code formatting

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

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.schema.oaf.utils;
 
 import java.util.*;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java

@@ -100,7 +100,7 @@ public class PrepareAffiliationRelations implements Serializable {
 		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
 		String outputPath) {
 		List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
-				.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
 			spark, crossrefInputPath, collectedfromOpenAIRE);
@@ -130,7 +130,8 @@ public class PrepareAffiliationRelations implements Serializable {
 				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 	}
 
-	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark, String inputPath,
+	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark,
+		String inputPath,
 		List<KeyValue> collectedfrom) {
 
 		Dataset<Row> df = spark
@@ -145,29 +146,28 @@ public class PrepareAffiliationRelations implements Serializable {
 	}
 
 	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
-																				   List<KeyValue> collectedfrom) {
+		List<KeyValue> collectedfrom) {
 
 		Dataset<Row> df = spark
-				.read()
-				.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-				.json(inputPath)
-				.where("DOI is not null");
-
+			.read()
+			.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
+			.json(inputPath)
+			.where("DOI is not null");
 
 		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
 
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
-																						  String inputPath,
-																						  List<KeyValue> collectedfrom) {
+		String inputPath,
+		List<KeyValue> collectedfrom) {
 
 		// load and parse affiliation relations from HDFS
 		Dataset<Row> df = spark
-				.read()
-				.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-				.json(inputPath)
-				.where("DOI is not null");
+			.read()
+			.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
+			.json(inputPath)
+			.where("DOI is not null");
 
 		return getTextTextJavaPairRDD(collectedfrom, df);
 	}
@@ -189,49 +189,49 @@ public class PrepareAffiliationRelations implements Serializable {
 	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
 		// unroll nested arrays
 		df = df
-				.withColumn("matching", functions.explode(new Column("Matchings")))
-				.select(
-						new Column("DOI").as("doi"),
-						new Column("matching.RORid").as("rorid"),
-						new Column("matching.Confidence").as("confidence"));
+			.withColumn("matching", functions.explode(new Column("Matchings")))
+			.select(
+				new Column("DOI").as("doi"),
+				new Column("matching.RORid").as("rorid"),
+				new Column("matching.Confidence").as("confidence"));
 
 		// prepare action sets for affiliation relations
 		return df
-				.toJavaRDD()
-				.flatMap((FlatMapFunction<Row, Relation>) row -> {
+			.toJavaRDD()
+			.flatMap((FlatMapFunction<Row, Relation>) row -> {
 
-					// DOI to OpenAIRE id
-					final String paperId = ID_PREFIX
-							+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(row.getAs("doi"))));
+				// DOI to OpenAIRE id
+				final String paperId = ID_PREFIX
+					+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", removePrefix(row.getAs("doi"))));
 
-					// ROR id to OpenAIRE id
-					final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
+				// ROR id to OpenAIRE id
+				final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
 
-					Qualifier qualifier = OafMapperUtils
-							.qualifier(
-									BIP_AFFILIATIONS_CLASSID,
-									BIP_AFFILIATIONS_CLASSNAME,
-									ModelConstants.DNET_PROVENANCE_ACTIONS,
-									ModelConstants.DNET_PROVENANCE_ACTIONS);
+				Qualifier qualifier = OafMapperUtils
+					.qualifier(
+						BIP_AFFILIATIONS_CLASSID,
+						BIP_AFFILIATIONS_CLASSNAME,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS);
 
-					// format data info; setting `confidence` into relation's `trust`
-					DataInfo dataInfo = OafMapperUtils
-							.dataInfo(
-									false,
-									BIP_INFERENCE_PROVENANCE,
-									true,
-									false,
-									qualifier,
-									Double.toString(row.getAs("confidence")));
+				// format data info; setting `confidence` into relation's `trust`
+				DataInfo dataInfo = OafMapperUtils
+					.dataInfo(
+						false,
+						BIP_INFERENCE_PROVENANCE,
+						true,
+						false,
+						qualifier,
+						Double.toString(row.getAs("confidence")));
 
-					// return bi-directional relations
-					return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
+				// return bi-directional relations
+				return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
 
