diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index b295bc1f1..4ee706169 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -29,6 +29,12 @@ spark-sql_2.11 + + eu.dnetlib.dhp + dhp-schemas + ${project.version} + + commons-cli commons-cli 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 3fa5fcbab..17482c019 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 @@ -94,7 +94,13 @@ public class AuthorMerger { if (r.getPid() == null) { r.setPid(new ArrayList<>()); } - r.getPid().add(a._1()); + + // 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); } } }); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java similarity index 79% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java index 84f88003b..12fbcc490 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java @@ -1,8 +1,9 @@ -package eu.dnetlib.dhp.oa.graph.clean; +package eu.dnetlib.dhp.schema.oaf; import java.util.LinkedHashMap; import java.util.Objects; +import java.util.Optional; import java.util.function.Function; import java.util.stream.Collectors; @@ -10,14 +11,13 @@ import org.apache.commons.lang3.StringUtils; import com.clearspring.analytics.util.Lists; -import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper; -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; public class CleaningFunctions { + public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/"; public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/"; + public static final String NONE = "none"; public static T fixVocabularyNames(T value) { if (value instanceof Datasource) { @@ -71,7 +71,7 @@ public class CleaningFunctions { return value; } - protected static T fixDefaults(T value) { + public static T fixDefaults(T value) { if (value instanceof Datasource) { // nothing to clean here } else if (value instanceof Project) { @@ -106,6 +106,20 @@ public class CleaningFunctions { .filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid())) .collect(Collectors.toList())); } + if (Objects.nonNull(r.getPid())) { + r + .setPid( + r + .getPid() + .stream() + .filter(Objects::nonNull) + .filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue()))) + .filter(sp -> NONE.equalsIgnoreCase(sp.getValue())) + .filter(sp -> Objects.nonNull(sp.getQualifier())) + .filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid())) + .map(CleaningFunctions::normalizePidValue) + .collect(Collectors.toList())); + } if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { r .setResourcetype( @@ -125,7 +139,7 @@ public class CleaningFunctions { } } if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) { - Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance()); + Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance()); if (Objects.isNull(bestaccessrights)) { r .setBestaccessright( @@ -201,4 +215,24 @@ public class CleaningFunctions { classid, classname, scheme, scheme); } + /** + * Utility method that normalises PID values on a per-type basis. + * @param pid the PID whose value will be normalised. + * @return the PID containing the normalised value. + */ + public static StructuredProperty normalizePidValue(StructuredProperty pid) { + String value = Optional + .ofNullable(pid.getValue()) + .map(String::trim) + .orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty")); + switch (pid.getQualifier().getClassid()) { + + // TODO add cleaning for more PID types as needed + case "doi": + pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, "")); + break; + } + return pid; + } + } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ModelHardLimits.java similarity index 70% rename from dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ModelHardLimits.java index 9bc3706cd..16fdc3760 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ModelHardLimits.java @@ -1,14 +1,14 @@ -package eu.dnetlib.dhp.oa.provision; +package eu.dnetlib.dhp.schema.oaf; -public class ProvisionConstants { +public class ModelHardLimits { public static final int MAX_EXTERNAL_ENTITIES = 50; public static final int MAX_AUTHORS = 200; public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000; public static final int MAX_TITLE_LENGTH = 5000; public static final int MAX_TITLES = 10; - public static final int MAX_ABSTRACT_LENGTH = 100000; + public static final int MAX_ABSTRACT_LENGTH = 150000; public static final int MAX_INSTANCES = 10; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java similarity index 84% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java index 84b29e3d4..f079c55af 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java @@ -1,11 +1,10 @@ -package eu.dnetlib.dhp.oa.graph.raw.common; +package eu.dnetlib.dhp.schema.oaf; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.List; -import java.util.Map; -import java.util.Objects; +import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES; + +import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.function.Function; import java.util.function.Predicate; @@ -13,15 +12,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.ExtraInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.OAIProvenance; -import eu.dnetlib.dhp.schema.oaf.OriginDescription; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.common.LicenseComparator; import eu.dnetlib.dhp.utils.DHPUtils; public class OafMapperUtils { @@ -270,4 +261,36 @@ public class OafMapperUtils { final Map seen = new ConcurrentHashMap<>(); return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null; } + + public static Qualifier createBestAccessRights(final List instanceList) { + return getBestAccessRights(instanceList); + } + + protected static Qualifier getBestAccessRights(final List instanceList) { + if (instanceList != null) { + final Optional min = instanceList + .stream() + .map(i -> i.getAccessright()) + .min(new LicenseComparator()); + + final Qualifier rights = min.isPresent() ? min.get() : new Qualifier(); + + if (StringUtils.isBlank(rights.getClassid())) { + rights.setClassid(UNKNOWN); + } + if (StringUtils.isBlank(rights.getClassname()) + || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { + rights.setClassname(NOT_AVAILABLE); + } + if (StringUtils.isBlank(rights.getSchemeid())) { + rights.setSchemeid(DNET_ACCESS_MODES); + } + if (StringUtils.isBlank(rights.getSchemename())) { + rights.setSchemename(DNET_ACCESS_MODES); + } + + return rights; + } + return null; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ResultTypeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ResultTypeComparator.java new file mode 100644 index 000000000..6c11d1a85 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ResultTypeComparator.java @@ -0,0 +1,49 @@ + +package eu.dnetlib.dhp.schema.oaf; + +import java.util.Comparator; + +import eu.dnetlib.dhp.schema.common.ModelConstants; + +public class ResultTypeComparator implements Comparator { + + @Override + public int compare(Result left, Result right) { + + if (left == null && right == null) + return 0; + if (left == null) + return 1; + if (right == null) + return -1; + + String lClass = left.getResulttype().getClassid(); + String rClass = right.getResulttype().getClassid(); + + if (lClass.equals(rClass)) + return 0; + + if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) + return -1; + if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) + return 1; + + if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) + return -1; + if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) + return 1; + + if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) + return -1; + if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) + return 1; + + if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) + return -1; + if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) + return 1; + + // Else (but unlikely), lexicographical ordering will do. + return lClass.compareTo(rClass); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java new file mode 100644 index 000000000..319cda0bf --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java @@ -0,0 +1,102 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import java.io.Serializable; +import java.util.Objects; +import java.util.Optional; +import java.util.regex.Pattern; + +import org.apache.commons.lang.StringUtils; + +import eu.dnetlib.dhp.schema.oaf.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.utils.DHPUtils; + +/** + * Factory class for OpenAIRE identifiers in the Graph + */ +public class IdentifierFactory implements Serializable { + + public static final String ID_SEPARATOR = "::"; + public static final String ID_PREFIX_SEPARATOR = "|"; + public final static String ID_REGEX = "^[0-9][0-9]\\" + ID_PREFIX_SEPARATOR + ".{12}" + ID_SEPARATOR + + "[a-zA-Z0-9]{32}$"; + + public final static String DOI_REGEX = "(^10\\.[0-9]{4,9}\\/[-._;()\\/:a-zA-Z0-9]+$)|" + + "(^10\\.1002\\/[^\\s]+$)|" + + "(^10\\.1021\\/[a-zA-Z0-9_][a-zA-Z0-9_][0-9]++$)|" + + "(^10\\.1207\\/[a-zA-Z0-9_]+\\&[0-9]+_[0-9]+$)"; + + public static final int ID_PREFIX_LEN = 12; + public static final String NONE = "none"; + + /** + * Creates an identifier from the most relevant PID (if available) in the given entity T. Returns entity.id + * when no PID is available + * @param entity the entity providing PIDs and a default ID. + * @param the specific entity type. Currently Organization and Result subclasses are supported. + * @return an identifier from the most relevant PID, entity.id otherwise + */ + public static String createIdentifier(T entity) { + + if (Objects.isNull(entity.getPid()) || entity.getPid().isEmpty()) { + return entity.getId(); + } + + return entity + .getPid() + .stream() + .filter(s -> pidFilter(s)) + .min(new PidComparator<>(entity)) + .map(s -> idFromPid(entity, s)) + .map(IdentifierFactory::verifyIdSyntax) + .orElseGet(entity::getId); + } + + protected static boolean pidFilter(StructuredProperty s) { + if (Objects.isNull(s.getQualifier()) || + StringUtils.isBlank(StringUtils.trim(s.getValue()))) { + return false; + } + try { + switch (PidType.valueOf(s.getQualifier().getClassid())) { + case doi: + final String doi = StringUtils.trim(StringUtils.lowerCase(s.getValue())); + return doi.matches(DOI_REGEX); + default: + return true; + } + } catch (IllegalArgumentException e) { + return false; + } + } + + private static String verifyIdSyntax(String s) { + if (StringUtils.isBlank(s) || !s.matches(ID_REGEX)) { + throw new RuntimeException(String.format("malformed id: '%s'", s)); + } else { + return s; + } + } + + private static String idFromPid(T entity, StructuredProperty s) { + return new StringBuilder() + .append(StringUtils.substringBefore(entity.getId(), ID_PREFIX_SEPARATOR)) + .append(ID_PREFIX_SEPARATOR) + .append(createPrefix(s.getQualifier().getClassid())) + .append(ID_SEPARATOR) + .append(DHPUtils.md5(CleaningFunctions.normalizePidValue(s).getValue())) + .toString(); + } + + // create the prefix (length = 12) + private static String createPrefix(String pidType) { + StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN)); + while (prefix.length() < ID_PREFIX_LEN) { + prefix.append("_"); + } + return prefix.substring(0, ID_PREFIX_LEN); + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java new file mode 100644 index 000000000..733d41bff --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java @@ -0,0 +1,27 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import java.util.Comparator; + +public class OrganizationPidComparator implements Comparator { + + @Override + public int compare(PidType pLeft, PidType pRight) { + if (pLeft.equals(PidType.GRID)) + return -1; + if (pRight.equals(PidType.GRID)) + return 1; + + if (pLeft.equals(PidType.mag_id)) + return -1; + if (pRight.equals(PidType.mag_id)) + return 1; + + if (pLeft.equals(PidType.urn)) + return -1; + if (pRight.equals(PidType.urn)) + return 1; + + return 0; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java new file mode 100644 index 000000000..34ce5563f --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import java.util.Comparator; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class PidComparator implements Comparator { + + private T entity; + + public PidComparator(T entity) { + this.entity = entity; + } + + @Override + public int compare(StructuredProperty left, StructuredProperty right) { + + if (left == null && right == null) + return 0; + if (left == null) + return 1; + if (right == null) + return -1; + + PidType lClass = PidType.valueOf(left.getQualifier().getClassid()); + PidType rClass = PidType.valueOf(right.getQualifier().getClassid()); + + if (lClass.equals(rClass)) + return 0; + + if (ModelSupport.isSubClass(entity, Result.class)) { + return compareResultPids(lClass, rClass); + } + if (ModelSupport.isSubClass(entity, Organization.class)) { + return compareOrganizationtPids(lClass, rClass); + } + + // Else (but unlikely), lexicographical ordering will do. + return lClass.compareTo(rClass); + } + + private int compareResultPids(PidType lClass, PidType rClass) { + return new ResultPidComparator().compare(lClass, rClass); + } + + private int compareOrganizationtPids(PidType lClass, PidType rClass) { + return new OrganizationPidComparator().compare(lClass, rClass); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java new file mode 100644 index 000000000..9a0196ccc --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import org.apache.commons.lang3.EnumUtils; + +public enum PidType { + + // Result + doi, pmid, pmc, handle, arXiv, NCID, GBIF, nct, pdb, + + // Organization + GRID, mag_id, urn, + + // Used by dedup + undefined, original; + + public static boolean isValid(String type) { + return EnumUtils.isValidEnum(PidType.class, type); + } + + public static PidType tryValueOf(String s) { + try { + return PidType.valueOf(s); + } catch (Exception e) { + return PidType.original; + } + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java new file mode 100644 index 000000000..0f65cca36 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java @@ -0,0 +1,57 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import java.util.Comparator; + +public class ResultPidComparator implements Comparator { + + @Override + public int compare(PidType pLeft, PidType pRight) { + if (pLeft.equals(PidType.doi)) + return -1; + if (pRight.equals(PidType.doi)) + return 1; + + if (pLeft.equals(PidType.pmid)) + return -1; + if (pRight.equals(PidType.pmid)) + return 1; + + if (pLeft.equals(PidType.pmc)) + return -1; + if (pRight.equals(PidType.pmc)) + return 1; + + if (pLeft.equals(PidType.handle)) + return -1; + if (pRight.equals(PidType.handle)) + return 1; + + if (pLeft.equals(PidType.arXiv)) + return -1; + if (pRight.equals(PidType.arXiv)) + return 1; + + if (pLeft.equals(PidType.NCID)) + return -1; + if (pRight.equals(PidType.NCID)) + return 1; + + if (pLeft.equals(PidType.GBIF)) + return -1; + if (pRight.equals(PidType.GBIF)) + return 1; + + if (pLeft.equals(PidType.nct)) + return -1; + if (pRight.equals(PidType.nct)) + return 1; + + if (pLeft.equals(PidType.urn)) + return -1; + if (pRight.equals(PidType.urn)) + return 1; + + return 0; + } +} diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java new file mode 100644 index 000000000..d458c613e --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java @@ -0,0 +1,47 @@ + +package eu.dnetlib.dhp.schema.oaf.utils; + +import static org.junit.jupiter.api.Assertions.