D-Net

package eu.dnetlib.data.claims.parser;

import com.google.gson.Gson;

import eu.dnetlib.data.claims.entity.Result;

import eu.dnetlib.data.claims.utils.ClaimUtils;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import org.w3c.dom.Document;

import org.w3c.dom.NodeList;

import org.xml.sax.InputSource;

import org.xml.sax.SAXException;

import javax.xml.parsers.DocumentBuilder;

import javax.xml.parsers.DocumentBuilderFactory;

import javax.xml.parsers.ParserConfigurationException;

import javax.xml.transform.Transformer;

import javax.xml.transform.TransformerFactory;

import javax.xml.transform.dom.DOMSource;

import javax.xml.transform.stream.StreamResult;

import javax.xml.xpath.XPath;

import javax.xml.xpath.XPathConstants;

import javax.xml.xpath.XPathExpressionException;

import javax.xml.xpath.XPathFactory;

import java.io.BufferedReader;

import java.io.IOException;

import java.io.StringReader;

import java.io.StringWriter;

import java.math.BigInteger;

import java.security.MessageDigest;

import java.security.NoSuchAlgorithmException;

import java.util.List;

/**

 * Created by kiatrop on 5/2/2016.

 */

public class ExternalRecordParser {

    /**

     * Gets the json response from crossref API

     * and returns a Result object

     * *

     * @param json

     * @return Result or null

     */

    private static final Logger logger = LogManager.getLogger(ExternalRecordParser.class);

    public static Result crossref2Result(String json) {

        Result result = null;

        if (json == null){

            return result;

        }

        BufferedReader br = new BufferedReader(new StringReader(json));

        //convert the json string back to object

        Gson gson = new Gson();

        CrossrefResponse obj = gson.fromJson(br, CrossrefResponse.class);

        if(obj!=null && obj.getMessage().getItems().size()>0){

            result= new Result();

            result.setMetadataRecord(json);

            result.setRecordFormat(ClaimUtils.FORMAT_JSON);

//            result.setFound(true);

            result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_CROSSREF);

            CrossrefResponse.Message.Item item = obj.getMessage().getItems().get(0);

            if (item.getTitle()!=null && item.getTitle().size()>0){

                result.setTitle(item.getTitle().get(0));

                if(item.getAuthor() != null) {

                    for (int i = 0; i < item.getAuthor().size(); i++) {

                        result.getAuthors().put(i + "", item.getAuthor().get(i).getGiven() + " " + item.getAuthor().get(i).getFamily());

                    }

                }

            }

//            System.out.println(item.getDOI());

            result.setDoi(item.getDOI());

            result.setOpenaireId(createOpenaireId(item.getDOI()));

            result.setExternalUrl(item.getUrl());

            if(result.getDoi()!=null&& result.getExternalUrl()==null){

                result.setExternalUrl(ClaimUtils.PREFIX_URL_FOR_DOI + result.getDoi());

            }

            result.setResultType(ClaimUtils.PUBLICATION);

        }

        return result;

    }

    public static Result dataciteJson2Result(String json) {

        Result result = null;

        if (json == null){

            return result;

        }

        BufferedReader br = new BufferedReader(new StringReader(json));

        //convert the json string back to object

        Gson gson = new Gson();

        DataciteResponse obj = gson.fromJson(br, DataciteResponse.class);

        System.out.println(json);

        if(obj!=null && obj.getData() != null ){

            result= new Result();

            result.setMetadataRecord(json);

            result.setRecordFormat(ClaimUtils.FORMAT_JSON);

//            result.setFound(true);

            result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_DATACITE);

            DataciteResponse.Data.Attributes item = obj.getData().getAttributes();

            if (item.getTitle()!=null){

                result.setTitle(item.getTitle());

                if(item.getAuthor() != null) {

                    for (int i = 0; i < item.getAuthor().size(); i++) {

                        result.getAuthors().put(i + "", (item.getAuthor().get(i).getGiven() != null)?(item.getAuthor().get(i).getGiven() + " " + item.getAuthor().get(i).getFamily()):item.getAuthor().get(i).getLiteral());

                    }

                }

            }

            System.out.println(item.getDoi());

            result.setDoi(item.getDoi());

            result.setOpenaireId(createOpenaireId(item.getDoi()));

            if(result.getDoi()!=null&& result.getExternalUrl()==null){

                result.setExternalUrl(ClaimUtils.PREFIX_URL_FOR_DOI + result.getDoi());

