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package eu.dnetlib.functionality.modular.ui.vocabularies.persistence;
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import java.io.IOException;
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import java.io.StringReader;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.Map;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import eu.dnetlib.functionality.modular.ui.vocabularies.model.Relation;
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import eu.dnetlib.functionality.modular.ui.vocabularies.model.Synonym;
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import eu.dnetlib.functionality.modular.ui.vocabularies.model.Term;
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import eu.dnetlib.functionality.modular.ui.vocabularies.model.Vocabulary;
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import eu.dnetlib.miscutils.datetime.DateUtils;
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import eu.dnetlib.rmi.enabling.*;
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import org.antlr.stringtemplate.StringTemplate;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringEscapeUtils;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.io.SAXReader;
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public class RegistryServiceVocabularyDAO extends VocabularyDAO {
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@Override
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public List<Vocabulary> getVocabularies() throws VocabularyException {
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try {
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final String query =
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"for $x in collection('/db/DRIVER/VocabularyDSResources/VocabularyDSResourceType') order by $x//VOCABULARY_NAME "
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+ "return concat ($x//RESOURCE_IDENTIFIER/@value,' §§§ ',$x//VOCABULARY_NAME,' §§§ ',$x//VOCABULARY_DESCRIPTION,' §§§ ',$x//VOCABULARY_NAME/@code)";
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final List<Vocabulary> vocabularies = Lists.transform(this.serviceLocator.getService(ISLookUpService.class).quickSearchProfile(query),
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s -> {
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final String[] tokens = s.split("§§§");
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return new Vocabulary(tokens[0].trim(), tokens[1].trim(), tokens[2].trim(), tokens[3].trim());
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});
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return vocabularies;
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} catch (final ISLookUpException e) {
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throw new VocabularyException(e);
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}
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}
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@Override
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public List<Term> getTerms(final String vocabularyId) throws VocabularyException {
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try {
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final String profile = this.serviceLocator.getService(ISLookUpService.class).getResourceProfile(vocabularyId);
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final Document doc = new SAXReader().read(new StringReader(profile));
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final Map<String, Term> terms = Maps.newHashMap();
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for (final Object t : doc.selectNodes("//TERM")) {
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final Element termNode = (Element) t;
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final String code = termNode.valueOf("@code");
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if (!terms.containsKey(code)) {
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final Term term = new Term();
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term.setEnglishName(termNode.valueOf("@english_name"));
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term.setNativeName(termNode.valueOf("@native_name"));
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term.setEncoding(termNode.valueOf("@encoding"));
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term.setCode(code);
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term.setSynonyms(new ArrayList<Synonym>());
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term.setRelations(new ArrayList<Relation>());
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terms.put(code, term);
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}
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final Term term = terms.get(code);
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for (final Object s : termNode.selectNodes(".//SYNONYM")) {
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final Element synNode = (Element) s;
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final Synonym syn = new Synonym();
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syn.setTerm(synNode.valueOf("@term"));
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syn.setEncoding(synNode.valueOf("@encoding"));
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term.getSynonyms().add(syn);
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}
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for (final Object r : termNode.selectNodes(".//RELATION")) {
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final Element relNode = (Element) r;
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final Relation rel = new Relation();
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rel.setCode(relNode.valueOf("@code"));
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rel.setType(relNode.valueOf("@type"));
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term.getRelations().add(rel);
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}
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Collections.sort(term.getSynonyms());
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Collections.sort(term.getRelations());
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}
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final List<Term> list = Lists.newArrayList(terms.values());
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Collections.sort(list);
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return list;
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} catch (final ISLookUpDocumentNotFoundException e) {
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throw new VocabularyException(e);
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} catch (final ISLookUpException e) {
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throw new VocabularyException(e);
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} catch (final DocumentException e) {
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throw new VocabularyException(e);
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}
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}
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@Override
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public void commitTerms(final List<Term> terms, final String vocabularyId) throws VocabularyException {
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try {
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// prepare terms for XML
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for (final Term t : terms) {
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t.setCode(StringEscapeUtils.escapeXml11(t.getCode()));
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t.setEncoding(StringEscapeUtils.escapeXml11(t.getEncoding()));
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t.setEnglishName(StringEscapeUtils.escapeXml11(t.getEnglishName()));
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t.setNativeName(StringEscapeUtils.escapeXml11(t.getNativeName()));
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for (final Synonym s : t.getSynonyms()) {
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s.setEncoding(StringEscapeUtils.escapeXml11(s.getEncoding()));
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s.setTerm(StringEscapeUtils.escapeXml11(s.getTerm()));
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}
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for (final Relation r : t.getRelations()) {
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r.setType(StringEscapeUtils.escapeXml11(r.getType()));
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r.setCode(StringEscapeUtils.escapeXml11(r.getCode()));
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}
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}
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final StringTemplate st =
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new StringTemplate(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/functionality/modular/templates/terms.xml.st")));
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st.setAttribute("terms", terms);
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this.serviceLocator.getService(ISRegistryService.class).updateProfileNode(vocabularyId, "//TERMS", st.toString());
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} catch (final IOException e) {
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throw new VocabularyException(e);
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} catch (final ISRegistryException e) {
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throw new VocabularyException(e);
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}
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}
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@Override
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public void commitVocabularyInfo(final Vocabulary voc, final String vocabularyId) throws VocabularyException {
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try {
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String xml = "<VOCABULARY_DESCRIPTION>{desc}</VOCABULARY_DESCRIPTION>";
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xml = xml.replace("{desc}", StringEscapeUtils.escapeXml11(voc.getDescription()));
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this.serviceLocator.getService(ISRegistryService.class).updateProfileNode(vocabularyId, "//VOCABULARY_DESCRIPTION", xml);
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} catch (final ISRegistryException e) {
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throw new VocabularyException(e);
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}
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}
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@Override
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public String createVocabulary(final Vocabulary voc) throws VocabularyException {
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try {
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final StringTemplate st = new StringTemplate(
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IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/functionality/modular/templates/vocabulary.xml.st")));
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st.setAttribute("name", voc.getName());
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st.setAttribute("description", voc.getDescription());
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st.setAttribute("code", voc.getCode());
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st.setAttribute("date", DateUtils.now_ISO8601());
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final String newVocabularyId = this.serviceLocator.getService(ISRegistryService.class).registerProfile(st.toString());
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return newVocabularyId;
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} catch (final IOException e) {
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throw new VocabularyException(e);
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} catch (final ISRegistryException e) {
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throw new VocabularyException(e);
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}
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}
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@Override
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public void dropVocabulary(final String vocabularyId) throws VocabularyException {
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try {
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this.serviceLocator.getService(ISRegistryService.class).deleteProfile(vocabularyId);
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} catch (final ISRegistryDocumentNotFoundException e) {
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throw new VocabularyException(e);
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} catch (final ISRegistryException e) {
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throw new VocabularyException(e);
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}
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}
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}
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