diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index aea046203a..0153e52d57 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -4,194 +4,318 @@ package eu.dnetlib.dhp.oa.merge; import java.text.Normalizer; import java.util.*; import java.util.stream.Collectors; - import org.apache.commons.lang3.StringUtils; - import com.wcohen.ss.JaroWinkler; - import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.pace.model.Person; import scala.Tuple2; + public class AuthorMerger { - private static final Double THRESHOLD = 0.95; + private static final Double THRESHOLD = 0.95; - private AuthorMerger() { - } + private AuthorMerger() { + } - public static List merge(List> authors) { + public static List merge(List> authors) { - authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2))); + authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2))); - List author = new ArrayList<>(); + List author = new ArrayList<>(); - for (List a : authors) { - author = mergeAuthor(author, a); - } + for (List a : authors) { + author = mergeAuthor(author, a); + } - return author; + return author; - } + } - public static List mergeAuthor(final List a, final List b, Double threshold) { - int pa = countAuthorsPids(a); - int pb = countAuthorsPids(b); - List base; - List enrich; - int sa = authorsSize(a); - int sb = authorsSize(b); + public static List mergeAuthor(final List a, final List b, Double threshold) { + int pa = countAuthorsPids(a); + int pb = countAuthorsPids(b); + List base; + List enrich; + int sa = authorsSize(a); + int sb = authorsSize(b); - if (sa == sb) { - base = pa > pb ? a : b; - enrich = pa > pb ? b : a; - } else { - base = sa > sb ? a : b; - enrich = sa > sb ? b : a; - } - enrichPidFromList(base, enrich, threshold); - return base; - } + if (sa == sb) { + base = pa > pb ? a : b; + enrich = pa > pb ? b : a; + } else { + base = sa > sb ? a : b; + enrich = sa > sb ? b : a; + } + enrichPidFromList(base, enrich, threshold); + return base; + } - public static List mergeAuthor(final List a, final List b) { - return mergeAuthor(a, b, THRESHOLD); - } + public static List mergeAuthor(final List a, final List b) { + return mergeAuthor(a, b, THRESHOLD); + } - private static void enrichPidFromList(List base, List enrich, Double threshold) { - if (base == null || enrich == null) - return; + private static void enrichPidFromList(List base, List enrich, Double threshold) { + if (base == null || enrich == null) + return; - // (if an Author has more than 1 pid, it appears 2 times in the list) - final Map basePidAuthorMap = base - .stream() - .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) - .flatMap( - a -> a - .getPid() - .stream() - .filter(Objects::nonNull) - .map(p -> new Tuple2<>(pidToComparableString(p), a))) - .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + // (if an Author has more than 1 pid, it appears 2 times in the list) + final Map basePidAuthorMap = base + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .flatMap( + a -> a + .getPid() + .stream() + .filter(Objects::nonNull) + .map(p -> new Tuple2<>(pidToComparableString(p), a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); - // (list of pid that are missing in the other list) - final List> pidToEnrich = enrich - .stream() - .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) - .flatMap( - a -> a - .getPid() - .stream() - .filter(Objects::nonNull) - .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) - .map(p -> new Tuple2<>(p, a))) - .collect(Collectors.toList()); + // (list of pid that are missing in the other list) + final List> pidToEnrich = enrich + .stream() + .filter(a -> a.getPid() != null && !a.getPid().isEmpty()) + .flatMap( + a -> a + .getPid() + .stream() + .filter(Objects::nonNull) + .filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p))) + .map(p -> new Tuple2<>(p, a))) + .collect(Collectors.toList()); - pidToEnrich - .forEach( - a -> { - Optional> simAuthor = base - .stream() - .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) - .max(Comparator.comparing(Tuple2::_1)); + pidToEnrich + .forEach( + a -> { + Optional> simAuthor = base + .stream() + .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) + .max(Comparator.comparing(Tuple2::_1)); - if (simAuthor.isPresent()) { - double th = threshold; - // increase the threshold if the surname is too short - if (simAuthor.get()._2().getSurname() != null - && simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0) - th = 0.99; + if (simAuthor.isPresent()) { + double th = threshold; + // increase the threshold if the surname is too short + if (simAuthor.get()._2().getSurname() != null + && simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0) + th = 0.99; - if (simAuthor.get()._1() > th) { - Author r = simAuthor.get()._2(); - if (r.getPid() == null) { - r.setPid(new ArrayList<>()); - } + if (simAuthor.get()._1() > th) { + Author r = simAuthor.get()._2(); + if (r.getPid() == null) { + r.setPid(new ArrayList<>()); + } - // TERRIBLE HACK but for some reason when we create and Array with Arrays.asList, - // it creates of fixed size, and the add method raise UnsupportedOperationException at - // java.util.AbstractList.add - final List tmp = new ArrayList<>(r.getPid()); - tmp.add(a._1()); - r.setPid(tmp); - } - } - }); - } + // TERRIBLE HACK but for some reason when we create and Array with Arrays.asList, + // it creates of fixed size, and the add method raise UnsupportedOperationException at + // java.util.AbstractList.add + final List tmp = new ArrayList<>(r.getPid()); + tmp.add(a._1()); + r.setPid(tmp); + } + } + }); + } - public static String pidToComparableString(StructuredProperty pid) { - final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() - : ""; - return (pid.getQualifier() != null ? classid : "") - + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); - } + public static String normalizeFullName(final String fullname) { + return nfd(fullname) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") - public static int countAuthorsPids(List authors) { - if (authors == null) - return 0; + .trim(); + } - return (int) authors.stream().filter(AuthorMerger::hasPid).count(); - } - private static int authorsSize(List authors) { - if (authors == null) - return 0; - return authors.size(); - } + private static String authorFieldToBeCompared(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return author.getSurname(); - private static Double sim(Author a, Author b) { + } + if (StringUtils.isNotBlank(author.getFullname())) { + return author.getFullname(); + } + return null; + } - final Person pa = parse(a); - final Person pb = parse(b); + /** + * This method tries to figure out when two author are the same in the contest + * of ORCID enrichment + * + * @param left Author in the OAF entity + * @param right Author ORCID + * @return based on a heuristic on the names of the authors if they are the same. + */ + public static boolean checkORCIDSimilarity(final Author left, final Author right) { + final Person pl = parse(left); + final Person pr = parse(right); - // if both are accurate (e.g. they have name and surname) - if (pa.isAccurate() & pb.isAccurate()) { - return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5 - + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5; - } else { - return new JaroWinkler() - .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); - } - } + // If one of them didn't have a surname we verify if they have the fullName not empty + // and verify if the normalized version is equal + if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && + pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) { - private static boolean hasPid(Author a) { - if (a == null || a.getPid() == null || a.getPid().isEmpty()) - return false; - return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); - } + if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null + && !pr.getFullname().isEmpty()) { + return pl + .getFullname() + .stream() + .anyMatch( + fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr)))); + } else { + return false; + } + } + // The Authors have one surname in common + if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { - private static Person parse(Author author) { - if (StringUtils.isNotBlank(author.getSurname())) { - return new Person(author.getSurname() + ", " + author.getName(), false); - } else { - if (StringUtils.isNotBlank(author.getFullname())) - return new Person(author.getFullname(), false); - else - return new Person("", false); - } - } + // If one of them has only a surname and is the same we can say that they are the same author + if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) || + (pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank))) + return true; + // The authors have the same initials of Name in common + if (pl + .getName() + .stream() + .anyMatch( + nl -> pr + .getName() + .stream() + .anyMatch(nr -> nr.equalsIgnoreCase(nl)))) + return true; + } - private static String normalize(final String s) { - String[] normalized = nfd(s) - .toLowerCase() - // do not compact the regexes in a single expression, would cause StackOverflowError - // in case - // of large input strings - .replaceAll("(\\W)+", " ") - .