new xslt adoption and changes in testing xslt's #101
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package eu.dnetlib.dhp.transformation.xslt;
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import static eu.dnetlib.dhp.transformation.xslt.XSLTTransformationFunction.QNAME_BASE_URI;
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import java.io.Serializable;
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// import java.nio.charset.Charset;
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import java.nio.charset.StandardCharsets;
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import java.text.Normalizer;
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import java.util.List;
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import java.util.Set;
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import com.google.common.base.Joiner;
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import com.google.common.base.Splitter;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.common.hash.Hashing;
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import eu.dnetlib.dhp.transformation.xslt.utils.Capitalize;
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import eu.dnetlib.dhp.transformation.xslt.utils.DotAbbreviations;
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import net.sf.saxon.s9api.ExtensionFunction;
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import net.sf.saxon.s9api.ItemType;
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import net.sf.saxon.s9api.OccurrenceIndicator;
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import net.sf.saxon.s9api.QName;
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import net.sf.saxon.s9api.SaxonApiException;
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import net.sf.saxon.s9api.SequenceType;
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import net.sf.saxon.s9api.XdmValue;
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//import eu.dnetlib.pace.clustering.NGramUtils;
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//import eu.dnetlib.pace.util.Capitalise;
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//import eu.dnetlib.pace.util.DotAbbreviations;
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public class PersonCleaner implements ExtensionFunction, Serializable {
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/**
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*
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*/
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private static final long serialVersionUID = 1L;
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private List<String> firstname = Lists.newArrayList();
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private List<String> surname = Lists.newArrayList();
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private List<String> fullname = Lists.newArrayList();
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private static Set<String> particles = null;
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public PersonCleaner() {
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}
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public String normalize(String s) {
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s = Normalizer.normalize(s, Normalizer.Form.NFD); // was NFD
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s = s.replaceAll("\\(.+\\)", "");
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s = s.replaceAll("\\[.+\\]", "");
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s = s.replaceAll("\\{.+\\}", "");
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s = s.replaceAll("\\s+-\\s+", "-");
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// s = s.replaceAll("[\\W&&[^,-]]", " ");
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// System.out.println("class Person: s: " + s);
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// s = s.replaceAll("[\\p{InCombiningDiacriticalMarks}&&[^,-]]", " ");
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s = s.replaceAll("[\\p{Punct}&&[^-,]]", " ");
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s = s.replace("\\d", " ");
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s = s.replace("\\n", " ");
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s = s.replace("\\.", " ");
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s = s.replaceAll("\\s+", " ");
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if (s.contains(",")) {
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// System.out.println("class Person: s: " + s);
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String[] arr = s.split(",");
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if (arr.length == 1) {
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fullname = splitTerms(arr[0]);
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} else if (arr.length > 1) {
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surname = splitTerms(arr[0]);
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firstname = splitTermsFirstName(arr[1]);
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// System.out.println("class Person: surname: " + surname);
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// System.out.println("class Person: firstname: " + firstname);
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fullname.addAll(surname);
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fullname.addAll(firstname);
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}
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} else {
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fullname = splitTerms(s);
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int lastInitialPosition = fullname.size();
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boolean hasSurnameInUpperCase = false;
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for (int i = 0; i < fullname.size(); i++) {
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String term = fullname.get(i);
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if (term.length() == 1) {
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lastInitialPosition = i;
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} else if (term.equals(term.toUpperCase())) {
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hasSurnameInUpperCase = true;
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}
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}
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if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini
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firstname = fullname.subList(0, lastInitialPosition + 1);
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System.out.println("name: " + firstname);
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surname = fullname.subList(lastInitialPosition + 1, fullname.size());
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} else if (hasSurnameInUpperCase) { // Case: Michele ARTINI
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for (String term : fullname) {
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if (term.length() > 1 && term.equals(term.toUpperCase())) {
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surname.add(term);
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} else {
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firstname.add(term);
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}
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}
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} else if (lastInitialPosition == fullname.size()) {
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surname = fullname.subList(lastInitialPosition - 1, fullname.size());
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firstname = fullname.subList(0, lastInitialPosition - 1);
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}
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}
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return null;
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}
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private List<String> splitTermsFirstName(String s) {
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List<String> list = Lists.newArrayList();
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for (String part : Splitter.on(" ").omitEmptyStrings().split(s)) {
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if (s.trim().matches("\\p{Lu}{2,3}")) {
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String[] parts = s.trim().split("(?=\\p{Lu})"); // (Unicode UpperCase)
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for (String p : parts) {
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if (p.length() > 0)
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list.add(p);
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}
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} else {
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list.add(part);
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}
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}
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return list;
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}
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private List<String> splitTerms(String s) {
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if (particles == null) {
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// particles = NGramUtils.loadFromClasspath("/eu/dnetlib/pace/config/name_particles.txt");
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}
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List<String> list = Lists.newArrayList();
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for (String part : Splitter.on(" ").omitEmptyStrings().split(s)) {
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// if (!particles.contains(part.toLowerCase())) {
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list.add(part);
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// }
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}
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return list;
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}
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public List<String> getFirstname() {
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return firstname;
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}
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public List<String> getSurname() {
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return surname;
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}
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public List<String> getFullname() {
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return fullname;
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}
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public String hash() {
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return Hashing.murmur3_128().hashString(getNormalisedFullname(), StandardCharsets.UTF_8).toString();
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}
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public String getNormalisedFullname() {
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return isAccurate() ? Joiner.on(" ").join(getSurname()) + ", " + Joiner.on(" ").join(getNameWithAbbreviations())
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: Joiner.on(" ").join(fullname);
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// return isAccurate() ?
