D-Net

package eu.dnetlib.dhp.common.java;

import java.util.Map;

import org.apache.hadoop.conf.Configuration;

import eu.dnetlib.dhp.common.java.porttype.PortType;

/** Workflow node written in Java.

 * 

 * The implementing class has to define a constructor with no parameters 

 * (possibly the default one) or a constructor with String[] as a single

 * parameter.

 * @author Mateusz Kobos

 */

public interface Process {

	/**

	 * Run the process.

	 * 

	 * The process ends with a success status if no exception is thrown, 

	 * otherwise it ends with an error status.

	 *

	 * @param parameters parameters of the process. Each parameter

	 * corresponds to a single entry in the map, its name is the key, its

	 * value is the value.

	 * @throws Exception if thrown, it means that the process finished

	 * with an error status

	 */

	void run(PortBindings portBindings, Configuration conf, 

			Map<String, String> parameters) throws Exception;

	/**

	 * @return map containing as the key: name of the port, as the value: type

	 * of the port 

	 */

	Map<String, PortType> getInputPorts();

	/**

	 * @return map containing as the key: name of the port, as the value: type

	 * of the port 

	 */

	Map<String, PortType> getOutputPorts();

}

package eu.dnetlib.dhp.common.oozie.property;

import java.io.File;

import java.io.FileOutputStream;

import java.io.OutputStream;

import java.util.Collections;

import java.util.Map;

import java.util.Properties;

import eu.dnetlib.dhp.common.java.PortBindings;

import eu.dnetlib.dhp.common.java.Process;

import eu.dnetlib.dhp.common.java.porttype.PortType;

import org.apache.hadoop.conf.Configuration;

import static eu.dnetlib.dhp.common.WorkflowRuntimeParameters.OOZIE_ACTION_OUTPUT_FILENAME;

/**

 * This process is a solution for setting dynamic properties in oozie workflow definition.

 * 

 * Expects three parameters to be provided: the first 'condition' parameter is boolean value 

 * based on which either first 'inCaseOfTrue' or second 'elseCase' parameter value is set as 

 * the 'result' property.

 *  

 * This can be understood as the: 

 * 

 * condition ? inCaseOfTrue : elseCase

 * 

 * java syntax equivalent.

 * 

 * @author mhorst

 *

 */

public class ConditionalPropertySetter implements Process {

	public static final String PARAM_CONDITION = "condition";

	public static final String PARAM_INCASEOFTRUE = "inCaseOfTrue";

	public static final String PARAM_ELSECASE = "elseCase";

	public static final String OUTPUT_PROPERTY_RESULT = "result";

	@Override

	public Map<String, PortType> getInputPorts() {

		return Collections.emptyMap();

	}

	@Override

	public Map<String, PortType> getOutputPorts() {

		return Collections.emptyMap();

	}

	@Override

	public void run(PortBindings portBindings, Configuration conf,

			Map<String, String> parameters) throws Exception {

		String condition = parameters.get(PARAM_CONDITION);

		if (condition == null) {

			throw new RuntimeException("unable to make decision: " + 

					PARAM_CONDITION + " parameter was not set!");

		}

		Properties props = new Properties();

        props.setProperty(OUTPUT_PROPERTY_RESULT, 

        		Boolean.parseBoolean(condition)?

        				parameters.get(PARAM_INCASEOFTRUE):

        					parameters.get(PARAM_ELSECASE));

        OutputStream os = new FileOutputStream(

        		new File(System.getProperty(OOZIE_ACTION_OUTPUT_FILENAME)));

        try {

        	props.store(os, "");	

        } finally {

        	os.close();	

        }

	}

}

package eu.dnetlib.dhp.common.string;

/**

 * Operations on {@link CharSequence} 

 * 

 * @author Łukasz Dumiszewski

*/

public final class CharSequenceUtils {

    //------------------------ CONSTRUCTORS --------------------------

    private CharSequenceUtils() {

        throw new IllegalStateException("may not be initialized");

    }

    //------------------------ LOGIC --------------------------

    /**

     * Converts the given {@link CharSequence} <code>value</code> to {@link String} by using {@link CharSequence#toString()}.

     * Returns empty string if <code>value</code> is null.

     */

    public static String toStringWithNullToEmpty(CharSequence value) {

        return value == null? "": value.toString();

    }

}

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</module>

package eu.dnetlib.dhp.common.counter;

import java.io.File;

import java.io.FileOutputStream;

import java.io.IOException;

import java.io.OutputStream;

import java.util.Properties;

/**

 * Writer of {@link NamedCounters} object into a properties file.