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") - .replaceAll("(\\p{Punct})+", " ") - .replaceAll("(\\d)+", " ") - .replaceAll("(\\n)+", " ") - .trim() - .split(" "); + // Sometimes we noticed that publication have author wrote in inverse order Surname, Name + // We verify if we have an exact match between name and surname + if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) && + pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl)))) + return true; + else + return false; + } + // - Arrays.sort(normalized); + /** + * Method to enrich ORCID information in one list of authors based on another list + * + * @param baseAuthor the Author List in the OAF Entity + * @param orcidAuthor The list of ORCID Author intersected + * @return The Author List of the OAF Entity enriched with the orcid Author + */ + public static List enrichOrcid(List baseAuthor, List orcidAuthor) { - return String.join(" ", normalized); - } + if (baseAuthor == null || baseAuthor.isEmpty()) + return orcidAuthor; - private static String nfd(final String s) { - return Normalizer.normalize(s, Normalizer.Form.NFD); - } + if (orcidAuthor == null || orcidAuthor.isEmpty()) + return baseAuthor; + + if (baseAuthor.size() == 1 && orcidAuthor.size() > 10) + return baseAuthor; + + final List oAuthor = new ArrayList<>(); + oAuthor.addAll(orcidAuthor); + + baseAuthor.forEach(ba -> { + Optional aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst(); + if (aMatch.isPresent()) { + final Author sameAuthor = aMatch.get(); + addPid(ba, sameAuthor.getPid()); + oAuthor.remove(sameAuthor); + } + }); + return baseAuthor; + } + + private static void addPid(final Author a, final List pids) { + + if (a.getPid() == null) { + a.setPid(new ArrayList<>()); + } + + a.getPid().addAll(pids); + + } + + public static String pidToComparableString(StructuredProperty pid) { + final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() + : ""; + return (pid.getQualifier() != null ? classid : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + } + + public static int countAuthorsPids(List authors) { + if (authors == null) + return 0; + + return (int) authors.stream().filter(AuthorMerger::hasPid).count(); + } + + private static int authorsSize(List authors) { + if (authors == null) + return 0; + return authors.size(); + } + + private static Double sim(Author a, Author b) { + + final Person pa = parse(a); + final Person pb = parse(b); + + // if both are accurate (e.g. they have name and surname) + if (pa.isAccurate() & pb.isAccurate()) { + return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5 + + new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5; + } else { + return new JaroWinkler() + .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); + } + } + + private static boolean hasPid(Author a) { + if (a == null || a.getPid() == null || a.getPid().isEmpty()) + return false; + return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue())); + } + + private static Person parse(Author author) { + if (StringUtils.isNotBlank(author.getSurname())) { + return new Person(author.getSurname() + ", " + author.getName(), false); + } else { + if (StringUtils.isNotBlank(author.getFullname())) + return new Person(author.getFullname(), false); + else + return new Person("", false); + } + } + + public static String normalize(final String s) { + String[] normalized = nfd(s) + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim() + .split(" "); + + Arrays.sort(normalized); + + return String.join(" ", normalized); + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } } diff --git a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java new file mode 100644 index 0000000000..c0a8d69279 --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java @@ -0,0 +1,114 @@ + +package eu.dnetlib.oa.merge; + +import static org.junit.jupiter.api.Assertions.*; + +import java.io.BufferedReader; +import java.io.InputStreamReader; +import java.util.List; +import java.util.Objects; + +import org.junit.jupiter.api.Test; +import org.junit.platform.commons.util.StringUtils; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.merge.AuthorMerger; +import eu.dnetlib.dhp.schema.oaf.Author; + +public class AuthorMergerTest { + + @Test + public void testEnrcichAuthor() throws Exception { + final ObjectMapper mapper = new ObjectMapper(); + + BufferedReader pr = new BufferedReader(new InputStreamReader( + Objects + .requireNonNull( + AuthorMergerTest.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); + BufferedReader or = new BufferedReader(new InputStreamReader( + Objects + .requireNonNull( + AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); + + TypeReference> aclass = new TypeReference>() { + }; + String pubLine; + + int i = 0; + while ((pubLine = pr.readLine()) != null) { + final String pubId = pubLine; + final String MatchPidOrcid = or.readLine(); + final String pubOrcid = or.readLine(); + + final String data = pr.readLine(); + + if (StringUtils.isNotBlank(data)) { + List publicationAuthors = mapper.readValue(data, aclass); + List orcidAuthors = mapper.readValue(or.readLine(), aclass); + System.out.printf("OAF ID = %s \n", pubId); + System.out.printf("ORCID Intersected ID = %s \n", pubOrcid); + System.out.printf("OAF Author Size = %d \n", publicationAuthors.size()); + System.out.printf("Oricd Author Size = %d \n", orcidAuthors.size()); + System.out.printf("Oricd Matched PID = %s \n", MatchPidOrcid); + + long originalAuthorWithPiD = publicationAuthors + .stream() + .filter( + a -> a.getPid() != null && a + .getPid() + .stream() + .anyMatch( + p -> p.getQualifier() != null + && p.getQualifier().getClassid().toLowerCase().contains("orcid"))) + .count(); + long start = System.currentTimeMillis(); + +// final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + final List enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors); + + long enrichedAuthorWithPid = enrichedList + .stream() + .filter( + a -> a.getPid() != null && a + .getPid() + .stream() + .anyMatch( + p -> p.getQualifier() != null + && p.getQualifier().getClassid().toLowerCase().contains("orcid"))) + .count(); + + long totalTime = (System.currentTimeMillis() - start) / 1000; + System.out + .printf( + "Enriched authors in %d seconds from %d pid to %d pid \n", totalTime, originalAuthorWithPiD, + enrichedAuthorWithPid); + + System.out.println("================="); + } + } + } + + @Test + public void checkSimilarityTest() { + final Author left = new Author(); + left.setName("Anand"); + left.setSurname("Rachna"); + left.setFullname("Anand, Rachna"); + + System.out.println(AuthorMerger.normalizeFullName(left.getFullname())); + + final Author right = new Author(); + right.setName("Rachna"); + right.setSurname("Anand"); + right.setFullname("Rachna, Anand"); +// System.out.println(AuthorMerger.normalize(right.getFullname())); + boolean same = AuthorMerger.checkORCIDSimilarity(left, right); + + assertTrue(same); + + } + +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json new file mode 100644 index 0000000000..ec521b3b70 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json @@ -0,0 +1,3 @@ +WrappedArray(arXiv1507.08202) +50|arXiv_dedup_::34e03f2336b8b28286550425e65634ea +[{"fullname":"Liron Barak","name":"Liron","surname":"Barak","rank":null,"pid":[{"value":"0000-0002-3436-2726","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Giuseppe Avolio","name":"Giuseppe","surname":"Avolio","rank":null,"pid":[{"value":"0000-0003-2664-3437","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Tobias Golling","name":"Tobias","surname":"Golling","rank":null,"pid":[{"value":"0000-0001-8535-6687","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Ivan Sykora","name":"Ivan","surname":"Sykora","rank":null,"pid":[{"value":"0000-0003-3447-5621","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Joao Carvalho","name":"Joao","surname":"Carvalho","rank":null,"pid":[{"value":"0000-0002-3015-7821","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jonathan David Long","name":"Jonathan David","surname":"Long","rank":null,"pid":[{"value":"0000-0002-2115-9382","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Heather Russell","name":"Heather","surname":"Russell","rank":null,"pid":[{"value":"0000-0003-4181-0678","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Alison Lister","name":"Alison","surname":"Lister","rank":null,"pid":[{"value":"0000-0002-1552-3651","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Malte Backhaus","name":"Malte","surname":"Backhaus","rank":null,"pid":[{"value":"0000-0002-5888-2304","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Xin Wu","name":"Xin","surname":"Wu","rank":null,"pid":[{"value":"0000-0001-7655-389X","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Luke Lambourne","name":"Luke","surname":"Lambourne","rank":null,"pid":[{"value":"0000-0002-7001-7575","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Kazunori Hanagaki","name":"Kazunori","surname":"Hanagaki","rank":null,"pid":[{"value":"0000-0003-0676-0441","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Krzysztof Sliwa","name":"Krzysztof","surname":"Sliwa","rank":null,"pid":[{"value":"0000-0002-1201-4771","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jiri Chudoba","name":"Jiri","surname":"Chudoba","rank":null,"pid":[{"value":"0000-0002-6425-2579","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jörn Große-Knetter","name":"Jörn","surname":"Große-Knetter","rank":null,"pid":[{"value":"0000-0003-3085-7067","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Katharine Leney","name":"Katharine","surname":"Leney","rank":null,"pid":[{"value":"0000-0002-1525-2695","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Michel 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Y.","surname":"Hostachy","rank":63,"pid":[],"affiliation":null},{"fullname":"Ledroit-Guillon, F.","name":"F.","surname":"Ledroit-Guillon","rank":64,"pid":[],"affiliation":null},{"fullname":"Lleres, A.","name":"A.","surname":"Lleres","rank":65,"pid":[],"affiliation":null},{"fullname":"Lucotte, A.","name":"A.","surname":"Lucotte","rank":66,"pid":[],"affiliation":null},{"fullname":"Malek, F.","name":"F.","surname":"Malek","rank":67,"pid":[],"affiliation":null},{"fullname":"Monini, C.","name":"C.","surname":"Monini","rank":68,"pid":[],"affiliation":null},{"fullname":"Stark, J.","name":"J.","surname":"Stark","rank":69,"pid":[],"affiliation":null},{"fullname":"Trocmé, B.","name":"B.","surname":"Trocmé","rank":70,"pid":[],"affiliation":null},{"fullname":"Wu, M.","name":"M.","surname":"Wu","rank":71,"pid":[],"affiliation":null},{"fullname":"Alio, L.","name":"L.","surname":"Alio","rank":72,"pid":[],"affiliation":null},{"fullname":"Barbero, M.","name":"M.","surname":"Barbero","rank":73,"pid":[],"affiliation":null},{"fullname":"Coadou, Y.","name":"Y.","surname":"Coadou","rank":74,"pid":[],"affiliation":null},{"fullname":"Diaconu, C.","name":"C.","surname":"Diaconu","rank":75,"pid":[],"affiliation":null},{"fullname":"Diglio, Sara","name":"Sara","surname":"Diglio","rank":76,"pid":[],"affiliation":null},{"fullname":"Djama, F.","name":"F.","surname":"Djama","rank":77,"pid":[],"affiliation":null},{"fullname":"Duccu, O.","name":"O.","surname":"Duccu","rank":78,"pid":[],"affiliation":null},{"fullname":"Feligioni, L.","name":"L.","surname":"Feligioni","rank":79,"pid":[