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dnet-hadoop
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cleanup

This commit is contained in:
Claudio Atzori 2020-04-29 19:09:07 +02:00
parent 77ac995770
commit 439c6255a2
30 changed files with 54 additions and 55 deletions
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2
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java
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@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test;
/** @author mhorst, claudio.atzori */
public class GenerateOoziePropertiesMojoTest {
private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
@BeforeEach
public void clearSystemProperties() {

2
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
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@ -366,7 +366,7 @@ public class WritePredefinedProjectPropertiesTest {
}
private Properties getStoredProperties(File testFolder)
throws FileNotFoundException, IOException {
throws IOException {
Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties;

2
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
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@ -21,7 +21,7 @@ public class DHPUtils {
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");

2
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java
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@ -17,7 +17,7 @@ public class NormalizeDate extends AbstractExtensionFunction {
"yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy"
};
private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
private static final String normalizeOutFormat = "yyyy-MM-dd'T'hh:mm:ss'Z'";
@Override
public String getName() {

2
dhp-common/src/main/java/eu/dnetlib/message/MessageManager.java
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@ -21,7 +21,7 @@ public class MessageManager {
private Connection connection;
private Map<String, Channel> channels = new HashMap<>();
private final Map<String, Channel> channels = new HashMap<>();
private boolean durable;

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java
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@ -16,7 +16,7 @@ public class AtomicActionDeserializer extends JsonDeserializer {
@Override
public Object deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException, JsonProcessingException {
throws IOException {
JsonNode node = jp.getCodec().readTree(jp);
String classTag = node.get("clazz").asText();
JsonNode payload = node.get("payload");

2
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java
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@ -13,7 +13,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class ModelSupport {
/** Defines the mapping between the actual entity type and the main entity type */
private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static {
entityMapping.put(EntityType.publication, MainEntityType.result);

2
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
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@ -32,7 +32,7 @@ public class ISClient implements Serializable {
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
private ISLookUpService isLookup;
private final ISLookUpService isLookup;
public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);

8
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
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@ -123,10 +123,10 @@ public class PromoteActionPayloadFunctions {
* @param <G> Type of graph table row
*/
public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
private SerializableSupplier<G> zeroFn;
private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
private Class<G> rowClazz;
private final SerializableSupplier<G> zeroFn;
private final SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
private final SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
private final Class<G> rowClazz;
public TableAggregator(
SerializableSupplier<G> zeroFn,

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/DnetCollectorWorkerApplication.java
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@ -20,7 +20,7 @@ public class DnetCollectorWorkerApplication {
private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
private static CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
private static ArgumentApplicationParser argumentParser;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java
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@ -9,7 +9,7 @@ public class CollectorPluginErrorLogList extends LinkedList<String> {
@Override
public String toString() {
String log = new String();
String log = "";
int index = 0;
for (final String errorMessage : this) {
log += String.format("Retry #%s: %s / ", index++, errorMessage);

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java
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@ -11,22 +11,22 @@ import java.util.regex.Pattern;
public class XmlCleaner {
/** Pattern for numeric entities. */
private static Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); // $NON-NLS-1$
private static final Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); // $NON-NLS-1$
// private static Pattern validCharacterEntityPattern = Pattern.compile("^&#?\\d{2,4};");
// //$NON-NLS-1$
// see https://www.w3.org/TR/REC-xml/#charsets , not only limited to &#11;
private static Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];");
private static final Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];");
/**
* Pattern that negates the allowable XML 4 byte unicode characters. Valid are: #x9 | #xA | #xD | [#x20-#xD7FF] |
* [#xE000-#xFFFD] | [#x10000-#x10FFFF]
*/
private static Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); // $NON-NLS-1$
private static final Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); // $NON-NLS-1$
// Map entities to their unicode equivalent
private static Set<String> goodEntities = new HashSet<>();
private static Map<String, String> badEntities = new HashMap<>();
private static final Set<String> goodEntities = new HashSet<>();
private static final Map<String, String> badEntities = new HashMap<>();
static {
// pre-defined XML entities