-				})
-				.map(p -> new AtomicAction(Relation.class, p))
-				.mapToPair(
-						aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-								new Text(OBJECT_MAPPER.writeValueAsString(aa))));
+			})
+			.map(p -> new AtomicAction(Relation.class, p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
 	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
@@ -292,7 +292,7 @@ public class PrepareAffiliationRelations implements Serializable {
 	}
 
 	private static String removePrefix(String doi) {
-		if(doi.startsWith(DOI_URL_PREFIX))
+		if (doi.startsWith(DOI_URL_PREFIX))
 			return doi.substring(DOI_URL_PREFIX_LENGTH);
 		return doi;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java

@@ -46,11 +46,11 @@ public class CollectorWorker extends ReportingJob {
 	private final HttpClientParams clientParams;
 
 	public CollectorWorker(
-			final ApiDescriptor api,
-			final FileSystem fileSystem,
-			final MDStoreVersion mdStoreVersion,
-			final HttpClientParams clientParams,
-			final AggregatorReport report) {
+		final ApiDescriptor api,
+		final FileSystem fileSystem,
+		final MDStoreVersion mdStoreVersion,
+		final HttpClientParams clientParams,
+		final AggregatorReport report) {
 		super(report);
 		this.api = api;
 		this.fileSystem = fileSystem;
@@ -69,22 +69,25 @@ public class CollectorWorker extends ReportingJob {
 		scheduleReport(counter);
 
 		try (SequenceFile.Writer writer = SequenceFile
-				.createWriter(this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
-						.keyClass(IntWritable.class), SequenceFile.Writer
-								.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
+			.createWriter(
+				this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
+					.keyClass(IntWritable.class),
+				SequenceFile.Writer
+					.valueClass(Text.class),
+				SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
 			final IntWritable key = new IntWritable(counter.get());
 			final Text value = new Text();
 			plugin
-					.collect(this.api, this.report)
-					.forEach(content -> {
-						key.set(counter.getAndIncrement());
-						value.set(content);
-						try {
-							writer.append(key, value);
-						} catch (final Throwable e) {
-							throw new RuntimeException(e);
-						}
-					});
+				.collect(this.api, this.report)
+				.forEach(content -> {
+					key.set(counter.getAndIncrement());
+					value.set(content);
+					try {
+						writer.append(key, value);
+					} catch (final Throwable e) {
+						throw new RuntimeException(e);
+					}
+				});
 		} catch (final Throwable e) {
 			this.report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
@@ -112,36 +115,36 @@ public class CollectorWorker extends ReportingJob {
 	private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
 
 		switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
-		case oai:
-			return new OaiCollectorPlugin(this.clientParams);
-		case rest_json2xml:
-			return new RestCollectorPlugin(this.clientParams);
-		case file:
-			return new FileCollectorPlugin(this.fileSystem);
-		case fileGzip:
-			return new FileGZipCollectorPlugin(this.fileSystem);
-		case baseDump:
-			return new BaseCollectorPlugin(this.fileSystem);
-		case gtr2Publications:
-			return new Gtr2PublicationsCollectorPlugin(this.clientParams);
-		case osfPreprints:
-			return new OsfPreprintsCollectorPlugin(this.clientParams);
-		case other:
-			final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
+			case oai:
+				return new OaiCollectorPlugin(this.clientParams);
+			case rest_json2xml:
+				return new RestCollectorPlugin(this.clientParams);
+			case file:
+				return new FileCollectorPlugin(this.fileSystem);
+			case fileGzip:
+				return new FileGZipCollectorPlugin(this.fileSystem);
+			case baseDump:
+				return new BaseCollectorPlugin(this.fileSystem);
+			case gtr2Publications:
+				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
+			case osfPreprints:
+				return new OsfPreprintsCollectorPlugin(this.clientParams);
+			case other:
+				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(this.api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
 					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
-			switch (plugin) {
-			case mdstore_mongodb_dump:
-				return new MongoDbDumpCollectorPlugin(this.fileSystem);
-			case mdstore_mongodb:
-				return new MDStoreCollectorPlugin();
+				switch (plugin) {
+					case mdstore_mongodb_dump:
+						return new MongoDbDumpCollectorPlugin(this.fileSystem);
+					case mdstore_mongodb:
+						return new MDStoreCollectorPlugin();
+					default:
+						throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
+				}
 			default:
-				throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
-			}
-		default:
-			throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
+				throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
 		}
 	}
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java