],"affiliation":null},{"fullname":"Gao, J.","name":"J.","surname":"Gao","rank":80,"pid":[],"affiliation":null},{"fullname":"Hallewell, G.D.","name":"G. D.","surname":"Hallewell","rank":81,"pid":[],"affiliation":null},{"fullname":"Hubaut, F.","name":"F.","surname":"Hubaut","rank":82,"pid":[],"affiliation":null},{"fullname":"Kahn, S.J.","name":"S. J.","surname":"Kahn","rank":83,"pid":[],"affiliation":null},{"fullname":"Knoops, E. B. F. G.","name":"E. B. F. G.","surname":"Knoops","rank":84,"pid":[],"affiliation":null},{"fullname":"Guirriec, E. Le","name":"E. Le","surname":"Guirriec","rank":85,"pid":[],"affiliation":null},{"fullname":"Liu, J.","name":"J.","surname":"Liu","rank":86,"pid":[],"affiliation":null},{"fullname":"Liu, K.","name":"K.","surname":"Liu","rank":87,"pid":[],"affiliation":null},{"fullname":"Madaffari, D.","name":"D.","surname":"Madaffari","rank":88,"pid":[],"affiliation":null},{"fullname":"Mochizuki, K.","name":"K.","surname":"Mochizuki","rank":89,"pid":[],"affiliation":null},{"fullname":"Monnier, E.","name":"E.","surname":"Monnier","rank":90,"pid":[],"affiliation":null},{"fullname":"Muanza, S.","name":"S.","surname":"Muanza","rank":91,"pid":[],"affiliation":null},{"fullname":"Nagai, Y.","name":"Y.","surname":"Nagai","rank":92,"pid":[],"affiliation":null},{"fullname":"Nagy, E.","name":"E.","surname":"Nagy","rank":93,"pid":[],"affiliation":null},{"fullname":"Pralavorio, P.","name":"P.","surname":"Pralavorio","rank":94,"pid":[],"affiliation":null},{"fullname":"Rozanov, A.","name":"A.","surname":"Rozanov","rank":95,"pid":[],"affiliation":null},{"fullname":"Serre, T.","name":"T.","surname":"Serre","rank":96,"pid":[],"affiliation":null},{"fullname":"Talby, M.","name":"M.","surname":"Talby","rank":97,"pid":[],"affiliation":null},{"fullname":"Torres, R.E. Ticse","name":"R. E. Ticse","surname":"Torres","rank":98,"pid":[],"affiliation":null},{"fullname":"Tiouchichine, E.","name":"E.","surname":"Tiouchichine","rank":99,"pid":[],"affiliation":null},{"fullname":"Tisserant, S.","name":"S.","surname":"Tisserant","rank":100,"pid":[],"affiliation":null},{"fullname":"Toth, J.","name":"J.","surname":"Toth","rank":101,"pid":[],"affiliation":null},{"fullname":"Touchard, F.","name":"F.","surname":"Touchard","rank":102,"pid":[],"affiliation":null},{"fullname":"Vacavant, L.","name":"L.","surname":"Vacavant","rank":103,"pid":[],"affiliation":null},{"fullname":"Boumediene, D.","name":"D.","surname":"Boumediene","rank":104,"pid":[],"affiliation":null},{"fullname":"Busato, Emmanuel","name":"Emmanuel","surname":"Busato","rank":105,"pid":[],"affiliation":null},{"fullname":"Calvet, D.","name":"D.","surname":"Calvet","rank":106,"pid":[],"affiliation":null},{"fullname":"Calvet, S.","name":"S.","surname":"Calvet","rank":107,"pid":[],"affiliation":null},{"fullname":"Donini, J.","name":"J.","surname":"Donini","rank":108,"pid":[],"affiliation":null},{"fullname":"Dubreuil, E.","name":"E.","surname":"Dubreuil","rank":109,"pid":[],"affiliation":null},{"fullname":"Gilles, G.","name":"G.","surname":"Gilles","rank":110,"pid":[],"affiliation":null},{"fullname":"Gris, Ph.","name":"Ph","surname":"Gris","rank":111,"pid":[],"affiliation":null},{"fullname":"Liao, H.","name":"H.","surname":"Liao","rank":112,"pid":[],"affiliation":null},{"fullname":"Madar, R.","name":"R.","surname":"Madar","rank":113,"pid":[],"affiliation":null},{"fullname":"Pallin, D.","name":"D.","surname":"Pallin","rank":114,"pid":[],"affiliation":null},{"fullname":"Saez, S.M. Romano","name":"S. M. Romano","surname":"Saez","rank":115,"pid":[],"affiliation":null},{"fullname":"Santoni, C.","name":"C.","surname":"Santoni","rank":116,"pid":[],"affiliation":null},{"fullname":"Simon, D.","name":"D.","surname":"Simon","rank":117,"pid":[],"affiliation":null},{"fullname":"Theveneaux-Pelzer, Timothée","name":"Timothée","surname":"Theveneaux-Pelzer","rank":118,"pid":[],"affiliation":null},{"fullname":"Vazeille, F.","name":"F.","surname":"Vazeille","rank":119,"pid":[],"affiliation":null},{"fullname":"Yatsenko, E.","name":"E.","surname":"Yatsenko","rank":120,"pid":[],"affiliation":null}] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java new file mode 100644 index 0000000000..69661bbf66 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDDumpApplication.java @@ -0,0 +1,102 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.InputStream; +import java.net.URL; +import java.net.URLConnection; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.http.client.config.RequestConfig; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClientBuilder; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.JsonNode; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class DownloadORCIDDumpApplication { + private static final Logger log = LoggerFactory.getLogger(DownloadORCIDDumpApplication.class); + + private final FileSystem fileSystem; + + public DownloadORCIDDumpApplication(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + DownloadORCIDDumpApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json")))); + argumentParser.parseArgument(args); + + final String hdfsuri = argumentParser.get("namenode"); + log.info("hdfsURI is {}", hdfsuri); + + final String targetPath = argumentParser.get("targetPath"); + log.info("targetPath is {}", targetPath); + + final String apiURL = argumentParser.get("apiURL"); + log.info("apiURL is {}", apiURL); + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsuri)); + + new DownloadORCIDDumpApplication(fileSystem).run(targetPath, apiURL); + + } + + private void downloadItem(final String name, final String itemURL, final String basePath) { + try { + final Path hdfsWritePath = new Path(String.format("%s/%s", basePath, name)); + final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true); + final HttpGet request = new HttpGet(itemURL); + final int timeout = 60; // seconds + final RequestConfig config = RequestConfig + .custom() + .setConnectTimeout(timeout * 1000) + .setConnectionRequestTimeout(timeout * 1000) + .setSocketTimeout(timeout * 1000) + .build(); + log.info("Downloading url {} into {}", itemURL, hdfsWritePath.getName()); + try (CloseableHttpClient client = HttpClientBuilder.create().setDefaultRequestConfig(config).build(); + CloseableHttpResponse response = client.execute(request)) { + int responseCode = response.getStatusLine().getStatusCode(); + log.info("Response code is {}", responseCode); + if (responseCode >= 200 && responseCode < 400) { + IOUtils.copy(response.getEntity().getContent(), fsDataOutputStream); + } + } catch (Throwable eu) { + throw new RuntimeException(eu); + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + protected void run(final String targetPath, final String apiURL) throws Exception { + final ObjectMapper mapper = new ObjectMapper(); + final URL url = new URL(apiURL); + URLConnection conn = url.openConnection(); + InputStream is = conn.getInputStream(); + final String json = IOUtils.toString(is); + JsonNode jsonNode = mapper.readTree(json); + jsonNode + .get("files") + .forEach(i -> downloadItem(i.get("name").asText(), i.get("download_url").asText(), targetPath)); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java new file mode 100644 index 0000000000..4aefdb5e9e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ExtractORCIDDump.java @@ -0,0 +1,71 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.List; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocatedFileStatus; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.fs.RemoteIterator; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class ExtractORCIDDump { + private static final Logger log = LoggerFactory.getLogger(ExtractORCIDDump.class); + + private final FileSystem fileSystem; + + public ExtractORCIDDump(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + + public static void main(String[] args) throws Exception { + final ArgumentApplicationParser argumentParser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + DownloadORCIDDumpApplication.class + .getResourceAsStream( + "/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json")))); + argumentParser.parseArgument(args); + + final String hdfsuri = argumentParser.get("namenode"); + log.info("hdfsURI is {}", hdfsuri); + + final String sourcePath = argumentParser.get("sourcePath"); + log.info("sourcePath is {}", sourcePath); + + final String targetPath = argumentParser.get("targetPath"); + log.info("targetPath is {}", targetPath); + + final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsuri)); + + new ExtractORCIDDump(fileSystem).run(sourcePath, targetPath); + + } + + public void run(final String sourcePath, final String targetPath) throws IOException, InterruptedException { + RemoteIterator ls = fileSystem.listFiles(new Path(sourcePath), false); + final List workers = new ArrayList<>(); + int i = 0; + while (ls.hasNext()) { + LocatedFileStatus current = ls.next(); + if (current.getPath().getName().endsWith("tar.gz")) { + workers.add(new ORCIDExtractor(fileSystem, "" + i++, current.getPath(), targetPath)); + } + } + workers.forEach(Thread::start); + for (ORCIDExtractor worker : workers) { + worker.join(); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java new file mode 100644 index 0000000000..11f4c55d84 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java @@ -0,0 +1,171 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.util.HashMap; +import java.util.Map; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveInputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.hadoop.io.IOUtils; +import org.apache.hadoop.io.SequenceFile; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.CompressionCodec; +import org.apache.hadoop.io.compress.CompressionCodecFactory; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +/**\ + * The ORCIDExtractor class extracts ORCID data from a TAR archive. + * The class creates a map of SequenceFile.Writer objects, one for each type of data that is to be extracted (e.g., employments, works, summaries). + * Then, it iterates over the TAR archive and writes each entry to the appropriate SequenceFile.Writer object. + * Finally, it closes all the SequenceFile.Writer objects. + */ +public class ORCIDExtractor extends Thread { + + private static final Logger log = LoggerFactory.getLogger(ORCIDExtractor.class); + + private