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// Joiner.on(" ").join(getCapitalSurname()) + ", " + Joiner.on(" ").join(getNameWithAbbreviations()) :
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// Joiner.on(" ").join(fullname);
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}
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public List<String> getCapitalSurname() {
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return Lists.newArrayList(Iterables.transform(surname, new Capitalize()));
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}
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public List<String> getNameWithAbbreviations() {
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return Lists.newArrayList(Iterables.transform(firstname, new DotAbbreviations()));
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}
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public boolean isAccurate() {
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return (firstname != null && surname != null && !firstname.isEmpty() && !surname.isEmpty());
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}
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@Override
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public QName getName() {
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return new QName(QNAME_BASE_URI + "/person", "person");
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}
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@Override
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public SequenceType getResultType() {
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return SequenceType.makeSequenceType(ItemType.STRING, OccurrenceIndicator.ZERO_OR_ONE);
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}
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@Override
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public SequenceType[] getArgumentTypes() {
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// TODO Auto-generated method stub
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return null;
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}
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@Override
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public XdmValue call(XdmValue[] arguments) throws SaxonApiException {
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// TODO Auto-generated method stub
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return null;
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}
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}
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@ -46,6 +46,7 @@ public class XSLTTransformationFunction implements MapFunction<MetadataRecord, M
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Processor processor = new Processor(false);
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processor.registerExtensionFunction(cleanFunction);
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processor.registerExtensionFunction(new DateCleaner());
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processor.registerExtensionFunction(new PersonCleaner());
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final XsltCompiler comp = processor.newXsltCompiler();
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XsltExecutable xslt = comp
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package eu.dnetlib.dhp.transformation.xslt.utils;
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// import org.apache.commons.text.WordUtils;
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// import org.apache.commons.text.WordUtils;
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import com.google.common.base.Function;
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public class Capitalize implements Function<String, String> {
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@Override
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public String apply(String s) {
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return org.apache.commons.lang3.text.WordUtils.capitalize(s.toLowerCase());
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}
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}
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package eu.dnetlib.dhp.transformation.xslt.utils;
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import com.google.common.base.Function;
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public class DotAbbreviations implements Function<String, String> {
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@Override
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public String apply(String s) {
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return s.length() == 1 ? s + "." : s;
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}
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}
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@ -103,15 +103,18 @@ public class TransformationJobTest extends AbstractVocabularyTest {
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}
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@Test
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@DisplayName("Test Transform record XML with xslt_cleaning_datarepo_datacite")
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@DisplayName("Test Transform record XML with xslt_cleaning_datarepo_datacite/oaiOpenAIRE")
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public void testTransformMostlyUsedScript() throws Exception {
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String xslTransformationScript = "";
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xslTransformationScript = "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_datarepo_datacite.xsl";
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// xslTransformationScript = "/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl";
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// We Set the input Record getting the XML from the classpath
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final MetadataRecord mr = new MetadataRecord();
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mr.setBody(IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/transform/input_itgv4.xml")));
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// We Load the XSLT transformation Rule from the classpath
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XSLTTransformationFunction tr = loadTransformationRule(
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"/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_datarepo_datacite.xsl");
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XSLTTransformationFunction tr = loadTransformationRule(xslTransformationScript);
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MetadataRecord result = tr.call(mr);
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@ -120,72 +123,6 @@ public class TransformationJobTest extends AbstractVocabularyTest {
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// TODO Create significant Assert
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}
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@Test
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@DisplayName("Test TransformSparkJobNode.main with oaiOpenaire_datacite (v4)")
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public void transformTestITGv4OAIdatacite(@TempDir Path testDir) throws Exception {
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SparkConf conf = new SparkConf();
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conf.setAppName(TransformationJobTest.class.getSimpleName());
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conf.setMaster("local");
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try (SparkSession spark = SparkSession.builder().config(conf).getOrCreate()) {