*; + +import java.io.IOException; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class IdentifierFactoryTest { + + private static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); + + @Test + public void testCreateIdentifierForPublication() throws IOException { + + verifyIdentifier("publication_doi.json", "50|doi_________::" + DHPUtils.md5("10.1016/j.cmet.2011.03.013")); + verifyIdentifier("publication_pmc.json", "50|pmc_________::" + DHPUtils.md5("21459329")); + verifyIdentifier( + "publication_urn.json", + "50|urn_________::" + DHPUtils.md5("urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2")); + + final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"; + verifyIdentifier("publication_3.json", defaultID); + verifyIdentifier("publication_4.json", defaultID); + verifyIdentifier("publication_5.json", defaultID); + } + + protected void verifyIdentifier(String filename, String expectedID) throws IOException { + final String json = IOUtils.toString(getClass().getResourceAsStream(filename)); + final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class); + + String id = IdentifierFactory.createIdentifier(pub); + + assertNotNull(id); + assertEquals(expectedID, id); + } + +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json new file mode 100644 index 000000000..6d33568f4 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_3.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json new file mode 100644 index 000000000..6617fe15f --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_4.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[]} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json new file mode 100644 index 000000000..700a10046 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_5.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi.json new file mode 100644 index 000000000..6865d0ff6 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc.json new file mode 100644 index 000000000..3e4ba2246 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn.json new file mode 100644 index 000000000..83e14e48d --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_urn.json @@ -0,0 +1 @@ +{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmcid"},"value":"21459329"}]} \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index b27fc9267..d759f0d55 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -39,15 +39,15 @@ public class ModelConstants { public static final String IS_SUPPLEMENT_TO = "isSupplementTo"; public static final String IS_SUPPLEMENTED_BY = "isSupplementedBy"; public static final String PART = "part"; - public static final String IS_PART_OF = "IsPartOf"; - public static final String HAS_PARTS = "HasParts"; + public static final String IS_PART_OF = "isPartOf"; + public static final String HAS_PARTS = "hasParts"; public static final String RELATIONSHIP = "relationship"; public static final String CITATION = "citation"; public static final String CITES = "cites"; - public static final String IS_CITED_BY = "IsCitedBy"; + public static final String IS_CITED_BY = "isCitedBy"; public static final String REVIEW = "review"; public static final String REVIEWS = "reviews"; - public static final String IS_REVIEWED_BY = "IsReviewedBy"; + public static final String IS_REVIEWED_BY = "isReviewedBy"; public static final String RESULT_PROJECT = "resultProject"; public static final String OUTCOME = "outcome"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java index 7f0ca983f..b2d3253d5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.project; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.HashMap; +import java.util.List; import java.util.Map; import java.util.Optional; @@ -11,6 +12,7 @@ import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.*; import org.slf4j.Logger; @@ -175,43 +177,54 @@ public class PrepareProgramme { return csvProgramme; }); - prepareClassification(h2020Programmes); + // prepareClassification(h2020Programmes); - h2020Programmes - .map(csvProgramme -> OBJECT_MAPPER.writeValueAsString(csvProgramme)) + JavaSparkContext jsc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD rdd = jsc.parallelize(prepareClassification(h2020Programmes), 1); + rdd + .map(csvProgramme -> { + String tmp = OBJECT_MAPPER.writeValueAsString(csvProgramme); + return tmp; + }) .saveAsTextFile(outputPath); } - private static void prepareClassification(JavaRDD h2020Programmes) { + private static List prepareClassification(JavaRDD h2020Programmes) { Object[] codedescription = h2020Programmes - .map(value -> new Tuple2<>(value.getCode(), value.getTitle())) + .map( + value -> new Tuple2<>(value.getCode(), + new Tuple2(value.getTitle(), value.getShortTitle()))) .collect() .toArray(); for (int i = 0; i < codedescription.length - 1; i++) { for (int j = i + 1; j < codedescription.length; j++) { - Tuple2 t2i = (Tuple2) codedescription[i]; - Tuple2 t2j = (Tuple2) codedescription[j]; + Tuple2> t2i = (Tuple2>) codedescription[i]; + Tuple2> t2j = (Tuple2>) codedescription[j]; if (t2i._1().compareTo(t2j._1()) > 0) { - Tuple2 temp = t2i; + Tuple2> temp = t2i; codedescription[i] = t2j; codedescription[j] = temp; } } } - Map map = new HashMap<>(); + Map> map = new HashMap<>(); for (int j = 0; j < codedescription.length; j++) { - Tuple2 entry = (Tuple2) codedescription[j]; + Tuple2> entry = (Tuple2>) codedescription[j]; String ent = entry._1(); if (ent.contains("Euratom-")) { ent = ent.replace("-Euratom-", ".Euratom."); } String[] tmp = ent.split("\\."); if (tmp.length <= 2) { - map.put(entry._1(), entry._2()); - + if (StringUtils.isEmpty(entry._2()._2())) { + map.put(entry._1(), new Tuple2(entry._2()._1(), entry._2()._1())); + } else { + map.put(entry._1(), entry._2()); + } } else { if (ent.endsWith(".")) { ent = ent.substring(0, ent.length() - 1); @@ -224,14 +237,14 @@ public class PrepareProgramme { key = key.substring(0, key.length() - 1); } } - String current = entry._2(); + String current = entry._2()._1(); if (!ent.contains("Euratom")) { String parent; String tmp_key = tmp[0] + "."; for (int i = 1; i < tmp.length - 1; i++) { tmp_key += tmp[i] + "."; - parent = map.get(tmp_key).toLowerCase().trim(); + parent = map.get(tmp_key)._1().toLowerCase().trim(); if (parent.contains("|")) { parent = parent.substring(parent.lastIndexOf("|") + 1).trim(); } @@ -246,18 +259,29 @@ public class PrepareProgramme { } } - map.put(ent + ".", map.get(key) + " | " + current); + String shortTitle = entry._2()._2(); + if (StringUtils.isEmpty(shortTitle)) { + shortTitle = current; + } + Tuple2 newEntry = new Tuple2<>(map.get(key)._1() + " | " + current, + map.get(key)._2() + " | " + shortTitle); + map.put(ent + ".", newEntry); } } - h2020Programmes.foreach(csvProgramme -> { - if (!csvProgramme.getCode().endsWith(".") && !csvProgramme.getCode().contains("Euratom") - && !csvProgramme.getCode().equals("H2020-EC")) - csvProgramme.setClassification(map.get(csvProgramme.getCode() + ".")); - else - csvProgramme.setClassification(map.get(csvProgramme.getCode())); - }); + return h2020Programmes.map(csvProgramme -> { + + String code = csvProgramme.getCode(); + if (!code.endsWith(".") && !code.contains("Euratom") + && !code.equals("H2020-EC")) + code += "."; + + csvProgramme.setClassification(map.get(code)._1()); + csvProgramme.setClassification_short(map.get(code)._2()); + + return csvProgramme; + }).collect(); } public static Dataset readPath( diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java index f2375e799..a583b7bfa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java @@ -9,7 +9,6 @@ import java.util.Objects; import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; @@ -138,7 +137,8 @@ public class SparkAtomicActionJob { pm.setCode(csvProject.getProgramme()); h2020classification.setClassification(ocsvProgramme.get().getClassification()); h2020classification.setH2020Programme(pm); - setLevelsAndProgramme(h2020classification, ocsvProgramme.get().getClassification()); + setLevelsandProgramme(h2020classification, ocsvProgramme.get().getClassification_short()); + // setProgramme(h2020classification, ocsvProgramme.get().getClassification()); pp.setH2020classification(Arrays.asList(h2020classification)); return pp; @@ -177,8 +177,8 @@ public class SparkAtomicActionJob { } - private static void setLevelsAndProgramme(H2020Classification h2020Classification, String classification) { - String[] tmp = classification.split(" \\| "); + private static void setLevelsandProgramme(H2020Classification h2020Classification, String classification_short) { + String[] tmp = classification_short.split(" \\| "); h2020Classification.setLevel1(tmp[0]); if (tmp.length > 1) { h2020Classification.setLevel2(tmp[1]); @@ -189,6 +189,12 @@ public class SparkAtomicActionJob { h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]); } +// private static void setProgramme(H2020Classification h2020Classification, String classification) { +// String[] tmp = classification.split(" \\| "); +// +// h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]); +// } + public static Dataset readPath( SparkSession spark, String inputPath, Class clazz) { return spark diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java index 6f9a59087..f991a4297 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java @@ -22,6 +22,15 @@ public class CSVProgramme implements Serializable { private String shortTitle; private String language; private String classification; + private String classification_short; + + public String getClassification_short() { + return classification_short; + } + + public void setClassification_short(String classification_short) { + this.classification_short = classification_short; + } public String getClassification() { return classification; diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java index fdc577687..59b536cd5 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/EXCELParserTest.java @@ -9,12 +9,14 @@ import java.util.List; import org.apache.poi.openxml4j.exceptions.InvalidFormatException; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import eu.dnetlib.dhp.actionmanager.project.httpconnector.CollectorServiceException; import eu.dnetlib.dhp.actionmanager.project.httpconnector.HttpConnector; import eu.dnetlib.dhp.actionmanager.project.utils.EXCELParser; +@Disabled public class EXCELParserTest { private static Path workingDir; diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareH2020ProgrammeTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareH2020ProgrammeTest.java index c5801bccc..256dc0521 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareH2020ProgrammeTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/PrepareH2020ProgrammeTest.java @@ -92,6 +92,8 @@ public class PrepareH2020ProgrammeTest { Assertions.assertEquals(0, verificationDataset.filter("classification = ''").count()); + // tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme))); + Assertions .assertEquals( "Societal challenges | Smart, Green And Integrated Transport | CLEANSKY2 | IADP Fast Rotorcraft", diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java index cfda7e718..42e494681 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/SparkUpdateProjectTest.java @@ -78,7 +78,7 @@ public class SparkUpdateProjectTest { "-programmePath", getClass() .getResource( - "/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_classification_whole.json.gz") + "/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz") .getPath(), "-projectPath", getClass().getResource("/eu/dnetlib/dhp/actionmanager/project/prepared_projects.json").getPath(), @@ -124,7 +124,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Societal challenges", + "Societal Challenges", execverification .filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'") .select("classification.level1") @@ -133,7 +133,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Smart, Green And Integrated Transport", + "Transport", execverification .filter("id = '40|corda__h2020::2c7298913008865ba784e5c1350a0aa5'") .select("classification.level2") @@ -188,7 +188,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Nurturing excellence by means of cross-border and cross-sector mobility", + "MSCA Mobility", execverification .filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'") .select("classification.h2020Programme.description") @@ -197,7 +197,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Excellent science", + "Excellent Science", execverification .filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'") .select("classification.level1") @@ -206,7 +206,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Marie Skłodowska-Curie Actions", + "Marie-Sklodowska-Curie Actions", execverification .filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'") .select("classification.level2") @@ -215,7 +215,7 @@ public class SparkUpdateProjectTest { .getString(0)); Assertions .assertEquals( - "Nurturing excellence by means of cross-border and cross-sector mobility", + "MSCA Mobility", execverification .filter("id = '40|corda__h2020::1a1f235fdd06ef14790baec159aa1202'") .select("classification.level3") diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java index 8bcf08906..90b3919ed 100644 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/project/httpconnector/HttpConnectorTest.java @@ -6,8 +6,10 @@ import org.apache.commons.logging.LogFactory; import org.apache.http.conn.ssl.SSLConnectionSocketFactory; import org.apache.http.ssl.SSLContextBuilder; import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; +@Disabled public class HttpConnectorTest { private static final Log log = LogFactory.getLog(HttpConnectorTest.class); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_classification_whole.json.