 * 

 * @author madryk

 */

public class NamedCountersFileWriter {

    //------------------------ LOGIC --------------------------

    /**

     * Writes {@link NamedCounters} as a properties file located under

     * provided filePath.

     * 

     * @throws IOException if writing to properties file resulted in an error

     */

    public void writeCounters(NamedCounters counters, String filePath) throws IOException {

        Properties counterProperties = buildPropertiesFromCounters(counters);

        File file = new File(filePath);

        try (OutputStream os = new FileOutputStream(file)) {

            counterProperties.store(os, null);

        }

    }

    //------------------------ PRIVATE --------------------------

    private Properties buildPropertiesFromCounters(NamedCounters counters) {

        Properties properties = new Properties();

        for (String counterName : counters.counterNames()) {

            long count = counters.currentValue(counterName);

            properties.put(counterName, String.valueOf(count));

        }

        return properties;

    }

}

package eu.dnetlib.dhp.common.counter;

import org.apache.spark.AccumulableParam;

import scala.Tuple2;

/**

 * Spark {@link AccumulableParam} for tracking multiple counter values using {@link NamedCounters}.

 * 

 * @author madryk

 */

public class NamedCountersAccumulableParam implements AccumulableParam<NamedCounters, Tuple2<String,Long>> {

    private static final long serialVersionUID = 1L;

    //------------------------ LOGIC --------------------------

    /**

     * Increments {@link NamedCounters} counter with the name same as the first element of passed incrementValue tuple

     * by value defined in the second element of incrementValue tuple.

     */

    @Override

    public NamedCounters addAccumulator(NamedCounters counters, Tuple2<String, Long> incrementValue) {

        counters.increment(incrementValue._1, incrementValue._2);

        return counters;

    }

    /**

     * Merges two passed {@link NamedCounters}.

     */

    @Override

    public NamedCounters addInPlace(NamedCounters counters1, NamedCounters counters2) {

        for (String counterName2 : counters2.counterNames()) {

            counters1.increment(counterName2, counters2.currentValue(counterName2));

        }

        return counters1;

    }

    /**

     * Returns passed initialCounters value without any modifications.

     */

    @Override

    public NamedCounters zero(NamedCounters initialCounters) {

        return initialCounters;

    }

}

package eu.dnetlib.dhp.common.java;

import java.util.Map;

import eu.dnetlib.dhp.common.java.porttype.PortType;

/**

 * A class that groups information about input and output ports, i.e.

 * their (name of the port -> type of the port) mappings. 

 * @author Mateusz Kobos

 */

public class Ports {

	private final Map<String, PortType> input;

	private final Map<String, PortType> output;

	public Ports(Map<String, PortType> input, Map<String, PortType> output){

		this.input = input;

		this.output = output;

	}

	public Map<String, PortType> getInput() {

		return input;

	}

	public Map<String, PortType> getOutput() {

		return output;

	}

}

package eu.dnetlib.dhp.common.java;

import java.util.HashMap;

import java.util.Map;

import java.util.Map.Entry;

import java.util.Properties;

import java.util.Set;

import org.apache.commons.cli.CommandLine;

import org.apache.hadoop.fs.Path;

/**

 * Handles parsing parameters passed to the {@link Process}

 * @author Mateusz Kobos

 *

 */

public class CmdLineParserForProcessRunParameters {

	/** Parse the command line arguments.

	 * 

	 * @param cmdLine command line arguments

	 * @param ports names of ports that ought to be extracted from command line

	 */

	public ProcessParameters run(CommandLine cmdLine, Ports ports) {

		Properties inputProperties = cmdLine.getOptionProperties(

				CmdLineParser.inputPrefix);

		assumePortNamesMatch(CmdLineParser.inputPrefix, inputProperties, 

				ports.getInput().keySet());

		Map<String, Path> inputBindings = getBindings(

				inputProperties, ports.getInput().keySet());

		Properties outputProperties = cmdLine.getOptionProperties(

				CmdLineParser.outputPrefix);

		assumePortNamesMatch(CmdLineParser.outputPrefix, outputProperties, 

				ports.getOutput().keySet());

		Map<String, Path> outputBindings = getBindings(

				outputProperties, ports.getOutput().keySet());

		PortBindings bindings = new PortBindings(inputBindings, outputBindings);