final FileSystem fileSystem; + + private final String id; + + private final Path sourcePath; + + private final String baseOutputPath; + + public ORCIDExtractor(FileSystem fileSystem, String id, Path sourcePath, String baseOutputPath) { + this.fileSystem = fileSystem; + this.id = id; + this.sourcePath = sourcePath; + this.baseOutputPath = baseOutputPath; + } + + /** + * creates a map of SequenceFile.Writer objects, + * one for each type of data that is to be extracted. The map is created based on the filename in the TAR archive. + * For example, if the filename is employments.json, the map will contain an entry for the SequenceFile.Writer + * object that writes employment data. + * @return the Map + */ + private Map createMap() { + try { + log.info("Thread {} Creating sequence files starting from this input Path {}", id, sourcePath.getName()); + Map res = new HashMap<>(); + if (sourcePath.getName().contains("summaries")) { + + final String summaryPath = String.format("%s/summaries_%s", baseOutputPath, id); + final SequenceFile.Writer summary_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(summaryPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + + log.info("Thread {} Creating only summary path here {}", id, summaryPath); + res.put("summary", summary_file); + return res; + } else { + String employmentsPath = String.format("%s/employments_%s", baseOutputPath, id); + final SequenceFile.Writer employments_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(employmentsPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + res.put("employments", employments_file); + log.info("Thread {} Creating employments path here {}", id, employmentsPath); + + final String worksPath = String.format("%s/works_%s", baseOutputPath, id); + final SequenceFile.Writer works_file = SequenceFile + .createWriter( + fileSystem.getConf(), + SequenceFile.Writer.file(new Path(worksPath)), + SequenceFile.Writer.keyClass(Text.class), + SequenceFile.Writer.valueClass(Text.class)); + res.put("works", works_file); + log.info("Thread {} Creating works path here {}", id, worksPath); + + return res; + } + } catch (Throwable e) { + throw new RuntimeException(e); + } + } + + @Override + public void run() { + + CompressionCodecFactory factory = new CompressionCodecFactory(fileSystem.getConf()); + CompressionCodec codec = factory.getCodec(sourcePath); + if (codec == null) { + System.err.println("No codec found for " + sourcePath.getName()); + System.exit(1); + } + + InputStream gzipInputStream = null; + try { + gzipInputStream = codec.createInputStream(fileSystem.open(sourcePath)); + final Map fileMap = createMap(); + iterateTar(fileMap, gzipInputStream); + + } catch (IOException e) { + throw new RuntimeException(e); + } finally { + log.info("Closing gzip stream"); + IOUtils.closeStream(gzipInputStream); + } + + } + + private SequenceFile.Writer retrieveFile(Map fileMap, final String path) { + if (sourcePath.getName().contains("summaries")) { + return fileMap.get("summary"); + } + + if (path.contains("works")) { + return fileMap.get("works"); + } + if (path.contains("employments")) + return fileMap.get("employments"); + return null; + } + + private void iterateTar(Map fileMap, InputStream gzipInputStream) throws IOException { + + int extractedItem = 0; + try (final TarArchiveInputStream tais = new TarArchiveInputStream(gzipInputStream)) { + + TarArchiveEntry entry; + while ((entry = tais.getNextTarEntry()) != null) { + + if (entry.isFile()) { + + final SequenceFile.Writer fl = retrieveFile(fileMap, entry.getName()); + if (fl != null) { + final Text key = new Text(entry.getName()); + final Text value = new Text( + org.apache.commons.io.IOUtils.toString(new BufferedReader(new InputStreamReader(tais)))); + fl.append(key, value); + extractedItem++; + if (extractedItem % 100000 == 0) { + log.info("Thread {}: Extracted {} items", id, extractedItem); + break; + } + } + } + } + } finally { + for (SequenceFile.Writer k : fileMap.values()) { + log.info("Thread {}: Completed processed {} items", id, extractedItem); + k.hflush(); + k.close(); + } + } + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java new file mode 100644 index 0000000000..159b8a5fca --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidParser.java @@ -0,0 +1,251 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.util.Arrays; +import java.util.Collections; +import java.util.List; + +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.ximpleware.*; + +import eu.dnetlib.dhp.collection.orcid.model.*; +import eu.dnetlib.dhp.parser.utility.VtdException; +import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; + +public class OrcidParser { + + final Logger log = LoggerFactory.getLogger(OrcidParser.class); + private VTDNav vn; + + private AutoPilot ap; + private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common"; + private static final String NS_COMMON = "common"; + private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person"; + private static final String NS_PERSON = "person"; + private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details"; + private static final String NS_DETAILS = "personal-details"; + private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name"; + private static final String NS_OTHER = "other-name"; + private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record"; + private static final String NS_RECORD = "record"; + private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error"; + private static final String NS_ACTIVITIES = "activities"; + private static final String NS_ACTIVITIES_URL = "http://www.orcid.org/ns/activities"; + private static final String NS_WORK = "work"; + private static final String NS_WORK_URL = "http://www.orcid.org/ns/work"; + + private static final String NS_ERROR = "error"; + private static final String NS_HISTORY = "history"; + private static final String NS_HISTORY_URL = "http://www.orcid.org/ns/history"; + private static final String NS_BULK_URL = "http://www.orcid.org/ns/bulk"; + private static final String NS_BULK = "bulk"; + private static final String NS_EXTERNAL = "external-identifier"; + private static final String NS_EXTERNAL_URL = "http://www.orcid.org/ns/external-identifier"; + + private void generateParsedDocument(final String xml) throws ParseException { + final VTDGen vg = new VTDGen(); + vg.setDoc(xml.getBytes()); + vg.parse(true); + this.vn = vg.getNav(); + this.ap = new AutoPilot(vn); + ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL); + ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL); + ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL); + ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL); + ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL); + ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL); + ap.declareXPathNameSpace(NS_HISTORY, NS_HISTORY_URL); + ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL); + ap.declareXPathNameSpace(NS_EXTERNAL, NS_EXTERNAL_URL); + ap.declareXPathNameSpace(NS_ACTIVITIES, NS_ACTIVITIES_URL); + } + + public Author parseSummary(final String xml) { + + try { + final Author author = new Author(); + generateParsedDocument(xml); + List recordNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, "//record:record", Arrays.asList("path")); + if (!recordNodes.isEmpty()) { + final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1); + author.setOrcid(oid); + } else { + return null; + } + List personNodes = VtdUtilityParser + .getTextValuesWithAttributes( + ap, vn, "//person:name", Arrays.asList("visibility")); + final String visibility = (personNodes.get(0).getAttributes().get("visibility")); + author.setVisibility(visibility); + final String name = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:given-names"); + author.setGivenName(name); + + final String surnames = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:family-name"); + author.setFamilyName(surnames); + + final String creditNames = VtdUtilityParser.getSingleValue(ap, vn, "//personal-details:credit-name"); + author.setCreditName(creditNames); + + final String biography = VtdUtilityParser + .getSingleValue(ap, vn, "//person:biography/personal-details:content"); + author.setBiography(biography); + + final List otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content"); + if (!otherNames.isEmpty()) { + author.setOtherNames(otherNames); + } + + ap.selectXPath("//external-identifier:external-identifier"); + + while (ap.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + + ap1.selectXPath("./common:external-id-type"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:external-id-value"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + author.addOtherPid(pid); + } + + return author; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + } + + public Work parseWork(final String xml) { + + try { + final Work work = new Work(); + generateParsedDocument(xml); + List workNodes = VtdUtilityParser + .getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "visibility")); + if (!workNodes.isEmpty()) { + final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1]; + work.setOrcid(oid); + } else { + return null; + } + + ap.selectXPath("//common:external-id"); + + while (ap.evalXPath() != -1) { + final Pid pid = new Pid(); + + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + + ap1.selectXPath("./common:external-id-type"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setSchema(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:external-id-value"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + pid.setValue(vn.toNormalizedString(it)); + } + + work.addPid(pid); + } + + work.setTitle(VtdUtilityParser.getSingleValue(ap, vn, "//work:title/common:title")); + + return work; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + + private String extractEmploymentDate(final String xpath) throws Exception { + + ap.selectXPath(xpath); + StringBuilder sb = new StringBuilder(); + while (ap.evalXPath() != -1) { + final AutoPilot ap1 = new AutoPilot(ap.getNav()); + ap1.selectXPath("./common:year"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:month"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append("-"); + sb.append(vn.toNormalizedString(it)); + } + ap1.selectXPath("./common:day"); + while (ap1.evalXPath() != -1) { + int it = vn.getText(); + sb.append("-"); + sb.append(vn.toNormalizedString(it)); + } + } + return sb.toString(); + + } + + public Employment parseEmployment(final String xml) { + try { + final Employment employment = new Employment(); + generateParsedDocument(xml); + final String oid = VtdUtilityParser + .getSingleValue(ap, vn, "//common:source-orcid/common:path"); + if (StringUtils.isNotBlank(oid)) { + employment.setOrcid(oid); + } else { + return null; + } + final String depName = VtdUtilityParser + .getSingleValue(ap, vn, "//common:department-name"); + final String rolTitle = VtdUtilityParser + .getSingleValue(ap, vn, "//common:role-title"); + if (StringUtils.isNotBlank(rolTitle)) + employment.setRoleTitle(rolTitle); + if (StringUtils.isNotBlank(depName)) + employment.setDepartmentName(depName); + else + employment + .setDepartmentName( + VtdUtilityParser + .getSingleValue(ap, vn, "//common:organization/common:name")); + + employment.setStartDate(extractEmploymentDate("//common:start-date")); + employment.setEndDate(extractEmploymentDate("//common:end-date")); + + final String affiliationId = VtdUtilityParser + .getSingleValue(ap, vn, "//common:disambiguated-organization-identifier"); + final String affiliationIdType = VtdUtilityParser + .getSingleValue(ap, vn, "//common:disambiguation-source"); + + if (StringUtils.isNotBlank(affiliationId) || StringUtils.isNotBlank(affiliationIdType)) + employment.setAffiliationId(new Pid(affiliationId, affiliationIdType)); + + return employment; + } catch (Throwable e) { + log.error("Error on parsing {}", xml); + log.error(e.getMessage()); + return null; + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java new file mode 100644 index 0000000000..32c321b41c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java @@ -0,0 +1,83 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +import java.util.ArrayList; +import java.util.List; + +public class Author extends ORCIDItem { + private String givenName; + private String familyName; + + private String visibility; + + private String creditName; + + private List otherNames; + + private List otherPids; + + private String biography; + + public String getBiography() { + return biography; + } + + public void setBiography(String biography) { + this.biography = biography; + } + + public String getGivenName() { + return givenName; + } + + public void setGivenName(String givenName) { + this.givenName = givenName; + } + + public String getFamilyName() { + return familyName; + } + + public void setFamilyName(String familyName) { + this.familyName = familyName; + } + + public String getCreditName() { + return creditName; + } + + public void setCreditName(String creditName) { + this.creditName = creditName; + } + + public List getOtherNames() { + return otherNames; + } + + public void setOtherNames(List otherNames) { + this.otherNames = otherNames; + } + + public String getVisibility() { + return visibility; + } + + public void setVisibility(String visibility) { + this.visibility = visibility; + } + + public List getOtherPids() { + return otherPids; + } + + public void setOtherPids(List otherPids) { + this.otherPids = otherPids; + } + + public void addOtherPid(final Pid pid) { + + if (otherPids == null) + otherPids = new ArrayList<>(); + otherPids.add(pid); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java new file mode 100644 index 0000000000..baee67d464 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Employment.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class Employment extends ORCIDItem { + + private String startDate; + private String EndDate; + + private Pid affiliationId; + + private String departmentName; + + private String roleTitle; + + public String getStartDate() { + return startDate; + } + + public void setStartDate(String startDate) { + this.startDate = startDate; + } + + public String getEndDate() { + return EndDate; + } + + public void setEndDate(String endDate) { + EndDate = endDate; + } + + public Pid getAffiliationId() { + return affiliationId; + } + + public void setAffiliationId(Pid affiliationId) { + this.affiliationId = affiliationId; + } + + public String getDepartmentName() { + return departmentName; + } + + public void setDepartmentName(String departmentName) { + this.departmentName = departmentName; + } + + public String getRoleTitle() { + return roleTitle; + } + + public void setRoleTitle(String roleTitle) { + this.roleTitle = roleTitle; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java new file mode 100644 index 0000000000..6bc47bc260 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java @@ -0,0 +1,14 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class ORCIDItem { + private String orcid; + + public String getOrcid() { + return orcid; + } + + public void setOrcid(String orcid) { + this.orcid = orcid; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java new file mode 100644 index 0000000000..077dc25504 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Pid.java @@ -0,0 +1,33 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +public class Pid { + + private String value; + + private String schema; + + public Pid() { + } + + public Pid(String value, String schema) { + this.value = value; + this.schema = schema; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getSchema() { + return schema; + } + + public void setSchema(String schema) { + this.schema = schema; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java new file mode 100644 index 0000000000..6701703237 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.collection.orcid.model; + +import java.util.ArrayList; +import java.util.List; + +public class Work extends ORCIDItem { + + private String title; + + private List pids; + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public List getPids() { + return pids; + } + + public void setPids(List pids) { + this.pids = pids; + } + + public void addPid(Pid pid) { + if (pids == null) + pids = new ArrayList<>(); + pids.add(pid); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json new file mode 100644 index 0000000000..4a84cbbb98 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/download_orcid_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the FIGSHARE API id URL to retrieve all the dump files", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json new file mode 100644 index 0000000000..4af3718753 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/extract_orcid_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH to extract files", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the PATH where the tar.gz files were downloaded", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json new file mode 100644 index 0000000000..01d81ea974 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "the master name", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH of the DF tables", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the PATH of the ORCID sequence file", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml new file mode 100644 index 0000000000..dd3c32c620 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/config-default.xml @@ -0,0 +1,23 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml new file mode 100644 index 0000000000..1a5f425e5a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/oozie_app/workflow.xml @@ -0,0 +1,81 @@ + + + + targetPath + the path to store the original ORCID dump + + + apiURL + The figshare API URL to retrieve the list file to download + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.collection.orcid.DownloadORCIDDumpApplication + --namenode${nameNode} + --targetPath${targetPath} + --apiURL${apiURL} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + + eu.dnetlib.dhp.collection.orcid.ExtractORCIDDump + -Xmx6g + --namenode${nameNode} + --sourcePath${targetPath} + --targetPath${targetPath}/extracted + + + + + + + + yarn + cluster + Generate ORCID Tables + eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${targetPath}/extracted + --targetPath${targetPath}/tables + --masteryarn + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json new file mode 100644 index 0000000000..4a84cbbb98 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/preprocess_orcid_dump_parameter.json @@ -0,0 +1,21 @@ +[ + { + "paramName": "n", + "paramLongName": "namenode", + "paramDescription": "the Name Node URI", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target PATH where download the files", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "apiURL", + "paramDescription": "the FIGSHARE API id URL to retrieve all the dump files", + "paramRequired": true + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala new file mode 100644 index 0000000000..f0c4cd2140 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/orcid/SparkGenerateORCIDTable.scala @@ -0,0 +1,101 @@ +package eu.dnetlib.dhp.collection.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.collection.orcid.model.