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_classification_whole.json.gz deleted file mode 100644 index d40bac8c6..000000000 Binary files a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_classification_whole.json.gz and /dev/null differ diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz index 1afa73061..01e804ff5 100644 Binary files a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz and b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/preparedProgramme_whole.json.gz differ diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz index 60c3bf05a..8b1982dee 100644 Binary files a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz and b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/project/whole_programme.json.gz differ diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 025745f12..99cd7c31f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -82,7 +82,7 @@ public class DedupRecordFactory { final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); - final List bestPids = Lists.newArrayList(); // best pids list + final List> bestPids = Lists.newArrayList(); // best pids list entities .forEachRemaining( @@ -90,7 +90,7 @@ public class DedupRecordFactory { T duplicate = t._2(); // prepare the list of pids to use for the id generation - bestPids.addAll(IdGenerator.bestPidToIdentifier(duplicate)); + bestPids.add(Identifier.newInstance(duplicate)); entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java index 405a9abf1..51e54ee4f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/IdGenerator.java @@ -1,124 +1,46 @@ package eu.dnetlib.dhp.oa.dedup; +import static org.apache.commons.lang3.StringUtils.substringAfter; +import static org.apache.commons.lang3.StringUtils.substringBefore; + import java.io.Serializable; -import java.text.ParseException; -import java.text.SimpleDateFormat; -import java.util.*; - -import org.apache.commons.lang.StringUtils; - -import com.google.common.collect.Lists; +import java.util.List; import eu.dnetlib.dhp.oa.dedup.model.Identifier; -import eu.dnetlib.dhp.oa.dedup.model.PidType; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Result; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; -import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; public class IdGenerator implements Serializable { - public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2"; - public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"; - public static String BASE_DATE = "2000-01-01"; - // pick the best pid from the list (consider date and pidtype) - public static String generate(List pids, String defaultID) { + public static String generate(List> pids, String defaultID) { if (pids == null || pids.size() == 0) return defaultID; - Optional bp = pids + Identifier bp = pids .stream() - .max(Identifier::compareTo); + .min(Identifier::compareTo) + .get(); - if (bp.get().isUseOriginal() || bp.get().getPid().getValue() == null) { - return bp.get().getOriginalID().split("\\|")[0] + "|dedup_wf_001::" - + DHPUtils.md5(bp.get().getOriginalID()); + String prefix = substringBefore(bp.getOriginalID(), "|"); + String ns = substringBefore(substringAfter(bp.getOriginalID(), "|"), "::"); + String suffix = substringAfter(bp.getOriginalID(), "::"); + + final String pidType = substringBefore(ns, "_"); + if (PidType.isValid(pidType)) { + return prefix + "|" + dedupify(ns) + "::" + suffix; } else { - return bp.get().getOriginalID().split("\\|")[0] + "|" - + createPrefix(bp.get().getPid().getQualifier().getClassid()) + "::" - + DHPUtils.md5(bp.get().getPid().getValue()); + return prefix + "|dedup_wf_001::" + suffix; } - } - public static ArrayList createBasePid(T entity, SimpleDateFormat sdf) { - - Date date; - try { - date = sdf.parse(BASE_DATE); - } catch (ParseException e) { - date = new Date(); - } - return Lists - .newArrayList( - new Identifier(new StructuredProperty(), date, PidType.original, entity.getCollectedfrom(), - EntityType.fromClass(entity.getClass()), entity.getId())); - } - - // pick the best pid from the entity. Returns a list (length 1) to save time in the call - public static List bestPidToIdentifier(T entity) { - - SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - - if (entity.getPid() == null || entity.getPid().size() == 0) - return createBasePid(entity, sdf); - - Optional bp = entity - .getPid() - .stream() - .filter(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()) != PidType.undefined) - .max(Comparator.comparing(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()))); - - return bp - .map( - structuredProperty -> Lists - .newArrayList( - new Identifier(structuredProperty, extractDate(entity, sdf), - PidType.classidValueOf(structuredProperty.getQualifier().getClassid()), - entity.getCollectedfrom(), EntityType.fromClass(entity.getClass()), entity.getId()))) - .orElseGet(() -> createBasePid(entity, sdf)); - - } - - // create the prefix (length = 12): dedup_+ pidType - public static String createPrefix(String pidType) { - - StringBuilder prefix = new StringBuilder("dedup_" + pidType); - + private static String dedupify(String ns) { + StringBuilder prefix = new StringBuilder(substringBefore(ns, "_")).append("_dedup"); while (prefix.length() < 12) { prefix.append("_"); } - return prefix.toString().substring(0, 12); - + return prefix.substring(0, 12); } - // extracts the date from the record. If the date is not available or is not wellformed, it returns a base date: - // 00-01-01 - public static Date extractDate(T duplicate, SimpleDateFormat sdf) { - - String date = BASE_DATE; - if (ModelSupport.isSubClass(duplicate, Result.class)) { - Result result = (Result) duplicate; - if (isWellformed(result.getDateofacceptance())) { - date = result.getDateofacceptance().getValue(); - } - } - - try { - return sdf.parse(date); - } catch (ParseException e) { - return new Date(); - } - - } - - public static boolean isWellformed(Field date) { - return date != null && StringUtils.isNotBlank(date.getValue()) - && date.getValue().matches(DatePicker.DATE_PATTERN) && DatePicker.inRange(date.getValue()); - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java index f5b2f48c5..39b26f919 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/Identifier.java @@ -2,93 +2,85 @@ package eu.dnetlib.dhp.oa.dedup.model; import java.io.Serializable; +import java.text.ParseException; +import java.text.SimpleDateFormat; import java.util.Date; import java.util.List; +import java.util.Optional; import java.util.Set; import java.util.stream.Collectors; +import org.apache.commons.lang3.StringUtils; + import com.google.common.collect.Sets; -import eu.dnetlib.dhp.oa.dedup.IdGenerator; + +import eu.dnetlib.dhp.oa.dedup.DatePicker; import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.PidComparator; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; -public class Identifier implements Serializable, Comparable { +public class Identifier implements Serializable, Comparable { - StructuredProperty pid; - Date date; - PidType type; - List collectedFrom; - EntityType entityType; - String originalID; + public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2"; + public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"; + public static String BASE_DATE = "2000-01-01"; - boolean useOriginal = false; // to know if the top identifier won because of the alphabetical order of the original - // ID + private static SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); - public Identifier(StructuredProperty pid, Date date, PidType type, List collectedFrom, - EntityType entityType, String originalID) { - this.pid = pid; - this.date = date; - this.type = type; - this.collectedFrom = collectedFrom; - this.entityType = entityType; - this.originalID = originalID; + private T entity; + + public static Identifier newInstance(T entity) { + return new Identifier(entity); } - public StructuredProperty getPid() { - return pid; + public Identifier(T entity) { + this.entity = entity; } - public void setPid(StructuredProperty pid) { - this.pid = pid; + public T getEntity() { + return entity; + } + + public void setEntity(T entity) { + this.entity = entity; } public Date getDate() { - return date; + String date = BASE_DATE; + if (ModelSupport.isSubClass(getEntity(), Result.class)) { + Result result = (Result) getEntity(); + if (isWellformed(result.getDateofacceptance())) { + date = result.getDateofacceptance().getValue(); + } + } + try { + return sdf.parse(date); + } catch (ParseException e) { + return new Date(); + } } - public void setDate(Date date) { - this.date = date; - } - - public PidType getType() { - return type; - } - - public void setType(PidType type) { - this.type = type; + private static boolean isWellformed(Field date) { + return date != null && StringUtils.isNotBlank(date.getValue()) + && date.getValue().matches(DatePicker.DATE_PATTERN) && DatePicker.inRange(date.getValue()); } public List getCollectedFrom() { - return collectedFrom; - } - - public void setCollectedFrom(List collectedFrom) { - this.collectedFrom = collectedFrom; + return entity.getCollectedfrom(); } public EntityType getEntityType() { - return entityType; - } - - public void setEntityType(EntityType entityType) { - this.entityType = entityType; + return EntityType.fromClass(entity.getClass()); } public String getOriginalID() { - return originalID; + return entity.getId(); } - public void setOriginalID(String originalID) { - this.originalID = originalID; - } - - public boolean isUseOriginal() { - return useOriginal; - } - - public void setUseOriginal(boolean useOriginal) { - this.useOriginal = useOriginal; + private PidType getPidType() { + return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_")); } @Override @@ -96,50 +88,50 @@ public class Identifier implements Serializable, Comparable { // priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4) // alphabetical order of the originalID - Set lKeys = Sets.newHashSet(); - if (this.collectedFrom != null) - lKeys = this.collectedFrom.stream().map(KeyValue::getKey).collect(Collectors.toSet()); + Set lKeys = Optional + .ofNullable(getCollectedFrom()) + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); - Set rKeys = Sets.newHashSet(); - if (i.getCollectedFrom() != null) - rKeys = i.getCollectedFrom().stream().map(KeyValue::getKey).collect(Collectors.toSet()); + final Optional> cf = Optional.ofNullable(i.getCollectedFrom()); + Set rKeys = cf + .map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet())) + .orElse(Sets.newHashSet()); - if (this.getType().compareTo(i.getType()) == 0) { // same type - if (entityType == EntityType.publication) { - if (isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID) - && !isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID)) - return 1; - if (isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID) - && !isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID)) + if (this.getPidType().compareTo(i.getPidType()) == 0) { // same type + if (getEntityType() == EntityType.publication) { + if (isFromDatasourceID(lKeys, CROSSREF_ID) + && !isFromDatasourceID(rKeys, CROSSREF_ID)) return -1; + if (isFromDatasourceID(rKeys, CROSSREF_ID) + && !isFromDatasourceID(lKeys, CROSSREF_ID)) + return 1; } - if (entityType == EntityType.dataset) { - if (isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID) - && !isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID)) - return 1; - if (isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID) - && !isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID)) + if (getEntityType() == EntityType.dataset) { + if (isFromDatasourceID(lKeys, DATACITE_ID) + && !isFromDatasourceID(rKeys, DATACITE_ID)) return -1; + if (isFromDatasourceID(rKeys, DATACITE_ID) + && !isFromDatasourceID(lKeys, DATACITE_ID)) + return 1; } if (this.getDate().compareTo(i.getDate()) == 0) {// same date - - if (this.originalID.compareTo(i.originalID) < 0) - this.useOriginal = true; - else - i.setUseOriginal(true); - // the minus because we need to take the alphabetically lower id - return -this.originalID.compareTo(i.originalID); + return this.getOriginalID().compareTo(i.getOriginalID()); } else // the minus is because we need to take the elder date - return -this.getDate().compareTo(i.getDate()); + return this.getDate().compareTo(i.getDate()); } else { - return this.getType().compareTo(i.getType()); + return new PidComparator<>(getEntity()).compare(toSP(getPidType()), toSP(i.getPidType())); } } + private StructuredProperty toSP(PidType pidType) { + return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo()); + } + public boolean isFromDatasourceID(Set collectedFrom, String dsId) { return collectedFrom.contains(dsId); } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/PidType.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/PidType.java deleted file mode 100644 index cb9b2bd15..000000000 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/PidType.java +++ /dev/null @@ -1,17 +0,0 @@ - -package eu.dnetlib.dhp.oa.dedup.model; - -public enum PidType { - - // from the less to the more important - undefined, original, orcid, ror, grid, pdb, arXiv, pmid, pmc, doi; - - public static PidType classidValueOf(String s) { - try { - return PidType.valueOf(s); - } catch (Exception e) { - return PidType.undefined; - } - } - -} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index bb4188f7e..3f10af5b8 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -9,6 +9,7 @@ import java.io.IOException; import java.io.Serializable; import java.nio.file.Paths; import java.util.