		Properties specialProperties = cmdLine.getOptionProperties(

				CmdLineParser.specialParametersPrefix);

		assumeContainAllMandatoryParameters(

				specialProperties, CmdLineParser.mandatorySpecialParameters);

		Properties rawProperties = cmdLine.getOptionProperties(

				CmdLineParser.processParametersPrefix);

		Map<String, String> processParameters = new HashMap<String, String>();

		for(Entry<Object, Object> entry: rawProperties.entrySet()){

			processParameters.put(

					(String)entry.getKey(),	(String)entry.getValue());

		}

		return new ProcessParameters(bindings, processParameters);

	}

	private static void assumeContainAllMandatoryParameters(

			Properties properties, String[] mandatoryParameters){

		for(String otherParameter: mandatoryParameters){

			if(!properties.containsKey(otherParameter)){

				throw new CmdLineParserException(String.format(

						"Not all mandatory properties are set using the \"%s\" "

						+ "option are given, e.g. \"-%s\" parameter is missing",

						CmdLineParser.specialParametersPrefix, otherParameter));

			}

		}

	}

	private static void assumePortNamesMatch(String cmdLineParamPrefix,

			Properties cmdLineProperties, Set<String> portNames) {

		for (String name : portNames) {

			if (!cmdLineProperties.containsKey(name)) {

				throw new CmdLineParserException(String.format(

					"The port with name \"%s\" is not specified in "

					+ "command line (command line option \"-%s\" is missing)",

					name, cmdLineParamPrefix + name));

			}

		}

		for (Object cmdLineKeyObject : cmdLineProperties.keySet()) {

			String name = (String) cmdLineKeyObject;

			if (!portNames.contains(name)) {

				throw new CmdLineParserException(String.format(

						"A port name \"%s\" which is not specified is given "

						+ "in the command line "

						+ "(command line option \"%s\" is excess)",

						name, cmdLineParamPrefix + name));

			}

		}

	}

	private static Map<String, Path> getBindings(

			Properties cmdLineProperties, Set<String> portNames) {

		Map<String, Path> bindings = new HashMap<String, Path>();

		for (String name : portNames) {

			Path path = new Path((String) cmdLineProperties.get(name));

			bindings.put(name, path);

		}

		return bindings;

	}

}

package eu.dnetlib.dhp.common.java;

import java.lang.reflect.Constructor;

import org.apache.commons.cli.CommandLine;

/**

 * Handles parsing the command line arguments provided by the Oozie

 * to create a {@link Process}

 * @author Mateusz Kobos

 *

 */

public class CmdLineParserForProcessConstruction {

	public Process run(CommandLine cmdLine){

		String[] args = cmdLine.getArgs();

		if(args.length != 1){

			throw new CmdLineParserException("The name of the class has "+

					"to be specified as the first agrument");

		}

		String className = args[0];

		String[] constructorParams = cmdLine.getOptionValues(

				CmdLineParser.constructorPrefix);

		if(constructorParams == null){

			constructorParams = new String[0];

		}

		try {

			Class<?> processClass = Class.forName(className);

			Constructor<?> processConstructor = null;

			if(constructorParams.length == 0){

				try{

					processConstructor = processClass.getConstructor();

					return (Process) processConstructor.newInstance();

				} catch(NoSuchMethodException ex){

				}

			}

			processConstructor = processClass.getConstructor(String[].class);

			return (Process) processConstructor.newInstance(

						(Object)constructorParams);

		} catch (Exception e) {

			throw new CmdLineParserException(String.format(

					"Problem while creating class \"%s\"", className), e);

		}

	}

}

package eu.dnetlib.dhp.common.java.jsonworkflownodes;

import java.util.HashMap;

import java.util.Map;

import org.apache.avro.Schema;

import eu.dnetlib.dhp.common.java.jsonworkflownodes.StringPortSpecificationExtractor.PortSpecification;

import eu.dnetlib.dhp.common.java.porttype.AvroPortType;

import eu.dnetlib.dhp.common.java.porttype.PortType;

import eu.dnetlib.dhp.common.utils.AvroUtils;

/**

 * @author Mateusz Kobos

 */

public class PortSpecifications {

	private static final String[] propertyRegexps = 

			new String[]{"[\\w\\.]+", "[\\w\\./_\\-]+"};

	private final Map<String, SpecificationValues> specs;

    public static class SpecificationValues {

        private final Schema schema;

        private final String jsonFilePath;

        public SpecificationValues(Schema schema, String jsonFilePath) {

            this.schema = schema;

            this.jsonFilePath = jsonFilePath;