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final String mdstore_input = this
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.getClass()
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.getResource("/eu/dnetlib/dhp/transform/mdstorenative")
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.getFile();
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final String mdstore_output = testDir.toString() + "/version";
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mockupTrasformationRule(
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"simpleTRule",
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"/eu/dnetlib/dhp/transform/scripts/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid.xsl");
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final Map<String, String> parameters = Stream.of(new String[][] {
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{
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"dateOfTransformation", "1234"
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},
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{
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"varOfficialName", "Publications at Bielefeld University"
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},
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{
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"varOfficialId", "opendoar____::2294"
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},
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{
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"transformationPlugin", "XSLT_TRANSFORM"
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},
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{
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"transformationRuleId", "simpleTRule"
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},
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}).collect(Collectors.toMap(data -> data[0], data -> data[1]));
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TransformSparkJobNode.transformRecords(parameters, isLookUpService, spark, mdstore_input, mdstore_output);
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// TODO introduce useful assertions
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final Encoder<MetadataRecord> encoder = Encoders.bean(MetadataRecord.class);
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final Dataset<MetadataRecord> mOutput = spark
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.read()
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.format("parquet")
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.load(mdstore_output + MDSTORE_DATA_PATH)
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.as(encoder);
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final Long total = mOutput.count();
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final long recordTs = mOutput
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.filter((FilterFunction<MetadataRecord>) p -> p.getDateOfTransformation() == 1234)
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.count();
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final long recordNotEmpty = mOutput
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.filter((FilterFunction<MetadataRecord>) p -> !StringUtils.isBlank(p.getBody()))
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.count();
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assertEquals(total, recordTs);
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assertEquals(total, recordNotEmpty);
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}
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}
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@Test
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@DisplayName("Test TransformSparkJobNode.main")
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public void transformTest(@TempDir Path testDir) throws Exception {
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@ -0,0 +1,297 @@
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<!-- complete literature v4: xslt_cleaning_REST_OmicsDI ; transformation script production , 2021-03-17 -->
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<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
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version="2.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns:oaf="http://namespace.openaire.eu/oaf"
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xmlns:dr="http://www.driver-repository.eu/namespace/dr"
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xmlns:datacite="http://datacite.org/schema/kernel-4"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:dri="http://www.driver-repository.eu/namespace/dri"
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xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
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xmlns:xs="http://www.w3.org/2001/XMLSchema"
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xmlns:vocabulary="http://eu/dnetlib/transform/clean"
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xmlns:dateCleaner="http://eu/dnetlib/transform/dateISO"
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xmlns:personCleaner="http://eu/dnetlib/transform/person"
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exclude-result-prefixes="xsl vocabulary dateCleaner personCleaner">
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<xsl:param name="varOfficialName" />
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<xsl:param name="varDsType" />
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<xsl:param name="varDataSourceId" />
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<xsl:param name="index" select="0"/>
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<xsl:param name="transDate" select="current-dateTime()"/>
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<xsl:variable name="vCodes">
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<codes>
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<code source="arrayexpress-repository" id="re3data_____::r3d100010222" name="ArrayExpress Archive of Functional Genomics Data" sourceUrl="https://www.ebi.ac.uk/arrayexpress/" urlTemplate="https://www.ebi.ac.uk/arrayexpress/experiments/" />
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<code source="atlas-experiments" id="re3data_____::r3d100010223" name="Expression Atlas Database" sourceUrl="http://www.ebi.ac.uk/gxa/home" urlTemplate="" />
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<code source="biomodels" id="re3data_____::r3d100010789" name="BioModels Database" sourceUrl="https://www.ebi.ac.uk/biomodels-main/" urlTemplate="" />
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<code source="dbgap" id="re3data_____::r3d100010788" name="dbGaP (database of Genotypes and Phenotypes)" sourceUrl="https://www.ncbi.nlm.nih.gov/gap" urlTemplate="" />
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<code source="ega" id="re3data_____::r3d100011242" name="EGA Database (European Genome-phenome Archive)" sourceUrl="https://ega-archive.org" urlTemplate="" />
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<code source="eva" id="re3data_____::r3d100011553" name="EVA database (European Variation Archive)" sourceUrl="https://www.ebi.ac.uk/eva/" urlTemplate="" />
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<code source="geo" id="re3data_____::r3d100010283" name="GEO (Gene Expression Omnibus)" sourceUrl="https://www.ncbi.nlm.nih.gov/geo/" urlTemplate="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" />
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<code source="gnps" id="omicsdi_____::gnps" name="GNPS Database (Global Natural Products Social Molecular Networking)" sourceUrl="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash2.jsp" urlTemplate="" />