*; +import java.util.stream.Collectors; import org.codehaus.jackson.map.ObjectMapper; import org.junit.jupiter.api.BeforeEach; @@ -21,16 +22,16 @@ import scala.Tuple2; public class EntityMergerTest implements Serializable { - List> publications; - List> publications2; - List> publications3; - List> publications4; - List> publications5; + private List> publications; + private List> publications2; + private List> publications3; + private List> publications4; + private List> publications5; - String testEntityBasePath; - DataInfo dataInfo; - String dedupId = "00|dedup_id::1"; - Publication pub_top; + private String testEntityBasePath; + private DataInfo dataInfo; + private String dedupId = "00|dedup_id::1"; + private Publication pub_top; @BeforeEach public void setUp() throws Exception { @@ -61,9 +62,9 @@ public class EntityMergerTest implements Serializable { Software merged = DedupRecordFactory .entityMerger(dedupId, softwares.iterator(), 0, dataInfo, Software.class); - assertEquals(merged.getBestaccessright().getClassid(), "OPEN SOURCE"); + assertEquals("OPEN SOURCE", merged.getBestaccessright().getClassid()); - assertEquals(merged.getId(), "50|dedup_doi___::0968af610a356656706657e4f234b340"); + assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", merged.getId()); } @@ -74,45 +75,45 @@ public class EntityMergerTest implements Serializable { .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); // verify id - assertEquals(pub_merged.getId(), "50|dedup_doi___::0968af610a356656706657e4f234b340"); + assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", pub_merged.getId()); - assertEquals(pub_merged.getJournal(), pub_top.getJournal()); - assertEquals(pub_merged.getBestaccessright().getClassid(), "OPEN"); - assertEquals(pub_merged.getResulttype(), pub_top.getResulttype()); - assertEquals(pub_merged.getLanguage(), pub_merged.getLanguage()); - assertEquals(pub_merged.getPublisher(), pub_top.getPublisher()); - assertEquals(pub_merged.getEmbargoenddate(), pub_top.getEmbargoenddate()); - assertEquals(pub_merged.getResourcetype().getClassid(), "0004"); - assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation()); - assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance()); - assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection()); - assertEquals(pub_merged.getInstance().size(), 3); - assertEquals(pub_merged.getCountry().size(), 2); - assertEquals(pub_merged.getSubject().size(), 0); - assertEquals(pub_merged.getTitle().size(), 2); - assertEquals(pub_merged.getRelevantdate().size(), 0); - assertEquals(pub_merged.getDescription().size(), 0); - assertEquals(pub_merged.getSource().size(), 0); - assertEquals(pub_merged.getFulltext().size(), 0); - assertEquals(pub_merged.getFormat().size(), 0); - assertEquals(pub_merged.getContributor().size(), 0); - assertEquals(pub_merged.getCoverage().size(), 0); - assertEquals(pub_merged.getContext().size(), 0); - assertEquals(pub_merged.getExternalReference().size(), 0); - assertEquals(pub_merged.getOriginalId().size(), 3); - assertEquals(pub_merged.getCollectedfrom().size(), 3); - assertEquals(pub_merged.getPid().size(), 1); - assertEquals(pub_merged.getExtraInfo().size(), 0); + assertEquals(pub_top.getJournal(), pub_merged.getJournal()); + assertEquals("OPEN", pub_merged.getBestaccessright().getClassid()); + assertEquals(pub_top.getResulttype(), pub_merged.getResulttype()); + assertEquals(pub_top.getLanguage(), pub_merged.getLanguage()); + assertEquals(pub_top.getPublisher(), pub_merged.getPublisher()); + assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate()); + assertEquals(pub_top.getResourcetype().getClassid(), ""); + assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation()); + assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance()); + assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection()); + assertEquals(3, pub_merged.getInstance().size()); + assertEquals(2, pub_merged.getCountry().size()); + assertEquals(0, pub_merged.getSubject().size()); + assertEquals(2, pub_merged.getTitle().size()); + assertEquals(0, pub_merged.getRelevantdate().size()); + assertEquals(0, pub_merged.getDescription().size()); + assertEquals(0, pub_merged.getSource().size()); + assertEquals(0, pub_merged.getFulltext().size()); + assertEquals(0, pub_merged.getFormat().size()); + assertEquals(0, pub_merged.getContributor().size()); + assertEquals(0, pub_merged.getCoverage().size()); + assertEquals(0, pub_merged.getContext().size()); + assertEquals(0, pub_merged.getExternalReference().size()); + assertEquals(3, pub_merged.getOriginalId().size()); + assertEquals(3, pub_merged.getCollectedfrom().size()); + assertEquals(1, pub_merged.getPid().size()); + assertEquals(0, pub_merged.getExtraInfo().size()); // verify datainfo - assertEquals(pub_merged.getDataInfo(), dataInfo); + assertEquals(dataInfo, pub_merged.getDataInfo()); // verify datepicker - assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30"); + assertEquals("2018-09-30", pub_merged.getDateofacceptance().getValue()); // verify authors - assertEquals(pub_merged.getAuthor().size(), 9); - assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4); + assertEquals(9, pub_merged.getAuthor().size()); + assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor())); // verify title int count = 0; @@ -120,7 +121,7 @@ public class EntityMergerTest implements Serializable { if (title.getQualifier().getClassid().equals("main title")) count++; } - assertEquals(count, 1); + assertEquals(1, count); } @Test @@ -130,9 +131,9 @@ public class EntityMergerTest implements Serializable { .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); // verify id - assertEquals("50|dedup_doi___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); + assertEquals("50|doi_dedup___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); - assertEquals(pub_merged.getAuthor().size(), 27); + assertEquals(27, pub_merged.getAuthor().size()); } @Test @@ -142,7 +143,7 @@ public class EntityMergerTest implements Serializable { .entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class); // verify id - assertEquals("50|dedup_doi___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); + assertEquals("50|doi_dedup___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); } @Test @@ -152,17 +153,24 @@ public class EntityMergerTest implements Serializable { .entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class); // verify id - assertEquals("50|dedup_wf_001::2d2bbbbcfb285e3fb3590237b79e2fa8", pub_merged.getId()); + assertEquals("50|dedup_wf_001::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); } @Test public void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException { + System.out + .println( + publications5 + .stream() + .map(p -> p._2().getId()) + .collect(Collectors.toList())); + Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications5.iterator(), 0, dataInfo, Publication.class); // verify id - assertEquals("50|dedup_wf_001::584b89679c3ccd1015b647ec63cc2699", pub_merged.getId()); + assertEquals("50|dedup_wf_001::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId()); } public DataInfo setDI() { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java index 403498aeb..a6604dd30 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/IdGeneratorTest.java @@ -7,96 +7,57 @@ import java.io.BufferedReader; import java.io.FileReader; import java.io.IOException; import java.nio.file.Paths; -import java.text.SimpleDateFormat; import java.util.ArrayList; -import java.util.Date; import java.util.List; import java.util.stream.Collectors; +import java.util.stream.Stream; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.jupiter.api.*; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.MethodOrderer; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.TestMethodOrder; +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.oa.dedup.model.Identifier; -import eu.dnetlib.dhp.oa.dedup.model.PidType; -import eu.dnetlib.dhp.schema.common.EntityType; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.pace.util.MapDocumentUtil; import scala.Tuple2; @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class IdGeneratorTest { - private static List bestIds; - private static List> pubs; + private static ObjectMapper OBJECT_MAPPER = new ObjectMapper() + .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - private static List bestIds2; - private static List bestIds3; + private static List> bestIds; + private static List> bestIds2; + private static List> bestIds3; private static String testEntityBasePath; - private static SimpleDateFormat sdf; - private static Date baseDate; - @BeforeAll public static void setUp() throws Exception { - - sdf = new SimpleDateFormat("yyyy-MM-dd"); - baseDate = sdf.parse("2000-01-01"); - - bestIds = new ArrayList<>(); - bestIds2 = Lists - .newArrayList( - new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original, - keyValue("key", "value"), EntityType.publication, "50|originalID1"), - new Identifier(pid("pid2", "original", "original"), baseDate, PidType.original, - keyValue("key", "value"), EntityType.publication, "50|originalID2"), - new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original, - keyValue("key", "value"), EntityType.publication, "50|originalID3")); - bestIds3 = Lists - .newArrayList( - new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original, - keyValue("key", "value"), EntityType.publication, "50|originalID1"), - new Identifier(pid("pid2", "doi", "doi"), baseDate, PidType.doi, keyValue("key", "value"), - EntityType.publication, "50|originalID2"), - new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original, - keyValue("key", "value"), EntityType.publication, "50|originalID3")); - testEntityBasePath = Paths .get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI()) .toFile() .getAbsolutePath(); - pubs = readSample(testEntityBasePath + "/publication_idgeneration.json", Publication.class); - + bestIds = createBestIds(testEntityBasePath + "/publication_idgeneration.json", Publication.class); + bestIds2 = createBestIds(testEntityBasePath + "/publication_idgeneration2.json", Publication.class); + bestIds3 = createBestIds(testEntityBasePath + "/publication_idgeneration3.json", Publication.class); } @Test - @Order(1) - public void bestPidToIdentifierTest() { - - List typesForAssertions = Lists - .newArrayList(PidType.pmc.toString(), PidType.doi.toString(), PidType.doi.toString()); - - for (Tuple2 pub : pubs) { - List ids = IdGenerator.bestPidToIdentifier(pub._2()); - assertEquals(typesForAssertions.get(pubs.indexOf(pub)), ids.get(0).getPid().getQualifier().getClassid()); - bestIds.addAll(ids); - } - } - - @Test - @Order(2) public void generateIdTest1() { String id1 = IdGenerator.generate(bestIds, "50|defaultID"); - System.out.println("id list 1 = " + bestIds.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList())); + System.out + .println("id list 1 = " + bestIds.stream().map(i -> i.getOriginalID()).collect(Collectors.toList())); - assertEquals("50|dedup_wf_001::9c5cfbf993d38476e0f959a301239719", id1); + assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", id1); } @Test @@ -104,13 +65,23 @@ public class IdGeneratorTest { String id1 = IdGenerator.generate(bestIds2, "50|defaultID"); String id2 = IdGenerator.generate(bestIds3, "50|defaultID"); - System.out.println("id list 2 = " + bestIds2.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList())); + System.out + .println("id list 2 = " + bestIds2.stream().map(i -> i.getOriginalID()).collect(Collectors.toList())); System.out.println("winner 2 = " + id1); - System.out.println("id list 3 = " + bestIds3.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList())); + System.out + .println("id list 3 = " + bestIds3.stream().map(i -> i.getOriginalID()).collect(Collectors.toList())); System.out.println("winner 3 = " + id2); - assertEquals("50|dedup_wf_001::2c56cc1914bffdb30fdff354e0099612", id1); - assertEquals("50|dedup_doi___::128ead3ed8d9ecf262704b6fcf592b8d", id2); + assertEquals("50|doi_dedup___::1a77a3bba737f8b669dcf330ad3b37e2", id1); + assertEquals("50|dedup_wf_001::0829b5191605bdbea36d6502b8c1ce1g", id2); + } + + protected static List> createBestIds(String path, Class clazz) { + final Stream> ids = readSample(path, clazz) + .stream() + .map(Tuple2::_2) + .map(Identifier::newInstance); + return ids.collect(Collectors.toList()); } public static List> readSample(String path, Class clazz) { @@ -124,7 +95,7 @@ public class IdGeneratorTest { .add( new Tuple2<>( MapDocumentUtil.getJPathString("$.id", line), - new ObjectMapper().readValue(line, clazz))); + OBJECT_MAPPER.readValue(line, clazz))); // read next line line = reader.readLine(); } @@ -137,23 +108,10 @@ public class IdGeneratorTest { } public static StructuredProperty pid(String pid, String classid, String classname) { - - StructuredProperty sp = new StructuredProperty(); - sp.setValue(pid); - Qualifier q = new Qualifier(); - q.setSchemeid(classid); - q.setSchemename(classname); - q.setClassname(classname); - q.setClassid(classid); - sp.setQualifier(q); - return sp; + return OafMapperUtils.structuredProperty(pid, classid, classname, "", "", new DataInfo()); } public static List keyValue(String key, String value) { - - KeyValue kv = new KeyValue(); - kv.setKey(key); - kv.setValue(value); - return Lists.newArrayList(kv); + return Lists.newArrayList(OafMapperUtils.keyValue(key, value)); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index b849160ff..c706061a0 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,12 +1,18 @@ package eu.dnetlib.dhp.oa.dedup; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.util.MapDocumentUtil; +import static java.nio.file.Files.createTempDirectory; + +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; + +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; + import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -25,19 +31,16 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.util.MapDocumentUtil; import scala.Tuple2; -import java.io.File; -import java.io.IOException; -import java.io.Serializable; -import java.net.URISyntaxException; -import java.nio.file.Paths; - -import