        }

        public Schema getSchema() {

            return schema;

        }

        public String getJsonFilePath() {

            return jsonFilePath;

        }

    }

	public PortSpecifications(String[] portSpecifications){

		StringPortSpecificationExtractor portSpecExtractor = 

				new StringPortSpecificationExtractor(propertyRegexps);

		specs = new HashMap<String, SpecificationValues>();

		for(int i = 0; i < portSpecifications.length; i++){

			PortSpecification portSpec = portSpecExtractor.getSpecification(portSpecifications[i]);

			Schema schema = AvroUtils.toSchema(portSpec.getProperties()[0]);

			String jsonPath = portSpec.getProperties()[1];

			specs.put(portSpec.getName(), new SpecificationValues(schema, jsonPath));

		}

	}

	public SpecificationValues get(String portName){

		return specs.get(portName);

	}

	public Map<String, PortType> getPortTypes(){

		Map<String, PortType> ports = new HashMap<String, PortType>();

		for(Map.Entry<String, SpecificationValues> e: specs.entrySet()){

			Schema schema = e.getValue().schema;

			ports.put(e.getKey(), new AvroPortType(schema));

		}

		return ports;	

	}

}

package eu.dnetlib.dhp.common.java;

/**

 * Process exception

 * @author Dominika Tkaczyk

 *

 */

public class ProcessException extends RuntimeException {

	private static final long serialVersionUID = 2758953138374438377L;

	public ProcessException(String message){

		super(message);

	}

	public ProcessException(String message, Throwable cause){

		super(message, cause);

	}

}

package eu.dnetlib.dhp.common;

import java.io.UnsupportedEncodingException;

/**

 * InfoSpaceConstants constants.

 * 

 * @author mhorst

 *

 */

public final class InfoSpaceConstants {

    public static final float CONFIDENCE_TO_TRUST_LEVEL_FACTOR = 0.9f;

    public static final String ENCODING_UTF8 = "utf-8";

    public static final char ROW_PREFIX_SEPARATOR = '|';

    public static final String ID_NAMESPACE_SEPARATOR = "::";

    public static final String CLASSIFICATION_HIERARCHY_SEPARATOR = ID_NAMESPACE_SEPARATOR;

    public static final String INFERENCE_PROVENANCE_SEPARATOR = ID_NAMESPACE_SEPARATOR;

    public static final String ROW_PREFIX_RESULT = "50|";

    public static final String ROW_PREFIX_PROJECT = "40|";

    public static final String ROW_PREFIX_PERSON = "30|";

    public static final String ROW_PREFIX_ORGANIZATION = "20|";

    public static final String ROW_PREFIX_DATASOURCE = "10|";

    public static final String QUALIFIER_BODY_STRING = "body";

    public static final byte[] QUALIFIER_BODY;

    public static final String SEMANTIC_CLASS_MAIN_TITLE = "main title";

    public static final String SEMANTIC_CLASS_PUBLICATION = "publication";

    public static final String SEMANTIC_CLASS_UNKNOWN = "UNKNOWN";

    public static final String SEMANTIC_SCHEME_DNET_PERSON_ROLES = "dnet:personroles";

    public static final String SEMANTIC_SCHEME_DNET_RELATIONS_RESULT_RESULT = "dnet:result_result_relations";

    public static final String SEMANTIC_SCHEME_DNET_RELATIONS_RESULT_PROJECT = "dnet:result_project_relations";

    public static final String SEMANTIC_SCHEME_DNET_TITLE = "dnet:dataCite_title";

    public static final String SEMANTIC_SCHEME_DNET_TITLE_TYPOLOGIES = "dnet:title_typologies";

    public static final String SEMANTIC_SCHEME_DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";

    public static final String SEMANTIC_SCHEME_DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";

    public static final String SEMANTIC_SCHEME_DNET_LANGUAGES = "dnet:languages";

    public static final String SEMANTIC_SCHEME_DNET_PID_TYPES = "dnet:pid_types";

    public static final String SEMANTIC_SCHEME_DNET_CLASSIFICATION_TAXONOMIES = "dnet:subject_classification_typologies";