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<code source="gpmdb" id="re3data_____::r3d100010883" name="GPMDB (Global Proteome Machine)" sourceUrl="http://gpmdb.thegpm.org/" urlTemplate="http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" />
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<code source="jpost" id="re3data_____::r3d100012349" name="JPOST Repository (Japan ProteOme STandard Repository/Database)" sourceUrl="https://jpostdb.org/" urlTemplate="https://repository.jpostdb.org/entry/JPST000228" />
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<code source="lincs" id="re3data_____::r3d100011833" name="LINCS (Big Data to Knowledge / Library of Integrated Network-based Cellular Signatures)" sourceUrl="http://lincsportal.ccs.miami.edu/dcic-portal/" urlTemplate="http://lincsportal.ccs.miami.edu/datasets/#/view/" />
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<code source="massive" id="omicsdi_____::massive" name="MassIVE Database (Mass Spectrometry Interactive Virtual Environment)" sourceUrl="https://massive.ucsd.edu/ProteoSAFe/datasets.jsp" urlTemplate="" />
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<code source="metabolights_dataset" id="opendoar____::2970" name="MetaboLights Database" sourceUrl="http://www.ebi.ac.uk/metabolights/" urlTemplate="" />
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<code source="metabolome_express" id="omicsdi_____::metabolome" name="MetabolomeExpress" sourceUrl="https://www.metabolome-express.org/" urlTemplate="https://www.metabolome-express.org/datasetview.php?datasetid=" />
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<code source="metabolomics_workbench" id="re3data_____::r3d100012314" name="Metabolomics Workbench Database" sourceUrl="http://www.metabolomicsworkbench.org/" urlTemplate="http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?StudyID=" />
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<code source="NCBI" id="omicsdi_____::ncbi" name="NCBI" sourceUrl="https://www.ncbi.nlm.nih.gov/bioproject/" urlTemplate="https://www.ncbi.nlm.nih.gov/bioproject/" />
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<code source="omics_ena_project" id="re3data_____::r3d100010527" name="ENA (European Nucleotide Archive)" sourceUrl="https://www.ebi.ac.uk/ena" urlTemplate="https://www.ebi.ac.uk/ena/data/view/" />
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<code source="paxdb" id="omicsdi_____::paxdb" name="PAXDB (protein abundance database)" sourceUrl="http://pax-db.org/" urlTemplate="" />
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<code source="peptide_atlas" id="re3data_____::r3d100010889" name="PeptideAtlas Database" sourceUrl="http://www.peptideatlas.org/" urlTemplate="" />
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<code source="pride" id="re3data_____::r3d100010137" name="PRIDE Database (PRoteomics IDEntifications)" sourceUrl="http://www.ebi.ac.uk/pride/archive/" urlTemplate="http://www.ebi.ac.uk/pride/archive/projects/PXD008134" />
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</codes>
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</xsl:variable>
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<!--
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gnps, jpost, massive, metabolome_express, paxdb: no id/OpenAIRE-entry found
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ncbi: several OpenAIRE-entries found - is one the right?
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-->
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<xsl:key name="kCodeByName" match="code" use="string(@source)"/>
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<xsl:template match="/">
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<xsl:variable name="datasourcePrefix"
|
||||
select="normalize-space(//oaf:datasourceprefix)" />
|
||||
<xsl:call-template name="validRecord" />
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template name="terminate">
|
||||
<xsl:message terminate="yes">
|
||||
record is not compliant, transformation is interrupted.
|
||||
</xsl:message>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template name="validRecord">
|
||||
<record>
|
||||
<xsl:apply-templates select="//*[local-name() = 'header']" />
|
||||
|
||||
<metadata>
|
||||
|
||||
<!--
|
||||
<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'datasets']"/>
|
||||
-->
|
||||
|
||||
<datacite:resource>
|
||||
|
||||
<!-- OmicsDI does not state: languages, projects,
|
||||
-->
|
||||
|
||||
<!-- landing page -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:alternateIdentifiers>
|
||||
<datacite:alternateIdentifier>
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'LandingPage'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:choose>
|
||||
<xsl:when test="//*[local-name() = 'source'][. = ('gnps','massive','paxdb','peptide_atlas')]">
|
||||
<xsl:value-of select="concat('https://www.omicsdi.org/#/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
|
||||
</xsl:when>
|
||||
<xsl:when test="//*[local-name() = 'source'][. = 'metabolome_express']">
|
||||
<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, substring-after(//*[local-name()='id'], 'MEX'))"/>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, //*[local-name()='id'])"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</datacite:alternateIdentifier>
|
||||
<datacite:alternateIdentifier>
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'local'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name()='id']"/>
|
||||
</datacite:alternateIdentifier>
|
||||
</datacite:alternateIdentifiers>
|
||||
</xsl:if>
|
||||
|
||||
<!-- identifier; ... -->
|
||||
<!-- URL hindered by _et_: https://www.omicsdi.org/ws/dataset/get_acc=E-MTAB-6546_et_database=arrayexpress-repository -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:identifier>
|
||||
<xsl:attribute name="identifierType">
|
||||
<xsl:value-of select="'URL'"/>
|
||||
</xsl:attribute>
|
||||
|
||||
<xsl:value-of select="concat('https://www.omicsdi.org/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
|
||||
|
||||
</datacite:identifier>
|
||||
</xsl:if>
|
||||
|
||||
<!-- title -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:titles>
|
||||
<datacite:title>
|
||||
<xsl:value-of select="//*[local-name() = 'title']"/>
|
||||
</datacite:title>
|
||||
</datacite:titles>
|
||||
</xsl:if>
|
||||
|
||||
<!-- no authors in OmicsDI -->
|
||||
<!--
|
||||
<xsl:call-template name="authors" />
|
||||
-->
|
||||
|
||||
<!--
|
||||
<xsl:call-template name="relatedPaper" />
|
||||
-->
|
||||
|
||||
<datacite:descriptions>
|
||||
<datacite:description>
|
||||
<xsl:attribute name="descriptionType">
|
||||
<xsl:value-of select="'Abstract'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name() = 'description']"/>
|
||||
</datacite:description>
|
||||
</datacite:descriptions>
|
||||
|
||||
<!-- subject -->
|
||||
<datacite:subjects>
|
||||
<xsl:for-each select="distinct-values(//*[local-name()='omicsType'])">
|
||||
<datacite:subject>
|
||||
<xsl:value-of select="."/>
|
||||
</datacite:subject>
|
||||
</xsl:for-each>
|
||||
</datacite:subjects>
|
||||
|
||||
</datacite:resource>
|
||||
|
||||
<xsl:choose>
|
||||
|
||||
<xsl:when test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<xsl:variable name='varCobjCategory'
|
||||
select="'0021'" />
|
||||
<dr:CobjCategory>
|
||||
<xsl:attribute name="type">
|
||||
<xsl:value-of select="vocabulary:clean($varCobjCategory, 'dnet:result_typologies')"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of
|
||||
select="$varCobjCategory" />
|
||||
</dr:CobjCategory>
|
||||
</xsl:when>
|
||||
|
||||
<xsl:otherwise>
|
||||
<!--
|
||||
<xsl:call-template name="terminate"/>
|
||||
-->
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
<!--
|
||||
// review status: no review indications found so far
|
||||
-->
|
||||
<!--
|
||||
OMICSDI is ‘including both open and controlled data source’.