4
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java
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@ -21,8 +21,8 @@ import eu.dnetlib.message.MessageManager;
public class DnetCollectorWorkerApplicationTests {
private ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);
private MessageManager messageManager = mock(MessageManager.class);
private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);
private final MessageManager messageManager = mock(MessageManager.class);
private DnetCollectorWorker worker;

3
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java
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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.oa.dedup;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.text.Normalizer;
import java.util.*;
@ -73,7 +74,7 @@ public class DedupUtility {
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");

2
dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java
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@ -15,7 +15,7 @@ public class SparkReporter implements Serializable, Reporter {
private final List<Tuple2<String, String>> relations = new ArrayList<>();
private Map<String, LongAccumulator> accumulators;
private final Map<String, LongAccumulator> accumulators;
public SparkReporter(Map<String, LongAccumulator> accumulators) {
this.accumulators = accumulators;

2
dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java
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@ -106,7 +106,7 @@ public class DedupUtility {
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8"));
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
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@ -410,14 +410,10 @@ public abstract class AbstractMdRecordToOafMapper {
final String identifier = n.valueOf("./*[local-name()='identifier']");
final String baseURL = n.valueOf("./*[local-name()='baseURL']");
;
final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
;
final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
final String datestamp = n.valueOf("./*[local-name()='datestamp']");
;
final String harvestDate = n.valueOf("@harvestDate");
;
return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
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@ -514,9 +514,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
if (arr.length == 3) {
final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;
;
final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;
;
if (issn != null || eissn != null || lissn != null) {
return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java
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@ -14,7 +14,7 @@ public class DbClient implements Closeable {
private static final Log log = LogFactory.getLog(DbClient.class);
private Connection connection;
private final Connection connection;
public DbClient(final String address, final String login, final String password) {

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java
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@ -2,6 +2,7 @@
package eu.dnetlib.dhp.oa.graph.raw.common;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.text.Normalizer;
import java.util.HashSet;
import java.util.List;
@ -141,7 +142,7 @@ public class PacePerson {
public String hash() {
return Hashing
.murmur3_128()
.hashString(getNormalisedFullname(), Charset.forName(UTF8))
.hashString(getNormalisedFullname(), StandardCharsets.UTF_8)
.toString();
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java
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@ -25,7 +25,7 @@ public abstract class AbstractScholexplorerParser {
protected static final Log log = LogFactory.getLog(AbstractScholexplorerParser.class);
static final Pattern pattern = Pattern.compile("10\\.\\d{4,9}/[-._;()/:A-Z0-9]+$", Pattern.CASE_INSENSITIVE);
private List<String> datasetSubTypes = Arrays
private final List<String> datasetSubTypes = Arrays
.asList(
"dataset",
"software",

2
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java
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@ -18,7 +18,7 @@ import eu.dnetlib.dhp.utils.DHPUtils;
public class CrossRefParserJSON {
private static List<ScholixCollectedFrom> collectedFrom = generateCrossrefCollectedFrom("complete");
private static final List<ScholixCollectedFrom> collectedFrom = generateCrossrefCollectedFrom("complete");
public static ScholixResource parseRecord(final String record) {
if (record == null)

2
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java
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@ -16,7 +16,7 @@ public class DataciteClient {
private String host;
private String index = "datacite";
private String indexType = "dump";
private Datacite2Scholix d2s;
private final Datacite2Scholix d2s;
public DataciteClient(String host) {
this.host = host;

2
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java
View File

@ -12,7 +12,7 @@ import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
*/
public class RelationPartitioner extends Partitioner {
private int numPartitions;
private final int numPartitions;
public RelationPartitioner(int numPartitions) {
this.numPartitions = numPartitions;