    // resultResult citation and similarity related

    public static final String SEMANTIC_SCHEME_DNET_DATASET_PUBLICATION_RELS = "dnet:dataset_publication_rels";

    public static final String SEMANTIC_CLASS_TAXONOMIES_ARXIV = "arxiv";

    public static final String SEMANTIC_CLASS_TAXONOMIES_WOS = "wos";

    public static final String SEMANTIC_CLASS_TAXONOMIES_DDC = "ddc";

    public static final String SEMANTIC_CLASS_TAXONOMIES_MESHEUROPMC = "mesheuropmc";

    public static final String SEMANTIC_CLASS_TAXONOMIES_ACM = "acm";

    public static final String EXTERNAL_ID_TYPE_INSTANCE_URL = "dnet:instance-url";

    public static final String EXTERNAL_ID_TYPE_UNKNOWN = "unknown";

    // publication types class ids

    public static final String SEMANTIC_CLASS_INSTANCE_TYPE_ARTICLE = "0001";

    public static final String SEMANTIC_CLASS_INSTANCE_TYPE_DATASET = "0021";

    static {

        try {

            QUALIFIER_BODY = QUALIFIER_BODY_STRING.getBytes(ENCODING_UTF8);

        } catch (UnsupportedEncodingException e) {

            throw new RuntimeException(e);

        }

    }

    private InfoSpaceConstants() {

    }

}

package eu.dnetlib.dhp.common.lock;

import java.security.InvalidParameterException;

import java.util.Collections;

import java.util.Map;

import java.util.concurrent.Semaphore;

import org.apache.commons.lang.StringUtils;

import org.apache.hadoop.conf.Configuration;

import org.apache.hadoop.ha.ZKFailoverController;

import org.apache.log4j.Logger;

import org.apache.zookeeper.CreateMode;

import org.apache.zookeeper.KeeperException;

import org.apache.zookeeper.Watcher.Event;

import org.apache.zookeeper.ZooDefs;

import org.apache.zookeeper.ZooKeeper;

import com.google.common.base.Preconditions;

import com.google.common.base.Stopwatch;

import eu.dnetlib.dhp.common.java.PortBindings;

import eu.dnetlib.dhp.common.java.porttype.PortType;

/**

 * Zookeeper lock managing process. Blocks until lock is released.

 * 

 * @author mhorst

 *

 */

public class LockManagingProcess implements eu.dnetlib.dhp.common.java.Process {

	public static final String DEFAULT_ROOT_NODE = "/cache";

	public static final String NODE_SEPARATOR = "/";

	public static final String PARAM_ZK_SESSION_TIMEOUT = "zk_session_timeout";

	public static final String PARAM_NODE_ID = "node_id";

	public static final String PARAM_LOCK_MODE = "mode";

	public static enum LockMode {

		obtain,

		release

	}

	public static final int DEFAULT_SESSION_TIMEOUT = 60000;

	public static final Logger log = Logger.getLogger(LockManagingProcess.class);

	@Override

	public Map<String, PortType> getInputPorts() {

		return Collections.emptyMap();

	}

	@Override

	public Map<String, PortType> getOutputPorts() {

		return Collections.emptyMap();

	}

	@Override

	public void run(PortBindings portBindings, Configuration conf,

			Map<String, String> parameters) throws Exception {

		Preconditions.checkArgument(parameters.containsKey(PARAM_NODE_ID), "node id not provided!");

		Preconditions.checkArgument(parameters.containsKey(PARAM_LOCK_MODE), "lock mode not provided!");

		String zkConnectionString = conf.get(ZKFailoverController.ZK_QUORUM_KEY);

		Preconditions.checkArgument(StringUtils.isNotBlank(zkConnectionString), 

		        "zookeeper quorum is unknown, invalid '%s' property value: %s", ZKFailoverController.ZK_QUORUM_KEY, zkConnectionString);

		int sessionTimeout = parameters.containsKey(PARAM_ZK_SESSION_TIMEOUT)?