            }

            result.setResultType(ClaimUtils.DATASET);

        }

        return result;

    }

    /**

     *

     * @param xml

     * @param orcidworkid The id from DMF identifier[@identifierType='orcidworkid'] {orcid + work-id}

     * @return Result or null

     */

    public static Result orcid2Result(String xml, String orcidworkid) {

         Result result = null;

        if (xml == null || orcidworkid == null){

            return result;

        }

        String orcidwork = orcidworkid.substring(20, orcidworkid.length());

        System.out.println();

        try {

            DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();

            DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();

            InputSource is = new InputSource(new StringReader(xml));

            Document document = dBuilder.parse(is);

            XPathFactory xPathfactory= XPathFactory.newInstance();

            XPath xpath = xPathfactory.newXPath();

            NodeList nl;

            System.out.println(orcidwork);

            NodeList worknl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']").evaluate(document,XPathConstants.NODESET);

            for( int n = 0; n<worknl.getLength(); n++){

                String code = (String) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']/@put-code").evaluate(worknl.item(n), XPathConstants.STRING);

                result = new Result();

                result.setResultType(ClaimUtils.PUBLICATION);

                nl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']/*[name()='work:title']/*[name()='common:title']/text()").evaluate(worknl.item(n), XPathConstants.NODESET);

                if (nl.getLength() > 0) {

                    result.setTitle(nl.item(0).getNodeValue());

                }

                nl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']//*[name()='common:external-id']").evaluate(worknl.item(n), XPathConstants.NODESET);

                for (int i = 0; i < nl.getLength(); i++) {

                    NodeList identifiersNl;

                    String type=null;

                    String id=null;

                    identifiersNl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']//*[name()='common:external-id-type']/text()").evaluate(nl.item(i), XPathConstants.NODESET);

                    if (identifiersNl.getLength() > 0) {

                        type=identifiersNl.item(0).getNodeValue();

                    }

                    identifiersNl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']//*[name()='common:external-id-value']/text()").evaluate(nl.item(i), XPathConstants.NODESET);

                    if (identifiersNl.getLength() > 0) {

                        id=identifiersNl.item(0).getNodeValue();

                    }

                    if(type != null && type.equals("doi") && id != null){

                        result.setDoi(id);

                        result.setExternalUrl(ClaimUtils.PREFIX_URL_FOR_DOI + id);

                    }

                    //more types (isbn)

                }

                if(result.getExternalUrl()==null) {

                    nl = (NodeList) xpath.compile("//*[name()='work:work'][@put-code='"+orcidwork+"']//*[name()='common:source']/*[name()='common:source-client-id']/*[name()='common:uri']/text()").evaluate(document, XPathConstants.NODESET);

                    if (nl.getLength() > 0) {

                        result.setExternalUrl(nl.item(0).getNodeValue());

                    }

                }

                nl = (NodeList) xpath.compile("//*[name()='work:work-summary'][@put-code='"+orcidwork+"']//*[name()='work:work-summary']").evaluate(document, XPathConstants.NODESET);

                for (int i = 0; i < nl.getLength(); i++) {

                    if(!worknl.item(0).isEqualNode(nl.item(i))) {

                        nl.item(i).getParentNode().removeChild(nl.item(i));

                    }

                }

                DOMSource domSource = new DOMSource(document);

                StringWriter writer = new StringWriter();

                StreamResult streamResult = new StreamResult(writer);

                TransformerFactory tf = TransformerFactory.newInstance();

                Transformer transformer = tf.newTransformer();

                transformer.transform(domSource, streamResult);

                result.setOrcidworkid(orcidworkid);

                result.setOpenaireId(createOpenaireId(orcidworkid));

                result.setMetadataRecord(writer.toString());

                result.setRecordFormat(ClaimUtils.FORMAT_XML);

                result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_ORCID);

//                result.setFound(true);

            }

        } catch (Exception e) {

            logger.error("Error parsing Orcid result\n"+xml,e);

        }

        return result;

    }

    /**

     *

     * @param xml

     * @return Result object or null

     */

    public static Result datacite2Result(String xml) {

        logger.debug("Datacite xml response:\n"+xml);