{Author, Employment, Pid, Work} +import org.apache.hadoop.io.Text +import org.apache.spark.SparkContext +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +class SparkGenerateORCIDTable(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + val sourcePath: String = parser.get("sourcePath") + log.info("found parameters sourcePath: {}", sourcePath) + val targetPath: String = parser.get("targetPath") + log.info("found parameters targetPath: {}", targetPath) + extractORCIDTable(spark, sourcePath, targetPath) + extractORCIDEmploymentsTable(spark, sourcePath, targetPath) + extractORCIDWorksTable(spark, sourcePath, targetPath) + } + + def extractORCIDTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidAuthor: Encoder[Author] = Encoders.bean(classOf[Author]) +// implicit val orcidPID:Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("summaries")) + .map { r => + val p = new OrcidParser + p.parseSummary(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Authors") + } + + def extractORCIDWorksTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidWorkAuthor: Encoder[Work] = Encoders.bean(classOf[Work]) + implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("works")) + .map { r => + val p = new OrcidParser + p.parseWork(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Works") + } + + def extractORCIDEmploymentsTable(spark: SparkSession, sourcePath: String, targetPath: String): Unit = { + val sc: SparkContext = spark.sparkContext + import spark.implicits._ + val df = sc + .sequenceFile(sourcePath, classOf[Text], classOf[Text]) + .map { case (x, y) => (x.toString, y.toString) } + .toDF + .as[(String, String)] + implicit val orcidEmploymentAuthor: Encoder[Employment] = Encoders.bean(classOf[Employment]) + implicit val orcidPID: Encoder[Pid] = Encoders.bean(classOf[Pid]) + df.filter(r => r._1.contains("employments")) + .map { r => + val p = new OrcidParser + p.parseEmployment(r._2) + } + .filter(p => p != null) + .write + .mode(SaveMode.Overwrite) + .save(s"$targetPath/Employments") + } +} + +object SparkGenerateORCIDTable { + + val log: Logger = LoggerFactory.getLogger(SparkGenerateORCIDTable.getClass) + + def main(args: Array[String]): Unit = { + + new SparkGenerateORCIDTable("/eu/dnetlib/dhp/collection/orcid/generate_orcid_table_parameter.json", args, log) + .initialize() + .run() + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index ee36609189..7603715b96 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -176,7 +176,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ), resourceType + ), + resourceType ) } if (schemaOrg != null && schemaOrg.nonEmpty) { @@ -188,7 +189,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ), schemaOrg + ), + schemaOrg ) } @@ -203,7 +205,8 @@ object DataciteToOAFTransformation { vocabularies.getSynonymAsQualifier( ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid - ), resourceTypeGeneral + ), + resourceTypeGeneral ) } @@ -228,7 +231,6 @@ object DataciteToOAFTransformation { itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) - typeQualifiers._2.getClassname match { case "dataset" => val r = new OafDataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index 89bc8d948b..df356548ab 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -593,7 +593,6 @@ object BioDBToOAF { itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) i.setInstanceTypeMapping(List(itm).asJava) - i.setCollectedfrom(collectedFromMap("ebi")) d.setInstance(List(i).asJava) i.setDateofacceptance( diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index f3f8b4f020..d59d73bd05 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -195,7 +195,7 @@ object PubMedToOaf { pubmedInstance.setInstanceTypeMapping(List(itm).asJava) } else { val i_type = article.getPublicationTypes.asScala - .map(s => (s.getValue,getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))) + .map(s => (s.getValue, getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))) .find(q => q._2 != null) if (i_type.isDefined) { @@ -205,8 +205,7 @@ object PubMedToOaf { itm.setOriginalType(i_type.get._1) itm.setVocabularyName(ModelConstants.OPENAIRE_COAR_RESOURCE_TYPES_3_1) pubmedInstance.setInstanceTypeMapping(List(itm).asJava) - } - else + } else return null } val result = createResult(pubmedInstance.getInstancetype, vocabularies) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java new file mode 100644 index 0000000000..868f4e92d0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/orcid/DownloadORCIDTest.java @@ -0,0 +1,119 @@ + +package eu.dnetlib.dhp.collection.orcid; + +import java.io.IOException; +import java.util.Arrays; +import java.util.List; +import java.util.Objects; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkContext; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.ximpleware.NavException; +import com.ximpleware.ParseException; +import com.ximpleware.XPathEvalException; +import com.ximpleware.XPathParseException; + +import eu.dnetlib.dhp.collection.orcid.model.Author; +import eu.dnetlib.dhp.collection.orcid.model.ORCIDItem; +import eu.dnetlib.dhp.parser.utility.VtdException; + +public class DownloadORCIDTest { + private final Logger log = LoggerFactory.getLogger(DownloadORCIDTest.class); + + @Test + public void testSummary() throws Exception { + final String xml = IOUtils + .toString( + Objects.requireNonNull(getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/orcid/summary.xml"))); + + final OrcidParser parser = new OrcidParser(); + ORCIDItem orcidItem = parser.parseSummary(xml); + + final ObjectMapper mapper = new ObjectMapper(); + System.out.println(mapper.writeValueAsString(orcidItem)); + + } + + @Test + public void testParsingWork() throws Exception { + + final List works_path = Arrays + .asList( + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml", + "/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml" + + ); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + works_path.stream().map(s -> { + try { + return IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream( + s))); + } catch (IOException e) { + throw new RuntimeException(e); + } + }).forEach(s -> { + try { + System.out.println(mapper.writeValueAsString(parser.parseWork(s))); + } catch (Exception e) { + throw new RuntimeException(e); + } + }); + } + + @Test + public void testParsingEmployments() throws Exception { + + final List works_path = Arrays + .asList( + "/eu/dnetlib/dhp/collection/orcid/employment.xml", + "/eu/dnetlib/dhp/collection/orcid/employment_2.xml", + "/eu/dnetlib/dhp/collection/orcid/employment_3.xml" + + ); + + final OrcidParser parser = new OrcidParser(); + final ObjectMapper mapper = new ObjectMapper(); + works_path.stream().map(s -> { + try { + return IOUtils + .toString( + Objects + .requireNonNull( + getClass() + .getResourceAsStream( + s))); + } catch (IOException e) { + throw new RuntimeException(e); + } + }).forEach(s -> { + try { + System.out.println(mapper.writeValueAsString(parser.parseEmployment(s))); + } catch (Exception e) { + throw new RuntimeException(e); + } + }); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml new file mode 100644 index 0000000000..2c89b83f6e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-2536-4498.xml @@ -0,0 +1,69 @@ + + + 2016-09-01T19:22:46.768Z + 2022-05-25T03:48:56.968Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + https://orcid.org/0000-0001-5010-5001 + 0000-0001-5010-5001 + orcid.org + + Quang Nguyen + + + Vision outcomes and major complications after endovascular coil embolization of ophthalmic segment aneurysms + + American Journal of Neuroradiology + + bibtex + @article{Nguyen2014,title = {Vision outcomes and major complications after endovascular coil embolization of ophthalmic segment aneurysms},journal = {American Journal of Neuroradiology},year = {2014},volume = {35},number = {11},pages = {2140-2145},author = {Durst, C. and Starke, R.M. and Gaughen, J. and Nguyen, Q. and Patrie, J. and Jensen, M.E. and Evans, A.J.}} + + journal-article + + 2014 + + + + doi + 10.3174/ajnr.A4032 + 10.3174/ajnr.a4032 + self + + + eid + 2-s2.0-84911865199 + 2-s2.0-84911865199 + self + + + http://www.scopus.com/inward/record.url?eid=2-s2.0-84911865199&partnerID=MN8TOARS + + + Durst, C. + + + Starke, R.M. + + + Gaughen, J. + + + Nguyen, Q. + + + Patrie, J. + + + Jensen, M.E. + + + Evans, A.J. + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml new file mode 100644 index 0000000000..63b4405f15 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0002-5982-8983.xml @@ -0,0 +1,79 @@ + + + 2018-11-01T19:49:45.562Z + 2018-11-01T19:49:45.562Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + + "Calling Out" in class: Degrees of candor in addressing social injustices in + racially homogenous and heterogeneous U.S. history classrooms + + Journal of Social Studies Research + + bibtex + @article{Massaro2018,title = {{"}Calling Out{"} in class: Degrees of + candor in addressing social injustices in racially homogenous and heterogeneous U.S. + history classrooms},journal = {Journal of Social Studies Research},year = {2018},author + = {Parkhouse, H. and Massaro, V.R.}} + + journal-article + + 2018 + + + + doi + 10.1016/j.jssr.2018.01.004 + 10.1016/j.jssr.2018.01.004 + self + + + eid + 2-s2.0-85041949043 + 2-s2.0-85041949043 + self + + + http://www.scopus.com/inward/record.url?eid=2-s2.0-85041949043&partnerID=MN8TOARS + + + Parkhouse, H. + + + Massaro, V.R. + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml new file mode 100644 index 0000000000..650d5a4cb4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191-similarity.xml @@ -0,0 +1,113 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Abdel-Dayem K + + first + author + + + + Abdel-Dayem Fake + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml new file mode 100644 index 0000000000..83752b1457 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191.xml @@ -0,0 +1,106 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + Khair Abde Daye + + first + author + + + + Eweda II + + first + author + + + + El-Sherbiny A + + first + author + + + + Dimitry MO + + first + author + + + + Nammas W + + first + author + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml new file mode 100644 index 0000000000..26e64aedae --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/activity_work_0000-0003-2760-1191_contributors.xml @@ -0,0 +1,101 @@ + + + 2016-12-12T23:02:05.233Z + 2016-12-13T09:08:16.412Z + + + https://orcid.org/0000-0002-9157-3431 + 0000-0002-9157-3431 + orcid.org + + Europe PubMed Central + + + Cutoff Value of Admission N-Terminal Pro-Brain Natriuretic Peptide Which + Predicts Poor Myocardial Perfusion after Primary Percutaneous Coronary Intervention for + ST-Segment-Elevation Myocardial Infarction. + + + formatted-unspecified + Abdel-Dayem K, Eweda II, El-Sherbiny A, Dimitry MO, Nammas W, Acta + Cardiologica Sinica, 2016, vol. 32, no. 6, pp. 649-655, 2016 + + journal-article + + 2016 + 11 + + + + pmid + 27899851 + 27899851 + self + + + pmc + PMC5126442 + PMC5126442 + self + + + http://europepmc.org/abstract/med/27899851 + + + + seq0 + role0 + + + + creditname1 + + + creditname2 + + seq2 + + + + + creditname3 + + + role3 + + + + + + seq4 + role4 + + + + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml new file mode 100644 index 0000000000..89c7f70201 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment.xml @@ -0,0 +1,50 @@ + + + 2016-09-01T19:21:05.791Z + 2016-09-01T19:21:05.791Z + + + https://orcid.org/0000-0001-5010-5001 + 0000-0001-5010-5001 + orcid.org + + Quang Nguyen + + + Beth Israel Deaconess Medical