|
||||
-->
|
||||
<oaf:accessrights>
|
||||
<xsl:text>UNKNOWN</xsl:text>
|
||||
</oaf:accessrights>
|
||||
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='NeuroVault__']">
|
||||
<oaf:concept>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="'ni'"/>
|
||||
</xsl:attribute>
|
||||
</oaf:concept>
|
||||
</xsl:if>
|
||||
|
||||
<oaf:hostedBy>
|
||||
<xsl:attribute name="name">
|
||||
<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@name"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@id"/>
|
||||
</xsl:attribute>
|
||||
</oaf:hostedBy>
|
||||
<oaf:collectedFrom>
|
||||
<xsl:attribute name="name">
|
||||
<xsl:value-of select="$varOfficialName"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="$varDataSourceId"/>
|
||||
</xsl:attribute>
|
||||
</oaf:collectedFrom>
|
||||
|
||||
<!-- date -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<oaf:dateAccepted>
|
||||
<xsl:value-of select="replace(//*[local-name() = 'publicationDate'][not(.='null')],'(\d{4})(\d{2})(\d{2})','$1-$2-$3')"/>
|
||||
</oaf:dateAccepted>
|
||||
</xsl:if>
|
||||
|
||||
</metadata>
|
||||
<xsl:copy-of select="//*[local-name() = 'about']" />
|
||||
</record>
|
||||
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="node()|@*">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'datasets']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'header']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
<xsl:element name="dr:dateOfTransformation">
|
||||
<xsl:value-of select="$transDate"/>
|
||||
</xsl:element>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
<!--
|
||||
no authors findable in OmicsDI">
|
||||
-->
|
||||
<!--
|
||||
<xsl:template match="//*[local-name() = 'authors']">
|
||||
-->
|
||||
<xsl:template name="authors">
|
||||
<xsl:choose>
|
||||
<xsl:when test="not(//*[local-name() = 'authors'][string-length(normalize-space(.)) > 0 and not(. = 'null')])">
|
||||
<xsl:call-template name="terminate" />
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:for-each select="tokenize(//*[local-name() = 'authors'], '(, and |,| and )')">
|
||||
|
||||
<xsl:element name="datacite:creator">
|
||||
|
||||
<xsl:element name="datacite:creatorName">
|
||||
<xsl:value-of select="TransformationFunction:convertString($tf, ., 'Person')"/>
|
||||
</xsl:element>
|
||||
|
||||
<xsl:element name="datacite:givenName">
|
||||
<xsl:value-of select="normalize-space(substring-after(personCleaner:normalize(.), ','))"/>
|
||||
</xsl:element>
|
||||
<xsl:element name="datacite:familyName">
|
||||
<xsl:value-of select="substring-before(personCleaner:normalize(.), ',')"/>
|
||||
</xsl:element>
|
||||
|
||||
</xsl:element>
|
||||
</xsl:for-each>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:template>
|
||||
|
||||
<!--
|
||||
<xsl:template match="//*[local-name() = 'DOI']">
|
||||
-->
|
||||
<xsl:template name="relatedPaper">
|
||||
<xsl:element name="datacite:relatedIdentifier">
|
||||
<xsl:attribute name="relatedIdentifierType">
|
||||
<xsl:value-of select="'DOI'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="relationType">
|
||||
<xsl:value-of select="'isReferencedBy'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name() = 'DOI']"/>
|
||||
</xsl:element>
|
||||
</xsl:template>
|
||||
|
||||
</xsl:stylesheet>
|
||||
|
|
@ -0,0 +1,292 @@
|
|||
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.1"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
|
||||
xmlns:dc="http://purl.org/dc/elements/1.1/"
|
||||
xmlns:datacite="http://datacite.org/schema/kernel-4"
|
||||
xmlns:TransformationFunction="eu.dnetlib.data.collective.transformation.core.xsl.ext.TransformationFunctionProxy"
|
||||
extension-element-prefixes="TransformationFunction"
|
||||
exclude-result-prefixes="TransformationFunction">
|
||||
|
||||
<xsl:param name="varOfficialName" />
|
||||
<xsl:param name="varDsType" />
|
||||
<xsl:param name="varDataSourceId" />
|
||||
<xsl:param name="index" select="0"/>
|
||||
<xsl:param name="transDate" select="current-dateTime()"/>
|
||||
<xsl:variable name="tf" select="TransformationFunction:getInstance()"/>
|
||||
|
||||
<xsl:variable name="vCodes">
|
||||
<codes>
|
||||