static java.nio.file.Files.createTempDirectory; -import static org.apache.spark.sql.functions.count; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; - @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest implements Serializable { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json index b2300acc6..4fc078204 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration.json @@ -1,3 +1,3 @@ -{"context": [], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:datasetarchive", "classname": "sysimport:crosswalk:datasetarchive", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.95"}, "resourcetype": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "pid": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "arXiv", "classname": "arXiv", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "arXivSampleID"} ,{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmc", "classname": "pmc", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "pmcsampleid"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}], "id": "50|a89337edbe55::4930db9e954866d70916cbfba9f81f97", "subject": [], "instance": [{"refereed": null, "hostedby": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}, "processingchargeamount": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "license": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "url": [], "distributionlocation": "", "processingchargecurrency": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "collectedfrom": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "Journal.fi", "key": "10|openaire____::6eef8049d0feedc089ee009abca55e35"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource"}}], "embargoenddate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Go\\u0308tz", "name": "Julia", "pid": [], "rank": 5, "affiliation": [], "fullname": "G\\u00f6tz, Julia"}, {"surname": "Wolff", "name": "Stephan", "pid": [], "rank": 6, "affiliation": [], "fullname": "Wolff, Stephan"}, {"surname": "Jansen", "name": "Olav", "pid": [], "rank": 7, "affiliation": [], "fullname": "Jansen, Olav"}, {"surname": "Dressler", "name": "Dirk", "pid": [{"qualifier": {"classid": "ORCID", "classname": "ORCID"}, "value": "0000-0000-0656-9999"},{"qualifier": {"classid": "id", "classname": "id"}, "value": "987654321"}], "rank": 8, "affiliation": [], "fullname": "Dressler, Dirk"}, {"surname": "Schneider", "name": "Susanne A.", "pid": [], "rank": 9, "affiliation": [], "fullname": "Schneider, Susanne A."}], "source": [], "dateofcollection": "2019-11-05T14:49:22.351Z", "fulltext": [], "dateoftransformation": "2019-11-05T16:10:58.988Z", "description": [], "format": [], "journal": {"issnPrinted": "1459-6067", "conferencedate": "", "conferenceplace": "", "name": "Agricultural and Food Science", "edition": "", "iss": "3", "sp": "", "vol": "27", "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "1795-1895", "ep": "", "issnLinking": ""}, "coverage": [], "publisher": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "eng", "classname": "English", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "country": [], "extraInfo": [], "originalId": [], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2018-09-30"}, "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Altered brain activation in a reversal learning task unmasks adaptive changes in cognitive control in writer's cramp"}]} -{"context": [], "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "sysimport:crosswalk:repository", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "dedup-similarity-result-levenstein", "invisible": false, "trust": "0.9"}, "resourcetype": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "pid": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "doi", "classname": "doi", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.1016/j.nicl.2015.11.006"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "arXiv", "classname": "arXiv", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "arXivSampleID"} ,{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "pmc", "classname": "pmc", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "pmcsampleid"}], "contributor": [], "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "relevantdate": [], "collectedfrom": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "BASE (Open Access Aggregator)", "key": "10|openaire____::df45502607927471ecf8a6ae83683ff5"}], "id": "50|base_oa_____::0968af610a356656706657e4f234b340", "subject": [], "instance": [{"refereed": null, "hostedby": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "NeuroImage: Clinical", "key": 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Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. 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In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. 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Urology"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"RC870-923"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open 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In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"dataInfo":null,"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed 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Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open 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Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. 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Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. 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Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"dataInfo":null,"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed 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"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556"}, "accessright": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0004", "classname": "Conference object", "schemename": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource"}}], "embargoenddate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "author": [{"surname": "Zeuner", "name": "Kirsten E.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Zeuner, Kirsten E."}, {"surname": "Knutzen", "name": "Arne", "pid": [], "rank": 2, "affiliation": [], "fullname": "Knutzen, Arne"}, {"surname": "Granert", "name": "Oliver", "pid": [{"qualifier": {"classid": "ORCID", "classname": "ORCID"}, "value": "0000-0002-0656-1023"}, {"qualifier": {"classid": "pubmed", "classname": "pubmed"}, "value": "pubmed.it"}], "rank": 3, "affiliation": [], "fullname": "Granert, Oliver"}, {"surname": "Sablowsky", "name": "Simone", "pid": [{"qualifier": {"classid": "id", "classname": "id"}, "value": "12345678"}], "rank": 4, "affiliation": [], "fullname": "Sablowsky, Simone"}, {"surname": "Go\\u0308tz", "name": "Julia", "pid": [], "rank": 5, "affiliation": [], "fullname": "G\\u00f6tz, Julia"}, {"surname": "Wolff", "name": "Stephan", "pid": [], "rank": 6, "affiliation": [], "fullname": "Wolff, Stephan"}, {"surname": "Jansen", "name": "Olav", "pid": [{"qualifier": {"classid": "ORCID", "classname": "ORCID"}, "value": "0000-0000-0656-1023"},{"qualifier": {"classid": "id", "classname": "id"}, "value": "987654321"}], "rank": 7, "affiliation": [], "fullname": "Jansen, Olav"}, {"surname": "Dressler", "name": "Dirk", "pid": [], "rank": 8, "affiliation": [], "fullname": "Dressler, Dirk"}, {"surname": "Schneider", "name": "Susanne A.", "pid": [], "rank": 9, "affiliation": [], "fullname": "Schneider, Susanne A."}], "source": [], "dateofcollection": "2020-03-10T15:05:38.685Z", "fulltext": [], "dateoftransformation": "2020-03-11T20:11:13.15Z", "description": [], "format": [], "coverage": [], "publisher": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "language": {"classid": "en", "classname": "en", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "bestaccessright": {"classid": "UNKNOWN", "classname": "unknown", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "country": [{"classid": "FI", "classname": "Finland", "schemeid": "dnet:countries", "schemename": "dnet:countries"}], "extraInfo": [], "originalId": ["(BISIS)113444", "https://www.cris.uns.ac.rs/record.jsf?recordId=113444&source=OpenAIRE&language=en"], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "2016-01-01"}, "title": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "qualifier": {"classid": "test title", "classname": "test title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Antichains of copies of ultrahomogeneous structures"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 772af010f..a29809fc0 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -1,13 +1,15 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset, Organization} +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.functions.col import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkGenerateDoiBoost { @@ -49,6 +51,7 @@ object SparkGenerateDoiBoost { val otherPub = item._2._2 if (otherPub != null) { crossrefPub.mergeFrom(otherPub) + crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)) } } crossrefPub diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala index 243719549..b3402ee9f 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala @@ -38,6 +38,8 @@ class QueryTest { def myQuery(spark:SparkSession, sc:SparkContext): Unit = { implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] + + val mapper = new ObjectMapper() mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index e295b9503..a15c2ee62 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -3,13 +3,9 @@ package eu.dnetlib.dhp.oa.graph.clean; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; -import java.io.BufferedInputStream; -import java.util.Objects; import java.util.Optional; -import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Dataset; @@ -23,10 +19,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; -import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper; -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5b6ae72f1..051225857 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -1,8 +1,8 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*; import java.util.*; @@ -12,10 +12,13 @@ import org.dom4j.DocumentFactory; import org.dom4j.DocumentHelper; import org.dom4j.Node; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.common.LicenseComparator; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public abstract class AbstractMdRecordToOafMapper { @@ -133,20 +136,34 @@ public abstract class AbstractMdRecordToOafMapper { final DataInfo info, final long lastUpdateTimestamp) { - final List oafs = new ArrayList<>(); + final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp); + final String id = IdentifierFactory.createIdentifier(entity); + if (!id.equals(entity.getId())) { + entity.getOriginalId().add(entity.getId()); + entity.setId(id); + } + final List oafs = Lists.newArrayList(entity); + + if (!oafs.isEmpty()) { + oafs.addAll(addProjectRels(doc, entity)); + oafs.addAll(addOtherResultRels(doc, entity)); + } + + return oafs; + } + + private OafEntity createEntity(Document doc, String type, List instances, KeyValue collectedFrom, + DataInfo info, long lastUpdateTimestamp) { switch (type.toLowerCase()) { case "publication": final Publication p = new Publication(); populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp); - p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); p.setJournal(prepareJournal(doc, info)); - oafs.add(p); - break; + return p; case "dataset": final Dataset d = new Dataset(); populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp); - d.setResulttype(DATASET_DEFAULT_RESULTTYPE); d.setStoragedate(prepareDatasetStorageDate(doc, info)); d.setDevice(prepareDatasetDevice(doc, info)); d.setSize(prepareDatasetSize(doc, info)); @@ -154,48 +171,34 @@ public abstract class AbstractMdRecordToOafMapper { d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info)); d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info)); d.setGeolocation(prepareDatasetGeoLocations(doc, info)); - oafs.add(d); - break; + return d; case "software": final Software s = new Software(); populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp); - s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info)); s.setLicense(prepareSoftwareLicenses(doc, info)); s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info)); s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info)); - oafs.add(s); - break; + return s; case "": case "otherresearchproducts": default: final OtherResearchProduct o = new OtherResearchProduct(); populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp); - o.setResulttype(ORP_DEFAULT_RESULTTYPE); o.setContactperson(prepareOtherResearchProductContactPersons(doc, info)); o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info)); o.setTool(prepareOtherResearchProductTools(doc, info)); - oafs.add(o); - break; + return o; } - - if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, collectedFrom, info, lastUpdateTimestamp)); - oafs.addAll(addOtherResultRels(doc, collectedFrom, info, lastUpdateTimestamp)); - } - - return oafs; } private List addProjectRels( final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { + final OafEntity entity) { final List res = new ArrayList<>(); - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + final String docId = entity.getId(); for (final Object o : doc.selectNodes("//oaf:projectid")) { @@ -207,13 +210,11 @@ public abstract class AbstractMdRecordToOafMapper { res .add( getRelation( - docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, - lastUpdateTimestamp)); + docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity)); res .add( getRelation( - projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, - lastUpdateTimestamp)); + projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity)); } } @@ -225,26 +226,22 @@ public abstract class AbstractMdRecordToOafMapper { final String relType, final String subRelType, final String relClass, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { + final OafEntity entity) { final Relation rel = new