        Result result = null;

        if (xml != null ) {

            try {

                DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();

                DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();

                InputSource is = new InputSource(new StringReader(xml));

                Document document = dBuilder.parse(is);

                XPathFactory xPathfactory = XPathFactory.newInstance();

                XPath xpath = xPathfactory.newXPath();

                NodeList nl;

                nl = (NodeList) xpath.compile("//*[local-name()='identifier']/text()").evaluate(document, XPathConstants.NODESET);

                if (nl.getLength() > 0) {

                    result = new Result();

                    result.setResultType(ClaimUtils.DATASET);

                    result.setDoi(nl.item(0).getNodeValue());

                    result.setExternalUrl("http://dx.doi.org/" + result.getDoi());

                    result.setOpenaireId(createOpenaireId(result.getDoi()));

                    nl = (NodeList) xpath.compile("//*[local-name()='title']/text()").evaluate(document, XPathConstants.NODESET);

                    if (nl.getLength() > 0) {

                        result.setTitle(nl.item(0).getNodeValue());

                    }

                    nl = (NodeList) xpath.compile("//*[local-name()='creator']/text()").evaluate(document, XPathConstants.NODESET);

                    if (nl.getLength() > 0) {

                        for (int i = 0; i < nl.getLength(); i++) {

                            result.getAuthors().put(i + "", nl.item(i).getNodeValue());

                        }

                    }

                    result.setMetadataRecord(xml);

                    result.setRecordFormat(ClaimUtils.FORMAT_XML);

                    result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_DATACITE);

//                result.setFound(true);

                    logger.debug("Datacite result" + result.toString());

                } else {

                  logger.error("Couldn't parse Datacite result\n" + xml);

                }

                } catch(ParserConfigurationException | IOException | XPathExpressionException |SAXException e){

                    logger.error("Error parsing Orcid result\n"+xml,e);

                }

        }

            return result;

    }

    public static String createOpenaireId(String id){

//        System.out.println("createOpenaireId from id:" +id);

        if(id==null){

            return null;

        }

        String openaireId=id;

        MessageDigest m= null;

        try {

            m = MessageDigest.getInstance("MD5");

            m.update(id.getBytes(),0,id.length());

            openaireId = new BigInteger(1,m.digest()).toString(16);

            while(openaireId.length() < 32 ){

                openaireId = "0"+openaireId;

            }

        } catch (NoSuchAlgorithmException e) {

            logger.error("Couldn't instatiate md5 algorithm",e);

        }

        openaireId ="userclaim___::"+openaireId;

        return openaireId;

    }

}

/**

 * The following classes display the crossref structure of API response

 * They are used for parsing the json CrossrefResponse

 */

class CrossrefResponse {

    String status;

    Message message;

    public String getStatus() {

        return status;

    }

    public Message getMessage() {

        return message;

    }

    class Message{

        List<Item> items;

        public List<Item> getItems() {

            return items;

        }

        class Item {

            private String DOI;

            private List<String> title;

            private List<Author> author;

            private String Url;

            private String type;

            private String source;

            public String getDOI() {

                return DOI;

            }

            public List<String> getTitle() {

                return title;

            }

            public List<Author> getAuthor() { return author;}

            public String getUrl() {

                return Url;

            }

            public String getType() {

                return type;

            }

            public String getSource() {

                return source;

            }

            class Author {

                String given;

                String family;

                public String getGiven() {

                    return given;

                }

                public String getFamily() {

                    return family;

                }

            }

        }

    }

}

class DataciteResponse {

    Data data;

    public Data getData() {

        return data;

    }

    class Data{

            private Attributes attributes;

            public Attributes getAttributes() {

                return attributes;

            }

            class Attributes{

                private String doi;

                private String containerTitle;

                private String published;

                private String title;

                private List<Author> author;

                public String getDoi() {

                    return doi;

                }

                public String getContainerTitle() {

                    return containerTitle;

                }

                public String getPublished() {

                    return published;

                }

                public String getTitle() {

                    return title;

                }

                public List<Author> getAuthor() {

                    return author;

                }

            }

            class Author {

                String given;

                String family;

                String literal;

                public String getGiven() {

                    return given;

                }

                public String getFamily() {

                    return family;

                }

                public String getLiteral() {

                    return literal;

                }

            }

        }

}