		        Integer.valueOf(parameters.get(PARAM_ZK_SESSION_TIMEOUT)) : DEFAULT_SESSION_TIMEOUT;

		final ZooKeeper zooKeeper = new ZooKeeper(zkConnectionString, sessionTimeout, (e) -> {

		 // we are not interested in generic events

		});

//		initializing root node if does not exist

		if (zooKeeper.exists(DEFAULT_ROOT_NODE, false) == null) {

			log.info("initializing root node: " + DEFAULT_ROOT_NODE);

			zooKeeper.create(DEFAULT_ROOT_NODE, new byte[0], ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);

			log.info("root node initialized");

		}

		final String nodePath = generatePath(parameters.get(PARAM_NODE_ID), DEFAULT_ROOT_NODE);

		final Semaphore semaphore = new Semaphore(1);

		semaphore.acquire();

		switch(LockMode.valueOf(parameters.get(PARAM_LOCK_MODE))) {

		    case obtain: {

		        obtain(zooKeeper, nodePath, semaphore);

		        break;

		    }

		    case release: {

		        release(zooKeeper, nodePath);

		        break;

		    }

		    default: {

		        throw new InvalidParameterException("unsupported lock mode: " + parameters.get(PARAM_LOCK_MODE));

		    }

		}

	}

	// ------------------------- PRIVATE --------------------------

	private void obtain(final ZooKeeper zooKeeper, final String nodePath, final Semaphore semaphore) throws KeeperException, InterruptedException {

        log.info("trying to obtain lock: " + nodePath);

        if (zooKeeper.exists(nodePath, (event) -> {

            if (Event.EventType.NodeDeleted == event.getType()) {

                try {

                    log.info(nodePath + " lock release detected");

                    log.info("creating new lock instance: " + nodePath + "...");

                    zooKeeper.create(nodePath, new byte[0], ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);

                    log.info("lock" + nodePath + " created");

                    semaphore.release();

                } catch (KeeperException e) {

                    throw new RuntimeException(e);

                } catch (InterruptedException e) {

                    throw new RuntimeException(e);

                }

            }

        }) == null) {

            log.info("lock not found, creating new lock instance: " + nodePath);

            zooKeeper.create(nodePath, new byte[0], ZooDefs.Ids.OPEN_ACL_UNSAFE, CreateMode.PERSISTENT);

            log.info("lock" + nodePath + " created");

            semaphore.release();

        } else {

            // waiting until node is removed by other lock manager

            log.info("waiting until lock is released");

            Stopwatch timer = new Stopwatch().start();

            semaphore.acquire();

            log.info("lock released, waited for " + timer.elapsedMillis() + " ms");

            semaphore.release();

        }

	}

	private void release(final ZooKeeper zooKeeper, final String nodePath) throws InterruptedException, KeeperException {

	    log.info("removing lock" + nodePath + "...");

        zooKeeper.delete(nodePath, -1);

        log.info("lock" + nodePath + " removed");

	}

	private static final String generatePath(String nodeId, String rootNode) {

		return rootNode + NODE_SEPARATOR + nodeId.replace('/', '_');

	}

}

/*

 * This file is part of CoAnSys project.

 * Copyright (c) 2012-2015 ICM-UW

 * 

 * CoAnSys is free software: you can redistribute it and/or modify

 * it under the terms of the GNU Affero General Public License as published by

 * the Free Software Foundation, either version 3 of the License, or

 * (at your option) any later version.

 * CoAnSys is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

 * GNU Affero General Public License for more details.

 * 

 * You should have received a copy of the GNU Affero General Public License

 * along with CoAnSys. If not, see <http://www.gnu.org/licenses/>.

 */

package eu.dnetlib.dhp.common.string;

import java.io.Serializable;

import java.util.List;

import org.apache.commons.lang3.StringUtils;

import com.google.common.collect.ImmutableList;

/**

 * An implementation of {@link StringNormalizer} that normalizes strings for non-strict comparisons

 * in which one does not care about characters other than letters and digits or about differently written diacritics.

 *

 * @author Łukasz Dumiszewski

 *

 */

public final class LenientComparisonStringNormalizer implements StringNormalizer, Serializable {

    private static final long serialVersionUID = 1L;

    private List<Character> whitelistCharacters;

    //------------------------ CONSTRUCTORS --------------------------

    public LenientComparisonStringNormalizer() {

        this(ImmutableList.of());

    }

    /**

     * @param whitelistCharacters - non alphanumeric characters that will not be removed

     *      during normalization

     */

    public LenientComparisonStringNormalizer(List<Character> whitelistCharacters) {

        this.whitelistCharacters = whitelistCharacters;

    }

    //------------------------ LOGIC --------------------------

    /**

     * Normalizes the given value. <br/>

     * The normalized strings are better suited for non-strict comparisons, in which one does NOT care about characters that are

     * neither letters nor digits; about accidental spaces or different diacritics etc. <br/><br/>

     * This method:

     * <ul>

     * <li>Replaces all characters that are not letters or digits with spaces (except those on whitelist characters list)</li>