<code source="arrayexpress-repository" id="re3data_____::r3d100010222" name="ArrayExpress Archive of Functional Genomics Data" sourceUrl="https://www.ebi.ac.uk/arrayexpress/" urlTemplate="https://www.ebi.ac.uk/arrayexpress/experiments/" />
|
||||
<code source="atlas-experiments" id="re3data_____::r3d100010223" name="Expression Atlas Database" sourceUrl="http://www.ebi.ac.uk/gxa/home" urlTemplate="" />
|
||||
<code source="biomodels" id="re3data_____::r3d100010789" name="BioModels Database" sourceUrl="https://www.ebi.ac.uk/biomodels-main/" urlTemplate="" />
|
||||
<code source="dbgap" id="re3data_____::r3d100010788" name="dbGaP (database of Genotypes and Phenotypes)" sourceUrl="https://www.ncbi.nlm.nih.gov/gap" urlTemplate="" />
|
||||
<code source="ega" id="re3data_____::r3d100011242" name="EGA Database (European Genome-phenome Archive)" sourceUrl="https://ega-archive.org" urlTemplate="" />
|
||||
<code source="eva" id="re3data_____::r3d100011553" name="EVA database (European Variation Archive)" sourceUrl="https://www.ebi.ac.uk/eva/" urlTemplate="" />
|
||||
<code source="geo" id="re3data_____::r3d100010283" name="GEO (Gene Expression Omnibus)" sourceUrl="https://www.ncbi.nlm.nih.gov/geo/" urlTemplate="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" />
|
||||
<code source="gnps" id="omicsdi_____::gnps" name="GNPS Database (Global Natural Products Social Molecular Networking)" sourceUrl="https://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash2.jsp" urlTemplate="" />
|
||||
<code source="gpmdb" id="re3data_____::r3d100010883" name="GPMDB (Global Proteome Machine)" sourceUrl="http://gpmdb.thegpm.org/" urlTemplate="http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=" />
|
||||
<code source="jpost" id="re3data_____::r3d100012349" name="JPOST Repository (Japan ProteOme STandard Repository/Database)" sourceUrl="https://jpostdb.org/" urlTemplate="https://repository.jpostdb.org/entry/JPST000228" />
|
||||
<code source="lincs" id="re3data_____::r3d100011833" name="LINCS (Big Data to Knowledge / Library of Integrated Network-based Cellular Signatures)" sourceUrl="http://lincsportal.ccs.miami.edu/dcic-portal/" urlTemplate="http://lincsportal.ccs.miami.edu/datasets/#/view/" />
|
||||
<code source="massive" id="omicsdi_____::massive" name="MassIVE Database (Mass Spectrometry Interactive Virtual Environment)" sourceUrl="https://massive.ucsd.edu/ProteoSAFe/datasets.jsp" urlTemplate="" />
|
||||
<code source="metabolights_dataset" id="opendoar____::2970" name="MetaboLights Database" sourceUrl="http://www.ebi.ac.uk/metabolights/" urlTemplate="" />
|
||||
<code source="metabolome_express" id="omicsdi_____::metabolome" name="MetabolomeExpress" sourceUrl="https://www.metabolome-express.org/" urlTemplate="https://www.metabolome-express.org/datasetview.php?datasetid=" />
|
||||
<code source="metabolomics_workbench" id="re3data_____::r3d100012314" name="Metabolomics Workbench Database" sourceUrl="http://www.metabolomicsworkbench.org/" urlTemplate="http://www.metabolomicsworkbench.org/data/DRCCMetadata.php?StudyID=" />
|
||||
<code source="NCBI" id="omicsdi_____::ncbi" name="NCBI" sourceUrl="https://www.ncbi.nlm.nih.gov/bioproject/" urlTemplate="https://www.ncbi.nlm.nih.gov/bioproject/" />
|
||||
<code source="omics_ena_project" id="re3data_____::r3d100010527" name="ENA (European Nucleotide Archive)" sourceUrl="https://www.ebi.ac.uk/ena" urlTemplate="https://www.ebi.ac.uk/ena/data/view/" />
|
||||
<code source="paxdb" id="omicsdi_____::paxdb" name="PAXDB (protein abundance database)" sourceUrl="http://pax-db.org/" urlTemplate="" />
|
||||
<code source="peptide_atlas" id="re3data_____::r3d100010889" name="PeptideAtlas Database" sourceUrl="http://www.peptideatlas.org/" urlTemplate="" />
|
||||
<code source="pride" id="re3data_____::r3d100010137" name="PRIDE Database (PRoteomics IDEntifications)" sourceUrl="http://www.ebi.ac.uk/pride/archive/" urlTemplate="http://www.ebi.ac.uk/pride/archive/projects/PXD008134" />
|
||||
</codes>
|
||||
</xsl:variable>
|
||||
|
||||
<!--
|
||||
gnps, jpost, massive, metabolome_express, paxdb: no id/OpenAIRE-entry found
|
||||
ncbi: several OpenAIRE-entries found - is one the right?
