.migration;
 
 import java.io.Closeable;
 import java.io.IOException;
+import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.stream.StreamSupport;
@@ -35,7 +36,7 @@ public class MdstoreClient implements Closeable {
 	public Map<String, String> validCollections(final String mdFormat, final String mdLayout, final String mdInterpretation) {
 
 		final Map<String, String> transactions = new HashMap<>();
-		for (final Document entry : getColl(db, COLL_METADATA_MANAGER).find()) {
+		for (final Document entry : getColl(db, COLL_METADATA_MANAGER, true).find()) {
 			final String mdId = entry.getString("mdId");
 			final String currentId = entry.getString("currentId");
 			if (StringUtils.isNoneBlank(mdId, currentId)) {
@@ -44,7 +45,7 @@ public class MdstoreClient implements Closeable {
 		}
 
 		final Map<String, String> res = new HashMap<>();
-		for (final Document entry : getColl(db, COLL_METADATA).find()) {
+		for (final Document entry : getColl(db, COLL_METADATA, true).find()) {
 			if (entry.getString("format").equals(mdFormat) && entry.getString("layout").equals(mdLayout)
 					&& entry.getString("interpretation").equals(mdInterpretation) && transactions.containsKey(entry.getString("mdId"))) {
 				res.put(entry.getString("mdId"), transactions.get(entry.getString("mdId")));
@@ -63,20 +64,26 @@ public class MdstoreClient implements Closeable {
 		return client.getDatabase(dbName);
 	}
 
-	private MongoCollection<Document> getColl(final MongoDatabase db, final String collName) {
+	private MongoCollection<Document> getColl(final MongoDatabase db, final String collName, final boolean abortIfMissing) {
 		if (!Iterables.contains(db.listCollectionNames(), collName)) {
 			final String err = String.format(String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
 			log.warn(err);
-			throw new RuntimeException(err);
+			if (abortIfMissing) {
+				throw new RuntimeException(err);
+			} else {
+				return null;
+			}
 		}
 		return db.getCollection(collName);
 	}
 
-	public Iterable<String> listRecords(final String coll) {
+	public Iterable<String> listRecords(final String collName) {
-		return () -> StreamSupport.stream(getColl(db, coll).find().spliterator(), false)
+		final MongoCollection<Document> coll = getColl(db, collName, false);
-				.filter(e -> e.containsKey("body"))
+		return coll == null ? new ArrayList<>()
-				.map(e -> e.getString("body"))
+				: () -> StreamSupport.stream(coll.find().spliterator(), false)
-				.iterator();
+						.filter(e -> e.containsKey("body"))
+						.map(e -> e.getString("body"))
+						.iterator();
 	}
 
 	@Override

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/migration/OdfMigrationExecutor.java

@@ -34,6 +34,7 @@ public class OdfMigrationExecutor extends AbstractMongoExecutor {
 
 	@Override
 	protected void registerNamespaces(final Map<String, String> nsContext) {
+		super.registerNamespaces(nsContext);
 		nsContext.put("dc", "http://datacite.org/schema/kernel-3");
 	}