Relation(); rel.setRelType(relType); rel.setSubRelType(subRelType); rel.setRelClass(relClass); rel.setSource(source); rel.setTarget(target); - rel.setCollectedfrom(Arrays.asList(collectedFrom)); - rel.setDataInfo(info); - rel.setLastupdatetimestamp(lastUpdateTimestamp); + rel.setCollectedfrom(entity.getCollectedfrom()); + rel.setDataInfo(entity.getDataInfo()); + rel.setLastupdatetimestamp(entity.getLastupdatetimestamp()); return rel; } protected abstract List addOtherResultRels( final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp); + final OafEntity entity); private void populateResultFields( final Result r, @@ -257,7 +254,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setLastupdatetimestamp(lastUpdateTimestamp); r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false)); - r.setOriginalId(Arrays.asList(findOriginalId(doc))); + r.setOriginalId(Lists.newArrayList(findOriginalId(doc))); r.setCollectedfrom(Arrays.asList(collectedFrom)); r.setPid(prepareResultPids(doc, info)); @@ -285,7 +282,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setInstance(instances); - r.setBestaccessright(getBestAccessRights(instances)); + r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances)); } protected abstract List prepareResultPids(Document doc, DataInfo info); @@ -370,38 +367,6 @@ public abstract class AbstractMdRecordToOafMapper { protected abstract Field prepareDatasetStorageDate(Document doc, DataInfo info); - public static Qualifier createBestAccessRights(final List instanceList) { - return getBestAccessRights(instanceList); - } - - protected static Qualifier getBestAccessRights(final List instanceList) { - if (instanceList != null) { - final Optional min = instanceList - .stream() - .map(i -> i.getAccessright()) - .min(new LicenseComparator()); - - final Qualifier rights = min.isPresent() ? min.get() : new Qualifier(); - - if (StringUtils.isBlank(rights.getClassid())) { - rights.setClassid(UNKNOWN); - } - if (StringUtils.isBlank(rights.getClassname()) - || UNKNOWN.equalsIgnoreCase(rights.getClassname())) { - rights.setClassname(NOT_AVAILABLE); - } - if (StringUtils.isBlank(rights.getSchemeid())) { - rights.setSchemeid(DNET_ACCESS_MODES); - } - if (StringUtils.isBlank(rights.getSchemename())) { - rights.setSchemename(DNET_ACCESS_MODES); - } - - return rights; - } - return null; - } - private Journal prepareJournal(final Document doc, final DataInfo info) { final Node n = doc.selectSingleNode("//oaf:journal"); if (n != null) { @@ -564,4 +529,5 @@ public abstract class AbstractMdRecordToOafMapper { } return res; } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java index 3568dc52a..27b57b2d1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java @@ -4,11 +4,9 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.IOException; -import java.util.Arrays; -import java.util.List; -import java.util.Objects; -import java.util.Optional; +import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -20,6 +18,7 @@ import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.sql.SparkSession; +import org.jetbrains.annotations.NotNull; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -29,16 +28,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Datasource; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.OafEntity; -import eu.dnetlib.dhp.schema.oaf.Organization; -import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; -import eu.dnetlib.dhp.schema.oaf.Project; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import scala.Tuple2; @@ -124,7 +114,18 @@ public class GenerateEntitiesApplication { private static Oaf merge(final Oaf o1, final Oaf o2) { if (ModelSupport.isSubClass(o1, OafEntity.class)) { - ((OafEntity) o1).mergeFrom((OafEntity) o2); + if (ModelSupport.isSubClass(o1, Result.class)) { + + return mergeResults((Result) o1, (Result) o2); + } else if (ModelSupport.isSubClass(o1, Datasource.class)) { + ((Datasource) o1).mergeFrom((Datasource) o2); + } else if (ModelSupport.isSubClass(o1, Organization.class)) { + ((Organization) o1).mergeFrom((Organization) o2); + } else if (ModelSupport.isSubClass(o1, Project.class)) { + ((Project) o1).mergeFrom((Project) o2); + } else { + throw new RuntimeException("invalid OafEntity subtype:" + o1.getClass().getCanonicalName()); + } } else if (ModelSupport.isSubClass(o1, Relation.class)) { ((Relation) o1).mergeFrom((Relation) o2); } else { @@ -133,6 +134,19 @@ public class GenerateEntitiesApplication { return o1; } + protected static Result mergeResults(Result o1, Result o2) { + Result r1 = o1; + Result r2 = o2; + + if (new ResultTypeComparator().compare(r1, r2) < 0) { + r1.mergeFrom(r2); + return r1; + } else { + r2.mergeFrom(r1); + return r2; + } + } + private static List convertToListOaf( final String id, final String s, diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index adf7b92be..16b0aa80b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -1,16 +1,6 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; -import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; @@ -19,19 +9,25 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; -import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION; -import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; -import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty; import java.io.Closeable; import java.io.IOException; @@ -445,22 +441,26 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i createOpenaireId(10, "infrastruct_::openaire", true), "OpenAIRE"); try { + final String targetType = rs.getString(TARGET_TYPE); if (rs.getString(SOURCE_TYPE).equals("context")) { final Result r; - if (rs.getString(TARGET_TYPE).equals("dataset")) { - r = new Dataset(); - r.setResulttype(DATASET_DEFAULT_RESULTTYPE); - } else if (rs.getString(TARGET_TYPE).equals("software")) { - r = new Software(); - r.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE); - } else if (rs.getString(TARGET_TYPE).equals("other")) { - r = new OtherResearchProduct(); - r.setResulttype(ORP_DEFAULT_RESULTTYPE); - } else { - r = new Publication(); - r.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE); + switch (targetType) { + case "dataset": + r = new Dataset(); + break; + case "software": + r = new Software(); + break; + case "other": + r = new OtherResearchProduct(); + break; + case "publication": + default: + r = new Publication(); + break; } + r.setId(createOpenaireId(50, rs.getString("target_id"), false)); r.setLastupdatetimestamp(lastUpdateTimestamp); r.setContext(prepareContext(rs.getString("source_id"), info)); @@ -470,7 +470,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i return Arrays.asList(r); } else { final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false); - final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false); + final String targetId = createOpenaireId(targetType, rs.getString("target_id"), false); final Relation r1 = new Relation(); final Relation r2 = new Relation(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java index dea80fabd..a1798e4fb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty; import java.util.ArrayList; import java.util.List; @@ -19,15 +19,8 @@ import com.google.common.collect.Lists; import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class OafToOafMapper extends AbstractMdRecordToOafMapper { @@ -93,7 +86,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List> prepareDescriptions(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//dc:description", info); + return prepareListFields(doc, "//dc:description", info) + .stream() + .map(d -> { + d.setValue(StringUtils.left(d.getValue(), ModelHardLimits.MAX_ABSTRACT_LENGTH)); + return d; + }) + .collect(Collectors.toList()); } @Override @@ -257,11 +256,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List addOtherResultRels( final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + final OafEntity entity) { + final String docId = entity.getId(); final List res = new ArrayList<>(); for (final Object o : doc.selectNodes("//*[local-name()='relatedDataset']")) { @@ -275,13 +272,11 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { res .add( getRelation( - docId, otherId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, collectedFrom, info, - lastUpdateTimestamp)); + docId, otherId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity)); res .add( getRelation( - otherId, docId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, collectedFrom, info, - lastUpdateTimestamp)); + otherId, docId, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO, entity)); } } return res; @@ -295,6 +290,10 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List prepareResultPids(final Document doc, final DataInfo info) { return prepareListStructPropsWithValidQualifier( - doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info); + doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info) + .stream() + .map(CleaningFunctions::normalizePidValue) + .collect(Collectors.toList()); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 6fe7bb971..b7ee2d546 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -1,34 +1,26 @@ package eu.dnetlib.dhp.oa.graph.raw; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field; -import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field; +import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty; import java.util.ArrayList; import java.util.Arrays; import java.util.HashSet; import java.util.List; import java.util.Set; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; -import com.google.common.collect.Lists; - import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.GeoLocation; -import eu.dnetlib.dhp.schema.oaf.Instance; -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @@ -198,7 +190,13 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List> prepareDescriptions(final Document doc, final DataInfo info) { - return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info); + return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info) + .stream() + .map(d -> { + d.setValue(StringUtils.left(d.getValue(), ModelHardLimits.MAX_ABSTRACT_LENGTH)); + return d; + }) + .collect(Collectors.toList()); } @Override @@ -314,11 +312,9 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List addOtherResultRels( final Document doc, - final KeyValue collectedFrom, - final DataInfo info, - final long lastUpdateTimestamp) { + final OafEntity entity) { - final String docId = createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false); + final String docId = entity.getId(); final List res = new ArrayList<>(); @@ -330,30 +326,26 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { final String otherId = createOpenaireId(50, originalId, false); final String type = ((Node) o).valueOf("@relationType"); - if (type.equalsIgnoreCase("IsSupplementTo")) { + if (type.equalsIgnoreCase(IS_SUPPLEMENT_TO)) { res .add( getRelation( - docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, - lastUpdateTimestamp)); + docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity)); res .add( getRelation( - otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, - lastUpdateTimestamp)); - } else if (type.equals("IsPartOf")) { - + otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity)); + } else if (type.equalsIgnoreCase(IS_PART_OF)) { res .add( getRelation( - docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, - lastUpdateTimestamp)); + docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity)); res .add( getRelation( - otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, - lastUpdateTimestamp)); + otherId, docId, RESULT_RESULT, PART, HAS_PARTS, entity)); } else { + // TODO catch more semantics } } } @@ -384,7 +376,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL' and @alternateIdentifierType != 'landingPage']", "@alternateIdentifierType", DNET_PID_TYPES, info)); - return Lists.newArrayList(res); + + return res + .stream() + .map(CleaningFunctions::normalizePidValue) + .collect(Collectors.toList()); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java index 9bf198c8b..bfc4fd6f1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java @@ -10,6 +10,7 @@ import org.apache.commons.lang3.StringUtils; import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.Qualifier; public class Vocabulary implements Serializable { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java index 334339d3b..32452bdc5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java @@ -7,6 +7,7 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala index d0df28b2d..822b16263 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala @@ -4,7 +4,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation} import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown} import eu.dnetlib.dhp.sx.ebi.EBIAggregator -import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal} import org.apache.commons.io.IOUtils import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.LoggerFactory @@ -18,38 +17,38 @@ object SparkSplitOafTODLIEntities { } - def main(args: Array[String]): Unit = { - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json"))) - val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass) - parser.parseArgument(args) - val workingPath: String = parser.get("workingPath") - logger.info(s"Working dir path = $workingPath") + def extract_dataset(spark:SparkSession, workingPath:String) :Unit = { + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset] + + val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf].repartition(4000) + + val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset].repartition(1000) + + + OAFDataset + .filter(s => s != null && s.isInstanceOf[DLIDataset]) + .map(s =>s.asInstanceOf[DLIDataset]) + .union(ebi_dataset) + .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) + .map(p => p._2) + .repartition(2000) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset") + + } + + def extract_publication(spark:SparkSession, workingPath:String) :Unit = { implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication] - implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset] - implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown] - implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] - - - - val spark:SparkSession = SparkSession - .builder() - .appName(SparkSplitOafTODLIEntities.getClass.getSimpleName) - .