     * <li>Replaces white spaces with spaces </li>

     * <li>Trims</li>

     * <li>Compacts multi-space gaps to one-space gaps</li>

     * <li>Removes diacritics</li>

     * <li>Changes characters to lower case</li>

     * </ul>

     * Returns "" if the passed value is null or blank

     *

     * @param value the string to normalize 

     * @see DiacriticsRemover#removeDiacritics(String, boolean)

     *

     *

     */

    public String normalize(String value) {

        if (StringUtils.isBlank(value)) {

            return "";

        }

        String result = value;

        result = DiacriticsRemover.removeDiacritics(result);

        result = removeNonLetterDigitCharacters(result);

        result = result.toLowerCase();

        result = result.trim().replaceAll(" +", " ");

        return result;

    }

    //------------------------ PRIVATE --------------------------

    private String removeNonLetterDigitCharacters(final String value) {

        StringBuilder sb = new StringBuilder();

        for (int i = 0; i < value.length(); ++i) {

            char c = value.charAt(i);

            if (Character.isLetterOrDigit(c) || whitelistCharacters.contains(c)) {

                sb.append(c);

            } else {

                sb.append(' ');

            }

        }

        return sb.toString();

    }

}

/*

 * This file is part of CoAnSys project.

 * Copyright (c) 2012-2015 ICM-UW

 * 

 * CoAnSys is free software: you can redistribute it and/or modify

 * it under the terms of the GNU Affero General Public License as published by

 * the Free Software Foundation, either version 3 of the License, or

 * (at your option) any later version.

 * CoAnSys is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

 * GNU Affero General Public License for more details.

 * 

 * You should have received a copy of the GNU Affero General Public License

 * along with CoAnSys. If not, see <http://www.gnu.org/licenses/>.

 */

package eu.dnetlib.dhp.common.string;

import java.text.Normalizer;

import java.util.HashMap;

import java.util.Map;

/**

 * Mapping to the basic Latin alphabet (a-z, A-Z). In most cases, a character is

 * mapped to the closest visual form, rather than functional one, e.g.: "ö" is

 * mapped to "o" rather than "oe", and "đ" is mapped to "d" rather than "dj" or

 * "gj". Notable exceptions include: "ĸ" mapped to "q", "ß" mapped to "ss", and

 * "Þ", "þ" mapped to "Y", "y".

 *

 * <p> Each character is processed as follows: <ol> <li>the character is

 * compatibility decomposed,</li> <li>all the combining marks are removed,</li>

 * <li>the character is compatibility composed,</li> <li>additional "manual"

 * substitutions are applied.</li> </ol> </p>

 *

 * <p> All the characters from the "Latin-1 Supplement" and "Latin Extended-A"

 * Unicode blocks are mapped to the "Basic Latin" block. Characters from other

 * alphabets are generally left intact, although the decomposable ones may be

 * affected by the procedure. </p>

 *

 * @author Lukasz Bolikowski (bolo@icm.edu.pl)

 * 

 * @author Łukasz Dumiszewski /just copied from coansys-commons/

 *

 */

public final class DiacriticsRemover {

    private static final Character[] from = {

        'Æ', 'Ð', 'Ø', 'Þ', 'ß', 'æ', 'ð', 'ø', 'þ', 'Đ', 'đ', 'Ħ',

        'ħ', 'ı', 'ĸ', 'Ł', 'ł', 'Ŋ', 'ŋ', 'Œ', 'œ', 'Ŧ', 'ŧ'};

    private static final String[] to = {

        "AE", "D", "O", "Y", "ss", "ae", "d", "o", "y", "D", "d", "H",

        "h", "i", "q", "L", "l", "N", "n", "OE", "oe", "T", "t"};

    private static Map<Character, String> lookup = buildLookup();

    //------------------------ CONSTRUCTORS -------------------

    private DiacriticsRemover() {}

    //------------------------ LOGIC --------------------------

    /**

     * Removes diacritics from a text.

     *

     * @param text Text to process.

     * @return Text without diacritics.

