Revision 54151
Added by Claudio Atzori over 5 years ago
OntologyLoader.java | ||
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package eu.dnetlib.utils.ontologies; |
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import javax.annotation.PostConstruct;
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import com.google.common.collect.Maps;
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import com.google.gson.Gson; |
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; |
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; |
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import eu.dnetlib.enabling.locators.UniqueServiceLocator; |
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import org.apache.commons.io.IOUtils; |
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import org.apache.commons.logging.Log; |
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import org.apache.commons.logging.LogFactory; |
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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.Node; |
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import org.dom4j.io.SAXReader; |
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import org.springframework.beans.factory.annotation.Autowired; |
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import org.springframework.core.io.support.PathMatchingResourcePatternResolver; |
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import org.springframework.stereotype.Component; |
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import javax.annotation.PostConstruct; |
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import java.io.IOException; |
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import java.io.InputStream; |
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import java.io.StringReader; |
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import java.util.Arrays; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.function.Function; |
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import java.util.stream.Collectors; |
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/** |
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* Created by claudio on 12/12/2016. |
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*/ |
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@Component |
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public class OntologyLoader { |
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private static UniqueServiceLocator staticServiceLocator;
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private static final Log log = LogFactory.getLog(OntologyLoader.class);
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@Autowired |
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private UniqueServiceLocator serviceLocator; |
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private static final String PATTERN = "classpath*:/eu/dnetlib/test/profiles/OntologyDSResources/OntologyDSResourceType/*.xml"; |
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// <TERM code="merges" encoding="organizationOrganization_dedup_merges" english_name="merges" native_name="merges"> |
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public static String fetchInverse(final String relType) throws ISLookUpException { |
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final String xquery = "let $x:= /RESOURCE_PROFILE[" |
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+ " .//RESOURCE_TYPE/@value = 'OntologyDSResourceType' and " |
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+ " .//TERM/@encoding='" + relType + "']" |
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+ "let $y:= $x//TERM[./@encoding='" + relType + "']//RELATION[./@type='inverseOf']/@code/string() " |
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+ "return $x//TERM[./@code = $y]/@encoding/string()"; |
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return staticServiceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xquery); |
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} |
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private static UniqueServiceLocator staticServiceLocator; |
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@PostConstruct |
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public void init() { |
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OntologyLoader.staticServiceLocator = serviceLocator; |
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} |
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@Autowired |
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private UniqueServiceLocator serviceLocator; |
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// <TERM code="merges" encoding="organizationOrganization_dedup_merges" english_name="merges" native_name="merges"> |
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public static String fetchInverse(final String relType) throws ISLookUpException { |
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final String xquery = "let $x:= /RESOURCE_PROFILE[" |
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+ " .//RESOURCE_TYPE/@value = 'OntologyDSResourceType' and " |
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+ " .//TERM/@encoding='" + relType + "']" |
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+ "let $y:= $x//TERM[./@encoding='" + relType + "']//RELATION[./@type='inverseOf']/@code/string() " |
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+ "return $x//TERM[./@code = $y]/@encoding/string()"; |
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return staticServiceLocator.getService(ISLookUpService.class).getResourceProfileByQuery(xquery); |
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} |
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@PostConstruct |
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public void init() { |
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OntologyLoader.staticServiceLocator = serviceLocator; |
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} |
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public static Ontology loadOntologyFromCp(final InputStream profile) { |
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return loadOntologyProfilefromPath(profile); |
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} |
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public static Ontologies loadOntologiesFromCp() throws IOException { |
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final PathMatchingResourcePatternResolver resolver = new PathMatchingResourcePatternResolver(); |
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final List<InputStream> files = Arrays.asList(resolver.getResources(PATTERN)).stream().map(r -> { |
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try { |
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return r.getInputStream(); |
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} catch (IOException e) { |
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throw new RuntimeException(e); |
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} |
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}).collect(Collectors.toList()); |
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return createOntologies(files); |
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} |
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public static Ontologies createOntologies(List<InputStream> files) { |
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final Ontologies ontologies = new Ontologies(); |
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files.stream().map( |
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s -> loadOntologyProfilefromPath(s)) |
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.collect(Collectors.toMap(Ontology::getCode, Function.identity())) |
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.entrySet() |
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.forEach(it -> ontologies.put(it.getKey(), it.getValue())); |
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return ontologies; |
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} |
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public static Ontologies loadOntologiesFromIS() throws ISLookUpException { |
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final ISLookUpService lookUpService = staticServiceLocator.getService(ISLookUpService.class); |
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List<String> files = lookUpService.quickSearchProfile("for $x in collection('/db/DRIVER/OntologyDSResources/OntologyDSResourceType') return $x"); |
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final Ontologies ontologies = new Ontologies(); |
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files.stream().map |
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(OntologyLoader::getOntologyFromProfile) |
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.collect(Collectors.toMap(Ontology::getCode, Function.identity())) |
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.entrySet() |
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.forEach(it -> ontologies.put(it.getKey(), it.getValue())); |
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return ontologies; |
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} |
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private static Ontology loadOntologyProfilefromPath(final InputStream profile) { |
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final String profileXML; |
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try { |
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profileXML = IOUtils.toString(profile); |
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} catch (IOException e) { |
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log.error(e); |
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return null; |
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} |
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return getOntologyFromProfile(profileXML); |
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} |
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private static Ontology getOntologyFromProfile(final String profile) { |
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SAXReader saxReader = new SAXReader(); |
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Document doc = null; |
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StringReader reader = new StringReader(profile); |
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try { |
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doc = saxReader.read(reader); |
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} catch (DocumentException e) { |
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e.printStackTrace(); |
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throw new RuntimeException(e); |
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} |
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return new Ontology() |
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.setCode(doc.valueOf("//ONTOLOGY_NAME/@code")) |
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.setDescription(doc.valueOf("//ONTOLOGY_DESCRIPTION/text()")) |
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.setTerms(asTerms(doc.selectNodes("//TERMS/TERM"))); |
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} |
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private static Map<String,OntologyTerm> asTerms(final List list) { |
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final Map<String, OntologyTerm> terms = Maps.newHashMap(); |
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if (list != null) { |
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list.forEach(o -> { |
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final Element e = (Element) o; |
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final OntologyTerm ot = OntologyTerm.newInstance() |
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.setCode(e.attributeValue("code")) |
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.setEncoding(e.attributeValue("encoding")) |
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.setEnglishName(e.attributeValue("english_name")) |
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.setNativeName(e.attributeValue("native_name")) |
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.setInverseCode(((Node) o).valueOf("./RELATIONS/RELATION[@type = 'inverseOf']/@code")); |
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terms.put(ot.getCode(), ot); |
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}); |
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} |
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return terms; |
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} |
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} |
Also available in: Unified diff
added utilities to load the ontology profiles and pass them to the M/R jobs