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer") - .master(parser.get("master")) - .getOrCreate() - - - val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf] - val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset] - val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication] - val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation] - + val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication].repartition(1000) OAFDataset @@ -60,20 +59,17 @@ object SparkSplitOafTODLIEntities { .groupByKey(_._1)(Encoders.STRING) .agg(EBIAggregator.getDLIPublicationAggregator().toColumn) .map(p => p._2) - .repartition(1000) + .repartition(2000) .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication") - OAFDataset - .filter(s => s != null && s.isInstanceOf[DLIDataset]) - .map(s =>s.asInstanceOf[DLIDataset]) - .union(ebi_dataset) - .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder)) - .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) - .map(p => p._2) - .repartition(1000) - .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset") + } + def extract_unknown(spark:SparkSession, workingPath:String) :Unit = { + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown] + + val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf] OAFDataset .filter(s => s != null && s.isInstanceOf[DLIUnknown]) @@ -82,9 +78,18 @@ object SparkSplitOafTODLIEntities { .groupByKey(_._1)(Encoders.STRING) .agg(EBIAggregator.getDLIUnknownAggregator().toColumn) .map(p => p._2) - .repartition(1000) .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown") + } + + + def extract_relations(spark:SparkSession, workingPath:String) :Unit = { + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] + + val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf] + val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation].repartition(2000) OAFDataset .filter(s => s != null && s.isInstanceOf[Relation]) @@ -94,9 +99,35 @@ object SparkSplitOafTODLIEntities { .groupByKey(_._1)(Encoders.STRING) .agg(EBIAggregator.getRelationAggregator().toColumn) .map(p => p._2) - .repartition(1000) + .repartition(4000) .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation") + } + + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json"))) + val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass) + parser.parseArgument(args) + + val workingPath: String = parser.get("workingPath") + val entity:String = parser.get("entity") + logger.info(s"Working dir path = $workingPath") + + val spark:SparkSession = SparkSession + .builder() + .appName(SparkSplitOafTODLIEntities.getClass.getSimpleName) + .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer") + .master(parser.get("master")) + .getOrCreate() + + + entity match { + case "publication" => extract_publication(spark, workingPath) + case "dataset" => extract_dataset(spark,workingPath) + case "relation" => extract_relations(spark, workingPath) + case "unknown" => extract_unknown(spark, workingPath) + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json index febcfc898..7878931af 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json @@ -1,4 +1,5 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the work dir path", "paramRequired": true} + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the work dir path", "paramRequired": true}, + {"paramName":"e", "paramLongName":"entity", "paramDescription": "the work dir path", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml index fabe7510b..9d06c42d6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml @@ -14,30 +14,103 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + ${jobTracker} ${nameNode} yarn-cluster cluster - Extract DLI Entities + Extract DLI Entities (Publication) eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities dhp-graph-mapper-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=5000 ${sparkExtraOPT} -mt yarn-cluster --workingPath${workingPath} + -epublication + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Extract DLI Entities (Dataset) + eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=5000 + ${sparkExtraOPT} + + -mt yarn-cluster + --workingPath${workingPath} + -edataset + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Extract DLI Entities (Unknown) + eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=5000 + ${sparkExtraOPT} + + -mt yarn-cluster + --workingPath${workingPath} + -eunknown + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + Extract DLI Entities (Relation) + eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=5000 + ${sparkExtraOPT} + + -mt yarn-cluster + --workingPath${workingPath} + -erelation diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java index 8a53c3a50..5ad8f2ac7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java @@ -7,8 +7,6 @@ import static org.mockito.Mockito.lenient; import java.io.IOException; import java.util.List; import java.util.Set; -import java.util.function.Predicate; -import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java new file mode 100644 index 000000000..a028738ea --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java @@ -0,0 +1,99 @@ + +package eu.dnetlib.dhp.oa.graph.raw; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; +import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class GenerateEntitiesApplicationTest { + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private VocabularyGroup vocs; + + @BeforeEach + public void setUp() throws IOException, ISLookUpException { + + lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); + lenient() + .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) + .thenReturn(synonyms()); + + vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); + } + + @Test + public void testMergeResult() throws IOException { + Result publication = getResult("oaf_record.xml", Publication.class); + Result dataset = getResult("odf_dataset.xml", Dataset.class); + Result software = getResult("odf_software.xml", Software.class); + Result orp = getResult("oaf_orp.xml", OtherResearchProduct.class); + + verifyMerge(publication, dataset, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + verifyMerge(dataset, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + + verifyMerge(publication, software, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + verifyMerge(software, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + + verifyMerge(publication, orp, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + verifyMerge(orp, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); + + verifyMerge(dataset, software, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); + verifyMerge(software, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); + + verifyMerge(dataset, orp, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); + verifyMerge(orp, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); + + verifyMerge(software, orp, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID); + verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID); + } + + protected void verifyMerge(Result publication, Result dataset, Class clazz, + String resultType) { + final Result merge = GenerateEntitiesApplication.mergeResults(publication, dataset); + assertTrue(clazz.isAssignableFrom(merge.getClass())); + assertEquals(resultType, merge.getResulttype().getClassid()); + } + + protected Result getResult(String xmlFileName, Class clazz) throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName)); + return new OdfToOafMapper(vocs, false) + .processMdRecord(xml) + .stream() + .filter(s -> clazz.isAssignableFrom(s.getClass())) + .map(s -> (Result) s) + .findFirst() + .get(); + } + + private List vocs() throws IOException { + return IOUtils + .readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); + } + + private List synonyms() throws IOException { + return IOUtils + .readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index af9fadb5a..1f5936ac3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -24,14 +24,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.Author; -import eu.dnetlib.dhp.schema.oaf.Dataset; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Oaf; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.schema.oaf.Software; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) @@ -71,7 +65,7 @@ public class MappersTest { assertValidId(p.getId()); - assertTrue(p.getOriginalId().size() == 1); + assertTrue(p.getOriginalId().size() == 2); assertEquals("10.3897/oneeco.2.e13718", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); @@ -123,22 +117,7 @@ public class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); - assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); - assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); + verifyRelations(p, r1, r2); // System.out.println(new ObjectMapper().writeValueAsString(p)); // System.out.println(new ObjectMapper().writeValueAsString(r1)); @@ -177,7 +156,7 @@ public class MappersTest { final Relation r2 = (Relation) list.get(2); assertValidId(d.getId()); - assertTrue(d.getOriginalId().size() == 1); + assertTrue(d.getOriginalId().size() == 2); assertEquals("oai:zenodo.org:3234526", d.getOriginalId().get(0)); assertValidId(d.getCollectedfrom().get(0).getKey()); assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); @@ -230,10 +209,19 @@ public class MappersTest { }); assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid()); + verifyRelations(d, r1, r2); + } + + private void verifyRelations(OafEntity e, Relation r1, Relation r2) { + assertEquals(e.getId(), r1.getSource()); + assertEquals(e.getId(), r2.getTarget()); + assertValidId(r1.getSource()); assertValidId(r1.getTarget()); assertValidId(r2.getSource()); assertValidId(r2.getTarget()); + assertValidId(r1.getCollectedfrom().get(0).getKey()); + assertValidId(r2.getCollectedfrom().get(0).getKey()); assertNotNull(r1.getDataInfo()); assertNotNull(r2.getDataInfo()); assertNotNull(r1.getDataInfo().getTrust()); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index f663d6095..3c0e2ce8e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -27,10 +27,10 @@ import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerAggregationTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerAggregationTest.scala index 4d83057f2..373683190 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerAggregationTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerAggregationTest.scala @@ -30,7 +30,7 @@ class SparkScholexplorerAggregationTest { implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication] - val spark: SparkSession = SparkSession.builder().appName("Test").master("local[*]").getOrCreate() + val spark: SparkSession = SparkSession.builder().appName("Test").master("local[*]").config("spark.driver.bindAddress", "127.0.0.1").getOrCreate() val ds: Dataset[DLIPublication] = spark.createDataset(spark.sparkContext.parallelize(s)).as[DLIPublication] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_orp.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_orp.xml new file mode 100644 index 000000000..c6b5d7b2e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_orp.xml @@ -0,0 +1,83 @@ + + +
+ pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2 + 10.3897/oneeco.2.e13718 + + + + + + 2020-03-23T00:20:51.392Z + 2020-03-23T00:26:59.078Z + pensoft_____ +
+ + Ecosystem Service capacity is higher in areas of multiple designation types + Nikolaidou,Charitini + Votsi,Nefta + Sgardelis,Steanos + Halley,John + Pantis,John + Tsiafouli,Maria + 2017 + The implementation of the Ecosystem Service (ES) concept into practice might be a challenging task as it has to take into account previous “traditional” policies and approaches that have evaluated nature and biodiversity differently. Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. This integration of “traditional” evaluation and designation and the “newer” ES concept forms a time- and cost-effective way to be adopted by stakeholders and policy-makers in order to start complying with new standards and demands for nature conservation and environmental management. + text/html + https://doi.org/10.3897/oneeco.2.e13718 + https://oneecosystem.pensoft.net/article/13718/ + eng + Pensoft Publishers + info:eu-repo/semantics/altIdentifier/eissn/2367-8194 + info:eu-repo/grantAgreement/EC/FP7/226852 + One Ecosystem 2: e13718 + One Ecosystem 2: e13718 + One Ecosystem 2: e13718 + Ecosystem Services hotspots + Natura 2000 + Quiet Protected Areas + Biodiversity + Agriculture + Elevation + Slope + Ecosystem Service trade-offs and synergies + cultural services + provisioning services + regulating services + supporting services + Research Artefact + 0020 + 2017-01-01 + corda_______::226852 + OPEN + + + 10.3897/oneeco.2.e13718 + https://oneecosystem.pensoft.net/article/13718/ + One Ecosystem + 0001 + + + + + http%3A%2F%2Fzookeys.pensoft.net%2Foai.php + 10.3897/oneeco.2.e13718 + 2017-09-08 + http://www.openarchives.org/OAI/2.0/oai_dc/ + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml index 05ca7d4ce..b287e9c88 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/pom.xml @@ -62,6 +62,10 @@ dhp-schemas ${project.version} + + org.apache.httpcomponents + httpmime + org.elasticsearch diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java new file mode 100644 index 000000000..95bea74a2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/MakeTar.java @@ -0,0 +1,111 @@ + +package eu.dnetlib.dhp.export.zenodo; + +import java.io.*; + +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class MakeTar implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(MakeTar.