D-Net

package eu.dnetlib.dli;

import java.util.List;

import java.util.Map;

import javax.annotation.PostConstruct;

import com.google.common.collect.HashBiMap;

import eu.dnetlib.data.transform.OntologyLoader;

import eu.dnetlib.rmi.enabling.ISLookUpService;

import org.apache.commons.lang3.tuple.Pair;

import org.springframework.beans.factory.annotation.Autowired;

import java.util.regex.Pattern;

    public static final Map<String, String> resolvedTypes = new HashMap<String, String>() {

        {

            put("pdb", "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s");

            put("ncbi-n", "http://www.ncbi.nlm.nih.gov/gquery/?term=%s");

            put("pmid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");

            put("pmcid", "http://www.ncbi.nlm.nih.gov/pmc/articles/%s");

            put("pubmedid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");

            put("doi", "http://dx.doi.org/%s");

            put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("nuccore", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("swiss-prot", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("arrayexpress", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("biomodels", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("bmrb", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("ena", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("geo", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("ensembl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("mgi", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("bind", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("pride", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("ddbj", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("bioproject", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("embl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

            put("sra", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");

        }

    private static DLIUtils instance;

    private Map<String, String> dataciteDatasource;

            relations = HashBiMap.create();

            relations.put("IsCitedBy", "Cites");

            relations.put("IsSupplementTo", "IsSupplementedBy");

            relations.put("IsReferencedBy", "References");

        }

        return relations;

    }

        if (datasources.keySet().size() == 0) {

            generateDSMap();

        }

        if (!datasources.containsKey(datasourcePrefix))

            return "";

        return datasources.get(datasourcePrefix).getRight();

    }

        if (datasources.keySet().size() == 0) {

            generateDSMap();

        }

        if (!datasources.containsKey(datasourcePrefix))

            return "";

        return datasources.get(datasourcePrefix).getLeft();

    }

        if (instance.getDataciteDatasource() != null) {

            return instance.getDataciteDatasource().get(publisher.trim().toLowerCase());

        }

        return "";

    }

        if (datasources.keySet().size() > 0)

            return;

                + "return concat($x//FIELD[./key='NamespacePrefix']/value/text(),'@--@',$x//FIELD[./key='DataSourceId']/value/text(),'@--@',$x//ENGLISH_NAME )";

        final List<String> results = lookupService.quickSearchProfile(query);

        datasources.clear();

            results.forEach(it -> {

                final String[] splitted = it.split("@--@");

                if (splitted.length == 3) {

                    datasources.put(splitted[0], new ImmutablePair<>(splitted[1], splitted[2]));

                }

            });

    }

        if (pidType != null && !pidType.toLowerCase().equals("doi")) {

            if (pid != null && pid.contains("http://dx.doi.org/") || pid.contains("http://doi.org/"))

                return "doi";

        }

        return pidType;

    }

        if (input != null) {

            return input.replace("http://dx.doi.org/", "").replace("http://doi.org/", "");

        }

        return null;

    }

    public static String geussPidType(final String pidType, final String pid ) {

        if (isValidDoi(pid)!= null){

            return "doi";

        }

        return pidType;

    }

    public static String geussPidValue(final String pid) {

        if (isValidDoi(pid)!= null){

            return isValidDoi(pid);

        }

        return pid;

    }

        PID correctPID = createCorrectPID(pid, pidType);

        correctPID.setResolvedUrl(resolvedUrl);

        return correctPID;

    }

        final String validDoi = isValidDoi(pid);

        if (validDoi!= null) {

            return new PID(validDoi.toLowerCase(), "doi");

        }

        return new PID(pid, pidType);

    }

    public static String isValidDoi(final String url) {

        final Pattern pattern = Pattern.compile(regex);

        final Matcher matcher = pattern.matcher(url);

        if (matcher.find())

            return matcher.group(0);

        return null;

    }

            return null;

        }

        return Character.toLowerCase(relation.charAt(0)) + relation.substring(1);

    public static String getInverse(final String relation) throws Exception {

        if (ontologies == null) {

            ontologies = OntologyLoader.loadOntologiesFromIS();

        }

        final String normalizedRelation = normalizeRelation(relation);

        try {

            System.out.println("Relation not found = " + normalizedRelation);

            return "related";

        }

    }

        if (StringUtils.isBlank(pid) || StringUtils.isBlank(pidtype))

            throw new RuntimeException("Error pid or pidtype cannot be null");

        return DnetXsltFunctions.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidtype.toLowerCase().trim()));

    }

     * This method is used only for test Scope

     *

     * @param mockInstance

     */

    public static void setInstance(final DLIUtils mockInstance) {

        instance = mockInstance;

    }

        instance = this;

        final InputStream inputStream = this.getClass().getResourceAsStream("/eu/dnetlib/transformation/data-center.json");

        dataciteDatasource = new Gson().fromJson(IOUtils.toString(inputStream), Map.class);

    }

        return serviceLocator;

    }

        this.serviceLocator = serviceLocator;

    }

    public Map<String, String> getDataciteDatasource() {

        return dataciteDatasource;

    }