     */

    public static String removeDiacritics(String text) {

        if (text == null) {

            return null;

        }

        String tmp = Normalizer.normalize(text, Normalizer.Form.NFKD);

        StringBuilder builder = new StringBuilder();

        for (int i = 0; i < tmp.length(); i++) {

            Character ch = tmp.charAt(i);

            if (Character.getType(ch) == Character.NON_SPACING_MARK) {

                continue;

            }

            if (lookup.containsKey(ch)) {

                builder.append(lookup.get(ch));

            } else {

                builder.append(ch);

            }

        }

        return builder.toString();

    }

    //------------------------ PRIVATE --------------------------

    private static Map<Character, String> buildLookup() {

        if (from.length != to.length) {

            throw new IllegalStateException();

        }

        Map<Character, String> _lookup = new HashMap<Character, String>();

        for (int i = 0; i < from.length; i++) {

            _lookup.put(from[i], to[i]);

        }

        return _lookup;

    }

}

package eu.dnetlib.dhp.common.report;

import eu.dnetlib.dhp.common.schemas.ReportEntry;

import eu.dnetlib.dhp.common.schemas.ReportEntryType;

/**

 * Factory of {@link ReportEntry} objects.

 * 

 * @author madryk

 */

public final class ReportEntryFactory {

    // ----------------------- CONSTRUCTORS -----------------------------

    private ReportEntryFactory() {}

    // ----------------------- LOGIC ------------------------------------

    /**

     * Creates {@link ReportEntry} with {@link ReportEntryType#COUNTER} type

     */

    public static ReportEntry createCounterReportEntry(String key, long count) {

        return new ReportEntry(key, ReportEntryType.COUNTER, String.valueOf(count));

    }

    /**

     * Creates {@link ReportEntry} with {@link ReportEntryType#DURATION} type

     */

    public static ReportEntry createDurationReportEntry(String key, long duration) {

        return new ReportEntry(key, ReportEntryType.DURATION, String.valueOf(duration));

    }

}

package eu.dnetlib.dhp.common.counter;

import java.io.Serializable;

import java.util.Collection;

import java.util.Map;

import com.google.common.base.Preconditions;

import com.google.common.collect.Maps;

/**

 * Class that groups several counters which are identified by name (<code>String</code> value).

 * 

 * @author madryk

 */

public class NamedCounters implements Serializable {

    private static final long serialVersionUID = 1L;

    private final Map<String, Long> counters;

    //------------------------ CONSTRUCTORS --------------------------

    /**

     * Creates {@link NamedCounters} with empty initial counters.

     */

    public NamedCounters() {

        this.counters = Maps.newHashMap();

    }

    /**

     * Creates {@link NamedCounters} with initial counters.<br/>

     * Starting value of initial counters is zero.

     * 

     * @param initialCounterNames - names of initial counters

     */

    public NamedCounters(String[] initialCounterNames) {

        Preconditions.checkNotNull(initialCounterNames);

        this.counters = Maps.newHashMap();

        for (String initialCounterName : initialCounterNames) {

            this.counters.put(initialCounterName, 0L);

        }

    }

    /**

     * Creates {@link NamedCounters} with initial counters.<br/>

     * Starting value of initial counters is zero.

     * 

     * @param initialCounterNamesEnumClass - enum class providing names of initial counters

     */

    public <E extends Enum<E>> NamedCounters(Class<E> initialCounterNamesEnumClass) {

        Preconditions.checkNotNull(initialCounterNamesEnumClass);

        this.counters = Maps.newHashMap();

        Enum<?>[] enumConstants = initialCounterNamesEnumClass.getEnumConstants();

        for (int i=0; i<enumConstants.length; ++i) {

            this.counters.put(enumConstants[i].name(), 0L);

        }

    }

    //------------------------ LOGIC --------------------------

    /**

     * Increments value by 1 of a counter with the name specified as parameter.<br/>

     * Internally uses {@link #increment(String, Long)} 

     */

    public void increment(String counterName) {

        increment(counterName, 1L);

    }

    /**

     * Increments value of a counter with the name specified as parameter by the given value.<br/>

     * If current instance of {@link NamedCounters} does not contain counter

     * with provided name, then before incrementing counter will be created with starting

     * value equal to zero.

     */

    public void increment(String counterName, Long incrementValue) {

        long oldValue = counters.getOrDefault(counterName, 0L);

        counters.put(counterName, oldValue + incrementValue);

    }

    /**

     * Returns current value of a counter with the name specified as parameter.

     * 

     * @throws IllegalArgumentException when {@link NamedCounters} does not contain counter

     *      with provided name

     */

    public long currentValue(String counterName) {

        if (!counters.containsKey(counterName)) {

            throw new IllegalArgumentException("Couldn't find counter with name: " + counterName);

        }

        return counters.get(counterName);