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + MakeTar.class + .getResourceAsStream( + "/eu/dnetlib/dhp/export/input_maketar_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String outputPath = parser.get("targetPath"); + log.info("hdfsPath: {}", outputPath); + + final String hdfsNameNode = parser.get("nameNode"); + log.info("nameNode: {}", hdfsNameNode); + + final String inputPath = parser.get("sourcePath"); + log.info("input path : {}", inputPath); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + makeTArArchive(fileSystem, inputPath, outputPath); + + } + + public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException { + + RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + + while (dir_iterator.hasNext()) { + LocatedFileStatus fileStatus = dir_iterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + + write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity); + } + + } + + private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name) + throws IOException { + + Path hdfsWritePath = new Path(outputPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath, true); + + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); + + TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream()); + + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(inputPath), true); + + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + if (!p_string.endsWith("_SUCCESS")) { + String name = p_string.substring(p_string.lastIndexOf("/") + 1); + TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz"); + entry.setSize(fileStatus.getLen()); + ar.putArchiveEntry(entry); + + InputStream is = fileSystem.open(fileStatus.getPath()); + + BufferedInputStream bis = new BufferedInputStream(is); + + int count; + byte data[] = new byte[1024]; + while ((count = bis.read(data, 0, data.length)) != -1) { + ar.write(data, 0, count); + } + bis.close(); + ar.closeArchiveEntry(); + + } + + } + + ar.close(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java new file mode 100644 index 000000000..1dcbf6ccc --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/zenodo/SendToZenodoHDFS.java @@ -0,0 +1,80 @@ + +package eu.dnetlib.dhp.export.zenodo; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.api.MissingConceptDoiException; +import eu.dnetlib.dhp.common.api.ZenodoAPIClient; + +public class SendToZenodoHDFS implements Serializable { + + private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); + + public static void main(final String[] args) throws Exception, MissingConceptDoiException { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SendToZenodoHDFS.class + .getResourceAsStream( + "/eu/dnetlib/dhp/export/upload_zenodo.json"))); + + parser.parseArgument(args); + + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("nameNode"); + final String access_token = parser.get("accessToken"); + final String connection_url = parser.get("connectionUrl"); + final String metadata = parser.get("metadata"); + final Boolean newDeposition = Boolean.valueOf(parser.get("newDeposition")); + final String concept_rec_id = Optional + .ofNullable(parser.get("conceptRecordId")) + .orElse(null); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(hdfsPath), true); + ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token); + if (newDeposition) { + zenodoApiClient.newDeposition(); + } else { + if (concept_rec_id == null) { + throw new MissingConceptDoiException("No concept record id has been provided"); + } + zenodoApiClient.newVersion(concept_rec_id); + } + + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + if (!p_string.endsWith("_SUCCESS")) { + // String tmp = p_string.substring(0, p_string.lastIndexOf("/")); + String name = p_string.substring(p_string.lastIndexOf("/") + 1); + log.info("Sending information for community: " + name); + FSDataInputStream inputStream = fileSystem.open(p); + zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); + + } + + } + + zenodoApiClient.sendMretadata(metadata); + zenodoApiClient.publish(); + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_maketar_parameters.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_maketar_parameters.json new file mode 100644 index 000000000..6d90ced2c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/input_maketar_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "n", + "paramLongName": "nameNode", + "paramDescription": "the Name Node", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the source path", + "paramRequired": true + }, + { + "paramName": "t", + "paramLongName": "targetPath", + "paramDescription": "the target path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/upload_zenodo.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/upload_zenodo.json new file mode 100644 index 000000000..66676005e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/export/upload_zenodo.json @@ -0,0 +1,45 @@ + +[ + { + "paramName":"nd", + "paramLongName":"newDeposition", + "paramDescription": "if it is a new deposition (true) or a new version (false)", + "paramRequired": true + }, + { + "paramName":"cri", + "paramLongName":"conceptRecordId", + "paramDescription": "The id of the concept record for a new version", + "paramRequired": false + }, + { + "paramName":"hdfsp", + "paramLongName":"hdfsPath", + "paramDescription": "the path of the folder tofind files to send to Zenodo", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "nameNode", + "paramDescription": "the name node", + "paramRequired": true + }, + { + "paramName": "at", + "paramLongName": "accessToken", + "paramDescription": "the access token for the deposition", + "paramRequired": false + }, + { + "paramName":"cu", + "paramLongName":"connectionUrl", + "paramDescription": "the url to connect to deposit", + "paramRequired": false + }, + { + "paramName":"m", + "paramLongName":"metadata", + "paramDescription": "metadata associated to the deposition", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/config-default.xml new file mode 100644 index 000000000..3b9aaca2a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/config-default.xml @@ -0,0 +1,48 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + oozie.wf.rerun.failnodes + false + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + spark2ExtraListeners + "com.cloudera.spark.lineage.NavigatorAppListener" + + + spark2SqlQueryExecutionListeners + "com.cloudera.spark.lineage.NavigatorQueryListener" + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml new file mode 100644 index 000000000..6d7056503 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/sx/zenodo/oozie_app/workflow.xml @@ -0,0 +1,53 @@ + + + + sourcePath + the source path + + + targetPath + the target path + + + metadata + the metadata + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.export.zenodo.MakeTar + -t${targetPath} + -n${nameNode} + -s${sourcePath} + + + + + + + + + eu.dnetlib.dhp.export.zenodo.SendToZenodoHDFS + --hdfsPath/user/dnet.scholexplorer/scholix/provision/scholix.tar/scholix-2020-10-16.tar + --nameNode${nameNode} + --accessTokenb6ddrY6b77WxcDEevn9gqVE5sL5sDNjdUijt75W3o7cQo5vpFFI48dMiu8Gv + --connectionUrlhttps://zenodo.org/api/deposit/depositions + --metadata${metadata} + --conceptRecordId1200252 + --newDepositionfalse + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala index cb04cf9e9..c62d169bc 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala @@ -3,14 +3,15 @@ package eu.dnetlib.dhp.export import java.time.LocalDateTime import java.time.format.DateTimeFormatter +import eu.dnetlib.dhp.provision.scholix.Scholix +import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary import eu.dnetlib.dhp.schema.oaf.Relation import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} - import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} import org.junit.jupiter.api.Test import scala.io.Source - +import scala.collection.JavaConverters._ class ExportDLITOOAFTest { val mapper = new ObjectMapper() @@ -22,12 +23,27 @@ class ExportDLITOOAFTest { } + def extractDatasources(s:Scholix):List[String]= { + s.getTarget.getCollectedFrom.asScala.map(c => c.getProvider.getName)(collection.breakOut) + } + + + def extractDatasources(s:ScholixSummary):List[String] = { + + s.getDatasources.asScala.map(c => c.getDatasourceName)(collection.breakOut) + + + } + + @Test def testMappingRele():Unit = { val r:Relation = new Relation r.setSource("60|fbff1d424e045eecf24151a5fe3aa738") r.setTarget("50|dedup_wf_001::ec409f09e63347d4e834087fe1483877") + r.setRelType("IsReferencedBy") + val r1 =DLIToOAF.convertDLIRelation(r) println(r1.getSource, r1.getTarget) diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java index b08e593f7..d404850eb 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java @@ -164,7 +164,7 @@ public class CreateRelatedEntitiesJob_phase1 { if (result.getTitle() != null && !result.getTitle().isEmpty()) { final StructuredProperty title = result.getTitle().stream().findFirst().get(); - title.setValue(StringUtils.left(title.getValue(), ProvisionConstants.MAX_TITLE_LENGTH)); + title.setValue(StringUtils.left(title.getValue(), ModelHardLimits.MAX_TITLE_LENGTH)); re.setTitle(title); } @@ -178,7 +178,7 @@ public class CreateRelatedEntitiesJob_phase1 { .getInstance() .stream() .filter(Objects::nonNull) - .limit(ProvisionConstants.MAX_INSTANCES) + .limit(ModelHardLimits.MAX_INSTANCES) .collect(Collectors.toList())); } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java index 7e175121e..e32fe020b 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java @@ -240,15 +240,15 @@ public class CreateRelatedEntitiesJob_phase2 { List refs = r .getExternalReference() .stream() - .limit(ProvisionConstants.MAX_EXTERNAL_ENTITIES) + .limit(ModelHardLimits.MAX_EXTERNAL_ENTITIES) .collect(Collectors.toList()); r.setExternalReference(refs); } if (r.getAuthor() != null) { List authors = Lists.newArrayList(); for (Author a : r.getAuthor()) { - a.setFullname(StringUtils.left(a.getFullname(), ProvisionConstants.MAX_AUTHOR_FULLNAME_LENGTH)); - if (authors.size() < ProvisionConstants.MAX_AUTHORS || hasORCID(a)) { + a.setFullname(StringUtils.left(a.getFullname(), ModelHardLimits.MAX_AUTHOR_FULLNAME_LENGTH)); + if (authors.size() < ModelHardLimits.MAX_AUTHORS || hasORCID(a)) { authors.add(a); } } @@ -260,7 +260,7 @@ public class CreateRelatedEntitiesJob_phase2 { .stream() .filter(Objects::nonNull) .map(d -> { - d.setValue(StringUtils.left(d.getValue(), ProvisionConstants.MAX_ABSTRACT_LENGTH)); + d.setValue(StringUtils.left(d.getValue(), ModelHardLimits.MAX_ABSTRACT_LENGTH)); return d; }) .collect(Collectors.toList()); @@ -272,10 +272,10 @@ public class CreateRelatedEntitiesJob_phase2 { .stream() .filter(Objects::nonNull) .map(t -> { - t.setValue(StringUtils.left(t.getValue(), ProvisionConstants.MAX_TITLE_LENGTH)); + t.setValue(StringUtils.left(t.getValue(), ModelHardLimits.MAX_TITLE_LENGTH)); return t; }) - .limit(ProvisionConstants.MAX_TITLES) + .limit(ModelHardLimits.MAX_TITLES) .collect(Collectors.toList()); r.setTitle(titles); } diff --git a/dhp-workflows/dhp-workflow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_prod_construction.xml b/dhp-workflows/dhp-workflow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_prod_construction.xml index 047433320..4eab12c73 100644 --- a/dhp-workflows/dhp-workflow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_prod_construction.xml +++ b/dhp-workflows/dhp-workflow-profiles/src/main/resources/eu/dnetlib/dhp/wf/profiles/graph_prod_construction.xml @@ -44,6 +44,7 @@ + Set the target path to store the RAW graph @@ -54,31 +55,45 @@ + + + Set the target path to store the first CLEANED graph + + firstCleanedGraphPath + /tmp/prod_provision/graph/02_graph_first_cleaned + + + + + + Set the target path to store the DEDUPED graph dedupGraphPath - /tmp/beta_provision/graph/02_graph_dedup + /tmp/beta_provision/graph/03_graph_dedup + Set the target path to store the INFERRED graph inferredGraphPath - /tmp/beta_provision/graph/03_graph_inferred + /tmp/beta_provision/graph/04_graph_inferred + Set the target path to store the CONSISTENCY graph consistentGraphPath - /tmp/beta_provision/graph/04_graph_consistent + /tmp/beta_provision/graph/05_graph_consistent @@ -89,7 +104,7 @@ Set the target path to store the ORCID enriched graph orcidGraphPath - /tmp/beta_provision/graph/05_graph_orcid + /tmp/beta_provision/graph/06_graph_orcid @@ -100,7 +115,7 @@ Set the target path to store the BULK TAGGED graph bulkTaggingGraphPath - /tmp/beta_provision/graph/06_graph_bulktagging + /tmp/beta_provision/graph/07_graph_bulktagging @@ -111,7 +126,7 @@ Set the target path to store the AFFILIATION from INSTITUTIONAL REPOS graph affiliationGraphPath - /tmp/beta_provision/graph/07_graph_affiliation + /tmp/beta_provision/graph/08_graph_affiliation @@ -122,7 +137,7 @@ Set the target path to store the COMMUNITY from SELECTED SOURCES graph communityOrganizationGraphPath - /tmp/beta_provision/graph/08_graph_comunity_organization + /tmp/beta_provision/graph/09_graph_comunity_organization @@ -133,7 +148,7 @@ Set the target path to store the FUNDING from SEMANTIC RELATION graph fundingGraphPath - /tmp/beta_provision/graph/09_graph_funding + /tmp/beta_provision/graph/10_graph_funding @@ -144,7 +159,7 @@ Set the target path to store the COMMUNITY from SEMANTIC RELATION graph communitySemRelGraphPath - /tmp/beta_provision/graph/10_graph_comunity_sem_rel + /tmp/beta_provision/graph/11_graph_comunity_sem_rel @@ -155,7 +170,7 @@ Set the target path to store the COUNTRY enriched graph countryGraphPath - /tmp/beta_provision/graph/11_graph_country + /tmp/beta_provision/graph/12_graph_country @@ -166,7 +181,7 @@ Set the target path to store the CLEANED graph cleanedGraphPath - /tmp/beta_provision/graph/12_graph_cleaned + /tmp/beta_provision/graph/13_graph_cleaned @@ -177,7 +192,7 @@ Set the target path to store the blacklisted graph blacklistedGraphPath - /tmp/beta_provision/graph/13_graph_blacklisted + /tmp/beta_provision/graph/14_graph_blacklisted @@ -324,6 +339,31 @@ build-report + + + + + + + clean the properties in the graph typed as Qualifier according to the vocabulary indicated in schemeid + + executeOozieJob + IIS + + { + 'graphInputPath' : 'rawGraphPath', + 'graphOutputPath': 'firstCleanedGraphPath', + 'isLookupUrl': 'isLookUpUrl' + } + + + { + 'oozie.wf.application.path' : '/lib/dnet/oa/graph/clean/oozie_app', + 'workingPath' : '/tmp/beta_provision/working_dir/first_clean' + } + + build-report + @@ -337,7 +377,7 @@ { 'actionSetId' : 'dedupConfig', - 'graphBasePath' : 'rawGraphPath', + 'graphBasePath' : 'firstCleanedGraphPath', 'dedupGraphPath': 'dedupGraphPath', 'isLookUpUrl' : 'isLookUpUrl' }