Center + + Boston + MA + US + + + 1859 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml new file mode 100644 index 0000000000..c0e88e236e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_2.xml @@ -0,0 +1,55 @@ + + + 2018-09-03T01:46:19.474Z + 2018-09-03T01:46:19.474Z + + + https://orcid.org/0000-0001-5011-3001 + 0000-0001-5011-3001 + orcid.org + + zhengyan li + + + 2008 + 09 + 01 + + + Anhui Academy of Agricultural Sciences + + Hefei + Anhui + CN + + + 125385 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml new file mode 100644 index 0000000000..8e7857fb88 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/employment_3.xml @@ -0,0 +1,62 @@ + + + 2021-03-11T14:48:29.603Z + 2021-03-11T14:48:29.603Z + + + https://orcid.org/0000-0001-5012-1001 + 0000-0001-5012-1001 + orcid.org + + Asma Bazzi + + Pathology and Laboratory Medicine + Medical Laboratory Technologist + + 1994 + 10 + 01 + + + 2000 + 06 + 30 + + + American University of Beirut + + Hamra + Beirut + LB + + + 11238 + RINGGOLD + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml new file mode 100644 index 0000000000..1f5a1bff11 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/orcid/summary.xml @@ -0,0 +1,581 @@ + + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + + es + + + Direct + 2023-01-17T23:50:40.215Z + 2023-09-04T17:51:57.749Z + true + true + true + + + + 2023-01-17T23:50:40.472Z + 2023-01-17T23:50:40.472Z + Patricio + Sánchez Quinchuela + + + + 2023-01-19T13:47:33.653Z + 2023-01-19T13:47:33.653Z + Especialista de vinculación con la sociedad y docente de la Universidad de las Artes. Magister en Economía Social y Solidaria por el IAEN; Magister en Proyectos Sociales y Productivos por la UNACH. Licenciado en Artes UCE. Licenciado en Castellano y Literatura por la UNACH. Doctorando del programa de Sociología de la UNED España. Larga trayectoria vinculado a las organizaciones sociales acompañando procesos de gestión cultural, formación de liderazgos y economía solidaria. + + + + + + + 2018-02-05T23:27:36.636Z + + 2013-03-08T03:20:39.347Z + 2018-02-05T23:27:36.636Z + + + https://orcid.org/client/0000-0002-5982-8983 + 0000-0002-5982-8983 + orcid.org + + Scopus - Elsevier + + https://orcid.org/0000-0001-7291-3210 + 0000-0001-7291-3210 + orcid.org + + Paolo Manghi + + Scopus Author ID + 6602255248 + http://www.scopus.com/inward/authorDetails.url?authorID=6602255248&partnerID=MN8TOARS + self + + + + + 2023-09-04T17:51:57.749Z + + 2023-01-19T13:49:48.482Z + + 2023-01-19T13:49:48.482Z + + + 2023-01-19T13:49:48.482Z + 2023-01-19T13:49:48.482Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Maestría + Becario del programa de Maestría en Economía Social y Solidaria + + 2014 + 10 + 20 + + + Instituto de Altos Estudios Nacionales + + Quito + Pichincha + EC + + + https://ror.org/011g3me54 + ROR + + + + + + + 2023-01-18T21:41:03.175Z + + 2023-01-18T21:41:03.175Z + + + 2023-01-18T21:41:03.175Z + 2023-01-18T21:41:03.175Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Doctorado en Sociología + Doctorando del Programa de Sociología + + 2020 + 11 + 06 + + + Universidad Nacional de Educación a Distancia Facultad de Ciencias Políticas y Sociología + + Madrid + Comunidad de Madrid + ES + + + 223339 + RINGGOLD + + + + + + + 2023-01-18T21:25:07.138Z + + 2023-01-18T21:22:21.513Z + + + 2023-01-17T23:57:08.246Z + 2023-01-18T21:22:21.513Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Dirección de Vinculación con la Sociedad + Especialista de Proyectos y docente + + 2021 + 11 + 01 + + + Universidad de las Artes + + Guayaquil + Guayas + EC + + + https://ror.org/016drwn73 + ROR + + + + + + 2023-01-18T21:25:07.138Z + + + 2023-01-18T21:25:07.138Z + 2023-01-18T21:25:07.138Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Dirección de Vinculación con la Sociedad + Director + + 2019 + 11 + 05 + + + 2021 + 10 + 31 + + + Universidad Regional Amazónica IKIAM + + Tena + Napo + EC + + + https://ror.org/05xedqd83 + ROR + + + http://ikiam.edu.ec + + + + + + + 2023-03-24T18:16:09.131Z + + 2023-03-24T18:16:09.131Z + + + 2023-03-24T18:16:09.131Z + 2023-03-24T18:16:09.131Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Artes Escénicas + Miembro + + 2000 + 07 + 15 + + + Casa de la Cultura Ecuatoriana + + Riobamba + Sierra Centro + EC + + + + + + + + 2023-01-18T21:45:07.379Z + + 2023-01-18T21:29:11.300Z + + + 2023-01-18T21:29:11.300Z + 2023-01-18T21:29:11.300Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Programa de Gobernabilidad + Magister en Economïa Social y Solidaria + + 2014 + 10 + 20 + + + 2017 + 01 + 26 + + + Instituto de Altos Estudios Nacionales + + Quito + Pichincha + EC + + + https://ror.org/011g3me54 + ROR + + + + + + 2023-01-18T21:34:32.093Z + + + 2023-01-18T21:34:32.093Z + 2023-01-18T21:34:32.093Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Posgrados + Magister en Proyectos Sociales y Productivos + + 2001 + 03 + 09 + + + 2003 + 02 + 27 + + + Universidad Nacional de Chimborazo + + Riobamba + Chimborazo + EC + + + https://ror.org/059wmd288 + ROR + + + + + + 2023-01-18T21:45:07.379Z + + + 2023-01-18T21:45:07.379Z + 2023-01-18T21:45:07.379Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Ciencias de la Educación + Licenciado en Ciencias de la Educación en Castellano y Literatura + + 1994 + 10 + 03 + + + 2000 + 01 + 31 + + + Universidad Nacional de Chimborazo + + Riobamba + Chimborazo + EC + + + https://ror.org/059wmd288 + ROR + + + + + + 2023-01-18T21:37:42.186Z + + + 2023-01-18T21:37:42.186Z + 2023-01-18T21:37:42.186Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + Facultad de Artes + Licenciado en Artes + + 1989 + 09 + 05 + + + 1997 + 08 + 07 + + + Universidad Central del Ecuador + + Quito + Pichincha + EC + + + http://dx.doi.org/10.13039/100019134 + FUNDREF + + + + + + + + + 2023-09-04T17:51:57.749Z + + 2023-06-09T22:15:12.910Z + + + 2023-03-24T18:36:56.180Z + 2023-06-09T22:15:12.910Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Experience in a non-capitalist way: solidarity funds that do not tax interest on the use of money + + + + isbn + 978-9942-29-089-2 + 9789942290892 + part-of + + + book-chapter + + 2023 + 06 + 07 + + Finanzas éticas y solidarias en América Latina: diagnósticos, debates y propuestas + + + + 2023-03-24T19:05:36.384Z + + + 2023-03-24T19:05:36.384Z + 2023-03-24T19:05:36.384Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Incidence of artistic practices in the social transformation of the territory. study of case: Hilarte Association, Guayaquil-Ecuador + + + conference-abstract + + 2022 + 10 + 06 + + + + + 2023-09-04T17:40:30.215Z + + + other-id + 2018 + 2018 + self + + + + 2023-09-04T17:40:30.215Z + 2023-09-04T17:40:30.215Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Más allá de la transferencia de conocimientos, un espacio para el interaprendizaje y el diálogo de saberes + + + + other-id + 2018 + 2018 + self + + + https://drive.google.com/drive/folders/1Tclz6isxGzSjTq-hfTnxe6M1nux-88wF?usp=drive_link + conference-poster + + 2018 + 11 + 30 + + Más allá de la transferencia de conocimientos, un espacio para el interaprendizaje y el diálogo de saberes + + + + 2023-03-24T18:57:10.095Z + + + 2023-03-24T18:57:10.095Z + 2023-03-24T18:57:10.095Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + Promotion of the popular and solidarity economy from the state: principles and challenges in the experience of Ecuador + + + dissertation-thesis + + 2017 + 01 + 26 + + + + + 2023-09-04T17:51:57.749Z + + + 2023-09-04T17:51:57.749Z + 2023-09-04T17:51:57.749Z + + + https://orcid.org/0000-0001-5045-1000 + 0000-0001-5045-1000 + orcid.org + + Patricio Sánchez Quinchuela + + + La Rebelión de los Dioses + + + https://drive.google.com/drive/folders/1Tclz6isxGzSjTq-hfTnxe6M1nux-88wF?usp=drive_link + registered-copyright + + 2001 + 08 + 28 + + Editorial pedagógica freire + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index 40a17b4869..ed6853229a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -133,32 +133,6 @@ --targetPath${inputPathMAG}/dataset --masteryarn-cluster - - - - - - - - yarn-cluster - cluster - Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkPreprocessORCID - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${inputPathOrcid} - --workingPath${workingPathOrcid} - --masteryarn-cluster - diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml index 29a12f4df4..8f28d706d5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/process/oozie_app/workflow.xml @@ -59,10 +59,10 @@ - - workingPathOrcid - the ORCID working path - + + + + @@ -170,32 +170,6 @@ --targetPath${workingPath}/uwPublication --masteryarn-cluster - - - - - - - - yarn-cluster - cluster - Convert ORCID to Dataset - eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF - dhp-doiboost-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --workingPath${workingPathOrcid} - --targetPath${workingPath}/orcidPublication - --masteryarn-cluster - diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 2cbd530979..9ffaeeeef7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -66,7 +66,7 @@ object SparkGenerateDoiBoost { Encoders.tuple(Encoders.STRING, mapEncoderPub) implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation] - logger.info("Phase 2) Join Crossref with UnpayWall") + logger.info("Phase 1) Join Crossref with UnpayWall") val crossrefPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/crossrefPublication").as[Publication].map(p => (p.getId, p)) @@ -91,20 +91,10 @@ object SparkGenerateDoiBoost { .write .mode(SaveMode.Overwrite) .save(s"$workingDirPath/firstJoin") - logger.info("Phase 3) Join Result with ORCID") - val fj: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p)) - val orcidPublication: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/orcidPublication").as[Publication].map(p => (p.getId, p)) - fj.joinWith(orcidPublication, fj("_1").equalTo(orcidPublication("_1")), "left") - .map(applyMerge) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingDirPath/secondJoin") - logger.info("Phase 4) Join Result with MAG") + logger.info("Phase 2) Join Result with MAG") val sj: Dataset[(String, Publication)] = - spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) + spark.read.load(s"$workingDirPath/firstJoin").as[Publication].map(p => (p.getId, p)) val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 