15
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java
View File

@ -46,7 +46,7 @@ public class StreamingInputDocumentFactory {
private static final String INDEX_RECORD_ID = INDEX_FIELD_PREFIX + "indexrecordidentifier";
private static final String outFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
private static final String outFormat = "yyyy-MM-dd'T'hh:mm:ss'Z'";
private static final List<String> dateFormats = Arrays
.asList("yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy");
@ -61,15 +61,18 @@ public class StreamingInputDocumentFactory {
private static final int MAX_FIELD_LENGTH = 25000;
private ThreadLocal<XMLInputFactory> inputFactory = ThreadLocal.withInitial(() -> XMLInputFactory.newInstance());
private final ThreadLocal<XMLInputFactory> inputFactory = ThreadLocal
.withInitial(() -> XMLInputFactory.newInstance());
private ThreadLocal<XMLOutputFactory> outputFactory = ThreadLocal.withInitial(() -> XMLOutputFactory.newInstance());
private final ThreadLocal<XMLOutputFactory> outputFactory = ThreadLocal
.withInitial(() -> XMLOutputFactory.newInstance());
private ThreadLocal<XMLEventFactory> eventFactory = ThreadLocal.withInitial(() -> XMLEventFactory.newInstance());
private final ThreadLocal<XMLEventFactory> eventFactory = ThreadLocal
.withInitial(() -> XMLEventFactory.newInstance());
private String version;
private final String version;
private String dsId;
private final String dsId;
private String resultName = DEFAULTDNETRESULT;

2
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java
View File

@ -17,7 +17,7 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
public class TemplateFactory {
private TemplateResources resources;
private final TemplateResources resources;
private static final char DELIMITER = '$';

12
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java
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@ -8,17 +8,17 @@ import com.google.common.io.Resources;
public class TemplateResources {
private String record = read("eu/dnetlib/dhp/oa/provision/template/record.st");
private final String record = read("eu/dnetlib/dhp/oa/provision/template/record.st");
private String instance = read("eu/dnetlib/dhp/oa/provision/template/instance.st");
private final String instance = read("eu/dnetlib/dhp/oa/provision/template/instance.st");
private String rel = read("eu/dnetlib/dhp/oa/provision/template/rel.st");
private final String rel = read("eu/dnetlib/dhp/oa/provision/template/rel.st");
private String webresource = read("eu/dnetlib/dhp/oa/provision/template/webresource.st");
private final String webresource = read("eu/dnetlib/dhp/oa/provision/template/webresource.st");
private String child = read("eu/dnetlib/dhp/oa/provision/template/child.st");
private final String child = read("eu/dnetlib/dhp/oa/provision/template/child.st");
private String entity = read("eu/dnetlib/dhp/oa/provision/template/entity.st");
private final String entity = read("eu/dnetlib/dhp/oa/provision/template/entity.st");
private static String read(final String classpathResource) throws IOException {
return Resources.toString(Resources.getResource(classpathResource), StandardCharsets.UTF_8);

8
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
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@ -48,13 +48,13 @@ import eu.dnetlib.dhp.schema.oaf.Result;
public class XmlRecordFactory implements Serializable {
public static final String REL_SUBTYPE_DEDUP = "dedup";
private Map<String, LongAccumulator> accumulators;
private final Map<String, LongAccumulator> accumulators;
private Set<String> specialDatasourceTypes;
private final Set<String> specialDatasourceTypes;
private ContextMapper contextMapper;
private final ContextMapper contextMapper;
private String schemaLocation;
private final String schemaLocation;
private boolean indent = false;

2
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
View File

@ -41,7 +41,7 @@ public class XmlSerializationUtils {
public static String mapStructuredProperty(String name, StructuredProperty t) {
return asXmlElement(
name, t.getValue(), t.getQualifier(), t.getDataInfo() != null ? t.getDataInfo() : null);
name, t.getValue(), t.getQualifier(), t.getDataInfo());
}
public static String mapQualifier(String name, Qualifier q) {

2
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java
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@ -9,7 +9,7 @@ import org.junit.jupiter.api.BeforeEach;
public class GraphJoinerTest {
private ClassLoader cl = getClass().getClassLoader();
private final ClassLoader cl = getClass().getClassLoader();
private Path workingDir;
private Path inputDir;
private Path outputDir;