@@ -31,17 +31,19 @@ public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
 		final String baseUrl = api.getBaseUrl();
 
 		final int pageSize = Optional
-				.ofNullable(api.getParams().get("pageSize"))
-				.filter(StringUtils::isNotBlank)
-				.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
-				.orElse(PAGE_SIZE_VALUE_DEFAULT);
+			.ofNullable(api.getParams().get("pageSize"))
+			.filter(StringUtils::isNotBlank)
+			.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
+			.orElse(PAGE_SIZE_VALUE_DEFAULT);
 
-		if (StringUtils.isBlank(baseUrl)) { throw new CollectorException("Param 'baseUrl' is null or empty"); }
+		if (StringUtils.isBlank(baseUrl)) {
+			throw new CollectorException("Param 'baseUrl' is null or empty");
+		}
 
 		final OsfPreprintsIterator it = new OsfPreprintsIterator(baseUrl, pageSize, getClientParams());
 
 		return StreamSupport
-				.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
+			.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
 	}
 
 	public HttpClientParams getClientParams() {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java

@@ -34,9 +34,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
 
 	public OsfPreprintsIterator(
-			final String baseUrl,
-			final int pageSize,
-			final HttpClientParams clientParams) {
+		final String baseUrl,
+		final int pageSize,
+		final HttpClientParams clientParams) {
 
 		this.clientParams = clientParams;
 		this.baseUrl = baseUrl;
@@ -54,7 +54,8 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	@Override
 	public boolean hasNext() {
 		synchronized (this.recordQueue) {
-			while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl) && this.currentUrl.startsWith("http")) {
+			while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl)
+				&& this.currentUrl.startsWith("http")) {
 				try {
 					this.currentUrl = downloadPage(this.currentUrl);
 				} catch (final CollectorException e) {
@@ -63,7 +64,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 				}
 			}
 
-			if (!this.recordQueue.isEmpty()) { return true; }
+			if (!this.recordQueue.isEmpty()) {
+				return true;
+			}
 
 			return false;
 		}
@@ -112,7 +115,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	}
 
 	private Document downloadUrl(final String url, final int attempt) throws CollectorException {
-		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
+		if (attempt > MAX_ATTEMPTS) {
+			throw new CollectorException("Max Number of attempts reached, url:" + url);
+		}
 
 		if (attempt > 0) {
 			final int delay = (attempt * 5000);

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

@@ -79,16 +79,16 @@ public class PrepareAffiliationRelationsTest {
 			.getPath();
 
 		String crossrefAffiliationRelationPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
-				.getPath();
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
+			.getPath();
 
 		String publisherAffiliationRelationPath = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
 			.getPath();
 
 		String publisherAffiliationRelationOldPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
-				.getPath();
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
+			.getPath();
 
 		String outputPath = workingDir.toString() + "/actionSet";
 
@@ -112,9 +112,8 @@ public class PrepareAffiliationRelationsTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-
 		// count the number of relations
-		assertEquals(150, tmp.count());//  18 + 24 *3 + 30 * 2 =
+		assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -173,18 +172,16 @@ public class PrepareAffiliationRelationsTest {
 							+ IdentifierFactory.md5("https://ror.org/03265fv13") + "'")
 					.count());
 
-
 		Assertions
-				.assertEquals(
-						3, execVerification
-								.filter(
-										"source = '" + ID_PREFIX
-												+ IdentifierFactory
-												.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
-												+ "' and target = '" + "20|ror_________::"
-												+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
-								.count());
-
+			.assertEquals(
+				3, execVerification
+					.filter(
+						"source = '" + ID_PREFIX
+							+ IdentifierFactory
+								.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
+							+ "' and target = '" + "20|ror_________::"
+							+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
+					.count());
 
 	}
 }

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java

@@ -50,9 +50,10 @@ public class OsfPreprintsCollectorPluginTest {
 	@Test
 	@Disabled
 	void test_one() throws CollectorException {
-		this.plugin.collect(this.api, new AggregatorReport())
-				.limit(1)
-				.forEach(log::info);
+		this.plugin
+			.collect(this.api, new AggregatorReport())
+			.limit(1)
+			.forEach(log::info);
 	}
 
 	@Test
@@ -95,7 +96,8 @@ public class OsfPreprintsCollectorPluginTest {
 		final HttpConnector2 connector = new HttpConnector2();
 
 		try {
-			final String res = connector.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
+			final String res = connector
+				.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
 			System.out.println(res);
 			fail();
 		} catch (final Throwable e) {