|
||||
-->
|
||||
|
||||
<xsl:key name="kCodeByName" match="code" use="string(@source)"/>
|
||||
|
||||
<xsl:template match="/">
|
||||
<xsl:variable name="datasourcePrefix"
|
||||
select="normalize-space(//oaf:datasourceprefix)" />
|
||||
<xsl:call-template name="validRecord" />
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template name="terminate">
|
||||
<xsl:message terminate="yes">
|
||||
record is not compliant, transformation is interrupted.
|
||||
</xsl:message>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template name="validRecord">
|
||||
<record>
|
||||
<xsl:apply-templates select="//*[local-name() = 'header']" />
|
||||
|
||||
<metadata>
|
||||
|
||||
<!--
|
||||
<xsl:apply-templates select="//*[local-name() = 'metadata']//*[local-name() = 'datasets']"/>
|
||||
-->
|
||||
|
||||
<datacite:resource>
|
||||
|
||||
<!-- OmicsDI does not state: languages, projects,
|
||||
-->
|
||||
|
||||
<!-- landing page -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:alternateIdentifiers>
|
||||
<datacite:alternateIdentifier>
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'LandingPage'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:choose>
|
||||
<xsl:when test="//*[local-name() = 'source'][. = ('gnps','massive','paxdb','peptide_atlas')]">
|
||||
<xsl:value-of select="concat('https://www.omicsdi.org/#/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
|
||||
</xsl:when>
|
||||
<xsl:when test="//*[local-name() = 'source'][. = 'metabolome_express']">
|
||||
<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, substring-after(//*[local-name()='id'], 'MEX'))"/>
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:value-of select="concat(key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@urlTemplate, //*[local-name()='id'])"/>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</datacite:alternateIdentifier>
|
||||
<datacite:alternateIdentifier>
|
||||
<xsl:attribute name="alternateIdentifierType">
|
||||
<xsl:value-of select="'local'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name()='id']"/>
|
||||
</datacite:alternateIdentifier>
|
||||
</datacite:alternateIdentifiers>
|
||||
</xsl:if>
|
||||
|
||||
<!-- identifier; ... -->
|
||||
<!-- URL hindered by _et_: https://www.omicsdi.org/ws/dataset/get_acc=E-MTAB-6546_et_database=arrayexpress-repository -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:identifier>
|
||||
<xsl:attribute name="identifierType">
|
||||
<xsl:value-of select="'URL'"/>
|
||||
</xsl:attribute>
|
||||
|
||||
<xsl:value-of select="concat('https://www.omicsdi.org/dataset/', //*[local-name() = 'source'], '/', //*[local-name() = 'id'])"/>
|
||||
|
||||
</datacite:identifier>
|
||||
</xsl:if>
|
||||
|
||||
<!-- title -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<datacite:titles>
|
||||
<datacite:title>
|
||||
<xsl:value-of select="//*[local-name() = 'title']"/>
|
||||
</datacite:title>
|
||||
</datacite:titles>
|
||||
</xsl:if>
|
||||
|
||||
<!-- no authors in OmicsDI -->
|
||||
<!--
|
||||
<xsl:call-template name="authors" />
|
||||
-->
|
||||
|
||||
<!--
|
||||
<xsl:call-template name="relatedPaper" />
|
||||
-->
|
||||
|
||||
<datacite:descriptions>
|
||||
<datacite:description>
|
||||
<xsl:attribute name="descriptionType">
|
||||
<xsl:value-of select="'Abstract'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name() = 'description']"/>
|
||||
</datacite:description>
|
||||
</datacite:descriptions>
|
||||
|
||||
<!-- subject -->
|
||||
<datacite:subjects>
|
||||
<xsl:for-each select="distinct-values(//*[local-name()='omicsType'])">
|
||||
<datacite:subject>
|
||||
<xsl:value-of select="."/>
|
||||
</datacite:subject>
|
||||
</xsl:for-each>
|
||||
</datacite:subjects>
|
||||
|
||||
</datacite:resource>
|
||||
|
||||
<xsl:choose>
|
||||
|
||||
<xsl:when test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<xsl:variable name='varCobjCategory'
|
||||
select="'0021'" />
|
||||
<dr:CobjCategory>
|
||||
<xsl:attribute name="type">
|
||||
<xsl:value-of select="TransformationFunction:convertString($tf, $varCobjCategory, 'SuperTypes')"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of
|
||||
select="$varCobjCategory" />
|
||||
</dr:CobjCategory>
|
||||
</xsl:when>
|
||||
|
||||
<xsl:otherwise>
|
||||
<!--
|
||||
<xsl:call-template name="terminate"/>
|
||||
-->
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
<!--
|
||||
// review status: no review indications found so far
|
||||
-->
|
||||
<!--
|
||||
OMICSDI is ‘including both open and controlled data source’.