65e3953570..53576fc106 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -107,7 +107,7 @@ case object Crossref2Oaf { .map(f => f.id) } - def mappingResult(result: Result, json: JValue, cobjCategory: String, originalType:String): Result = { + def mappingResult(result: Result, json: JValue, cobjCategory: String, originalType: String): Result = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID @@ -372,7 +372,7 @@ case object Crossref2Oaf { objectType, mappingCrossrefSubType.getOrElse(objectSubType, "0038 Other literature type") ) - mappingResult(result, json, cOBJCategory, originalType) + mappingResult(result, json, cOBJCategory, objectSubType) if (result == null || result.getId == null) return List() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json new file mode 100644 index 0000000000..765c0e8ff8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "orcidPath", + "paramDescription": "the path of the orcid Table generated by the dump", + "paramRequired": true + }, + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "the path of the graph we want to apply enrichment", + "paramRequired": true + }, + { + "paramName": "tp", + "paramLongName": "targetPath", + "paramDescription": "the output path of the graph enriched", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml new file mode 100644 index 0000000000..8a7bc8942d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml new file mode 100644 index 0000000000..a4330b966b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml @@ -0,0 +1,88 @@ + + + + orcidPath + the path of the orcid Table generated by the dump + + + graphPath + the path of the graph we want to apply enrichment + + + targetPath + the output path of the graph enriched + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Enrich Graph with ORCID + eu.dnetlib.dhp.enrich.orcid.SparkEnrichGraphWithOrcidAuthors + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.executor.memoryOverhead=2g + --conf spark.sql.shuffle.partitions=3000 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --orcidPath + ${orcidPath} + --targetPath + ${targetPath} + --graphPath + ${graphPath} + --master + yarn + + + + + + + + ${nameNode}/${graphPath}/datasource + ${nameNode}/${targetPath}/datasource + + + + + + + ${nameNode}/${graphPath}/organization + ${nameNode}/${targetPath}/organization + + + + + + + ${nameNode}/${graphPath}/project + ${nameNode}/${targetPath}/project + + + + + + + ${nameNode}/${graphPath}/relation + ${nameNode}/${targetPath}/relation + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala new file mode 100644 index 0000000000..15513c8af7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/AuthorEnricher.scala @@ -0,0 +1,40 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import eu.dnetlib.dhp.schema.sx.OafUtils +import org.apache.spark.sql.Row + +import scala.collection.JavaConverters._ + +object AuthorEnricher extends Serializable { + + def createAuthor(givenName: String, familyName: String, orcid: String): Author = { + val a = new Author + a.setName(givenName) + a.setSurname(familyName) + a.setFullname(s"$givenName $familyName") + val pid = OafUtils.createSP(orcid, ModelConstants.ORCID, ModelConstants.ORCID) + pid.setDataInfo(OafUtils.generateDataInfo()) + pid.getDataInfo.setProvenanceaction(OafUtils.createQualifier("ORCID_ENRICHMENT", "ORCID_ENRICHMENT")) + a.setPid(List(pid).asJava) + a + } + + def toOAFAuthor(r: Row): java.util.List[Author] = { + r.getList[Row](1) + .asScala + .map(s => createAuthor(s.getAs[String]("givenName"), s.getAs[String]("familyName"), s.getAs[String]("orcid"))) + .toList + .asJava + } + +// def enrichAuthor(p:Publication,r:Row): Unit = { +// val k:Map[String, OAuthor] =r.getList[Row](1).asScala.map(s => (s.getAs[String]("orcid"), OAuthor(s.getAs[String]("givenName") ,s.getAs[String]("familyName") ))).groupBy(_._1).mapValues(_.map(_._2).head) +// println(k) +// +// +// +// } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala new file mode 100644 index 0000000000..4822059c65 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -0,0 +1,138 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software} +import org.apache.spark.sql.functions._ +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ + +class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String], log: Logger) + extends AbstractScalaApplication(propertyPath, args, log: Logger) { + + /** Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + val graphPath = parser.get("graphPath") + log.info(s"graphPath is '$graphPath'") + val orcidPath = parser.get("orcidPath") + log.info(s"orcidPath is '$orcidPath'") + val targetPath = parser.get("targetPath") + log.info(s"targetPath is '$targetPath'") + val orcidPublication: Dataset[Row] = generateOrcidTable(spark, orcidPath) +// ModelSupport.entityTypes.entrySet().asScala.filter(k => k.getKey.getClass isInstance(Result)) + + enrichResult( + spark, + s"$graphPath/publication", + orcidPublication, + s"$targetPath/publication", + Encoders.bean(classOf[Publication]) + ) + enrichResult( + spark, + s"$graphPath/dataset", + orcidPublication, + s"$targetPath/dataset", + Encoders.bean(classOf[eu.dnetlib.dhp.schema.oaf.Dataset]) + ) + enrichResult( + spark, + s"$graphPath/software", + orcidPublication, + s"$targetPath/software", + Encoders.bean(classOf[Software]) + ) + enrichResult( + spark, + s"$graphPath/otherresearchproduct", + orcidPublication, + s"$targetPath/otherresearchproduct", + Encoders.bean(classOf[OtherResearchProduct]) + ) + } + + private def enrichResult[T <: Result]( + spark: SparkSession, + graphPath: String, + orcidPublication: Dataset[Row], + outputPath: String, + enc: Encoder[T] + ): Unit = { + + val entities = spark.read + .schema(enc.schema) + .json(graphPath) + .select(col("id"), col("datainfo"), col("instance")) + .where("datainfo.deletedbyinference != true") + .drop("datainfo") + .withColumn("instances", explode(col("instance"))) + .withColumn("pids", explode(col("instances.pid"))) + .select( + col("pids.qualifier.classid").alias("pid_schema"), + col("pids.value").alias("pid_value"), + col("id").alias("dnet_id") + ) + + val orcidDnet = orcidPublication + .join( + entities, + lower(col("schema")).equalTo(lower(col("pid_schema"))) && + lower(col("value")).equalTo(lower(col("pid_value"))), + "inner" + ) + .groupBy(col("dnet_id")) + .agg(collect_set(orcidPublication("author")).alias("orcid_authors")) + .select("dnet_id", "orcid_authors") + .cache() + orcidDnet.count() + val result = spark.read.schema(enc.schema).json(graphPath).as[T](enc) + + result + .joinWith(orcidDnet, result("id").equalTo(orcidDnet("dnet_id")), "left") + .map { + case (r: T, null) => + r + case (p: T, r: Row) => + p.setAuthor(AuthorMerger.enrichOrcid(p.getAuthor, AuthorEnricher.toOAFAuthor(r))) + p + }(enc) + .write + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath) + } + + private def generateOrcidTable(spark: SparkSession, inputPath: String): Dataset[Row] = { + val orcidAuthors = + spark.read.load(s"$inputPath/Authors").select("orcid", "familyName", "givenName", "creditName", "otherNames") + val orcidWorks = spark.read + .load(s"$inputPath/Works") + .select(col("orcid"), explode(col("pids")).alias("identifier")) + .where( + "identifier.schema IN('doi','pmid','pmc','arxiv','handle')" + ) + val orcidPublication = orcidAuthors + .join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) + .select( + col("identifier.schema").alias("schema"), + col("identifier.value").alias("value"), + struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") + ) + orcidPublication.cache() + } +} + +object SparkEnrichGraphWithOrcidAuthors { + + val log: Logger = LoggerFactory.getLogger(SparkEnrichGraphWithOrcidAuthors.getClass) + + def main(args: Array[String]): Unit = { + new SparkEnrichGraphWithOrcidAuthors("/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json", args, log) + .initialize() + .run() + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala new file mode 100644 index 0000000000..cb05332b24 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/EnrichOrcidTest.scala @@ -0,0 +1,77 @@ +package eu.dnetlib.dhp.enrich.orcid + +import eu.dnetlib.dhp.schema.oaf.{Author, Publication} +import org.apache.spark.sql.{Column, Encoder, Encoders, Row, SparkSession} +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} +import org.apache.spark.sql.functions._ + +class EnrichOrcidTest { + + val log: Logger = LoggerFactory.getLogger(getClass) + + def test() = { + val spark = SparkSession.builder().master("local[*]").getOrCreate() +// spark.sparkContext.setLogLevel("ERROR") + +// new SparkEnrichGraphWithOrcidAuthors(null, null, null) +// .enrichResult( +// spark, +// "/Users/sandro/orcid_test/publication", +// "", +// "/tmp/graph/", +// Encoders.bean(classOf[Publication]) +// ) + + val schema = Encoders.bean(classOf[Publication]).schema +// +// val simplifyAuthor = udf((r: Seq[Row]) => { +// r +// .map(k => +// AuthorPid( +// k.getAs[String]("fullname"), +// k.getAs[Seq[Row]]("pid") +// .map(p => Pid(p.getAs[Row]("qualifier").getAs[String]("classid"), p.getAs[String]("value"))) +// .toList +// ) +// ) +// .filter(l => l.pids.nonEmpty) +// .toList +// }) +// +// val wrong_orcid_intersection = udf((a: Seq[Row]) => { +// a.map(author => { +// val pids_with_orcid: Seq[Row] = author +// .getAs[Seq[Row]]("pids") +// .filter(p => +// p.getAs[String]("pidScheme") != null && p.getAs[String]("pidScheme").toLowerCase.contains("orcid") +// ) +// if (pids_with_orcid.exists(p => p.getAs[String]("pidScheme").equals("ORCID"))) { +// if (pids_with_orcid.map(p => p.getAs[String]("pidValue").toLowerCase).distinct.size > 1) { +// AuthorPid( +// author.getAs[String]("fullName"), +// pids_with_orcid.map(p => Pid(p.getAs[String]("pidScheme"), p.getAs[String]("pidValue"))).toList +// ) +// +// } else +// null +// } else +// null +// }).filter(author => author != null) +// }) + + Encoders + import spark.implicits._ + +// val enriched = spark.read +// .schema(schema) +// .json("/Users/sandro/orcid_test/publication_enriched") +// .select(col("id"), explode(col("author")).as("authors")) +// .withColumn("ap", col("authors.pid.qualifier.classid")) +// .withColumn("dp", col("authors.pid.datainfo.provenanceAction.classid")) +// +// .show() + + } + +}