|
||||
-->
|
||||
<oaf:accessrights>
|
||||
<xsl:text>UNKNOWN</xsl:text>
|
||||
</oaf:accessrights>
|
||||
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='NeuroVault__']">
|
||||
<oaf:concept>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="'ni'"/>
|
||||
</xsl:attribute>
|
||||
</oaf:concept>
|
||||
</xsl:if>
|
||||
|
||||
<oaf:hostedBy>
|
||||
<xsl:attribute name="name">
|
||||
<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@name"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="key('kCodeByName', string(//*[local-name()='source']), $vCodes)/@id"/>
|
||||
</xsl:attribute>
|
||||
</oaf:hostedBy>
|
||||
<oaf:collectedFrom>
|
||||
<xsl:attribute name="name">
|
||||
<xsl:value-of select="$varOfficialName"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="id">
|
||||
<xsl:value-of select="$varDataSourceId"/>
|
||||
</xsl:attribute>
|
||||
</oaf:collectedFrom>
|
||||
|
||||
<!-- date -->
|
||||
<xsl:if test="//*[local-name() = 'datasourceprefix'][.='_____OmicsDI']">
|
||||
<oaf:dateAccepted>
|
||||
<xsl:value-of select="replace(//*[local-name() = 'publicationDate'][not(.='null')],'(\d{4})(\d{2})(\d{2})','$1-$2-$3')"/>
|
||||
</oaf:dateAccepted>
|
||||
</xsl:if>
|
||||
|
||||
</metadata>
|
||||
<xsl:copy-of select="//*[local-name() = 'about']" />
|
||||
</record>
|
||||
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="node()|@*">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'metadata']//*[local-name() = 'datasets']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
|
||||
<xsl:template match="//*[local-name() = 'header']">
|
||||
<xsl:copy>
|
||||
<xsl:apply-templates select="node()|@*"/>
|
||||
<xsl:element name="dr:dateOfTransformation">
|
||||
<xsl:value-of select="$transDate"/>
|
||||
</xsl:element>
|
||||
</xsl:copy>
|
||||
</xsl:template>
|
||||
<!--
|
||||
no authors findable in OmicsDI">
|
||||
-->
|
||||
<!--
|
||||
<xsl:template match="//*[local-name() = 'authors']">
|
||||
-->
|
||||
<xsl:template name="authors">
|
||||
<xsl:choose>
|
||||
<xsl:when test="not(//*[local-name() = 'authors'][string-length(normalize-space(.)) > 0 and not(. = 'null')])">
|
||||
<xsl:call-template name="terminate" />
|
||||
</xsl:when>
|
||||
<xsl:otherwise>
|
||||
<xsl:for-each select="tokenize(//*[local-name() = 'authors'], '(, and |,| and )')">
|
||||
|
||||
<xsl:element name="datacite:creator">
|
||||
|
||||
<xsl:element name="datacite:creatorName">
|
||||
<xsl:value-of select="TransformationFunction:convertString($tf, ., 'Person')"/>
|
||||
</xsl:element>
|
||||
|
||||
<xsl:element name="datacite:givenName">
|
||||
<xsl:value-of select="normalize-space(substring-after(TransformationFunction:convertString($tf, ., 'Person'), ','))"/>
|
||||
</xsl:element>
|
||||
<xsl:element name="datacite:familyName">
|
||||
<xsl:value-of select="substring-before(TransformationFunction:convertString($tf, ., 'Person'), ',')"/>
|
||||
</xsl:element>
|
||||
|
||||
</xsl:element>
|
||||
</xsl:for-each>
|
||||
</xsl:otherwise>
|
||||
</xsl:choose>
|
||||
</xsl:template>
|
||||
|
||||
<!--
|
||||
<xsl:template match="//*[local-name() = 'DOI']">
|
||||
-->
|
||||
<xsl:template name="relatedPaper">
|
||||
<xsl:element name="datacite:relatedIdentifier">
|
||||
<xsl:attribute name="relatedIdentifierType">
|
||||
<xsl:value-of select="'DOI'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:attribute name="relationType">
|
||||
<xsl:value-of select="'isReferencedBy'"/>
|
||||
</xsl:attribute>
|
||||
<xsl:value-of select="//*[local-name() = 'DOI']"/>
|
||||
</xsl:element>
|
||||
</xsl:template>
|
||||
|
||||
</xsl:stylesheet>
|
||||
Loading…
Reference in New Issue