From e5da4ee9b18842bc46a3a0a080fef943b051d3fa Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 4 Nov 2020 15:02:02 +0100 Subject: [PATCH] dedup workflow using the common PidComparator --- .../oaf/utils/OrganizationPidComparator.java | 27 +++ .../dhp/schema/oaf/utils/PidComparator.java | 64 +------ .../dnetlib/dhp/schema/oaf/utils/PidType.java | 13 +- .../schema/oaf/utils/ResultPidComparator.java | 57 +++++++ .../dhp/oa/dedup/DedupRecordFactory.java | 4 +- .../eu/dnetlib/dhp/oa/dedup/IdGenerator.java | 118 +++---------- .../dhp/oa/dedup/model/Identifier.java | 159 +++++++++--------- .../dnetlib/dhp/oa/dedup/model/PidType.java | 17 -- .../dhp/oa/dedup/EntityMergerTest.java | 106 ++++++------ .../dnetlib/dhp/oa/dedup/IdGeneratorTest.java | 111 ++++-------- .../dedup/json/publication_idgeneration.json | 6 +- .../dedup/json/publication_idgeneration2.json | 3 + .../dedup/json/publication_idgeneration3.json | 3 + .../dhp/dedup/json/publication_merge.json | 2 +- .../dhp/dedup/json/publication_merge2.json | 7 +- .../dhp/dedup/json/publication_merge3.json | 6 +- .../dhp/dedup/json/software_merge.json | 6 +- 17 files changed, 304 insertions(+), 405 deletions(-) create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java delete mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/model/PidType.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration2.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration3.json 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 index d0a8f87ce..34ce5563f 100644 --- 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 @@ -45,70 +45,10 @@ public class PidComparator 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-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 dcbeb57f5..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 @@ -2,94 +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 @@ -97,50 +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 6089babf7..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 @@ -7,97 +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())); + .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 @@ -106,14 +66,22 @@ public class IdGeneratorTest { String id2 = IdGenerator.generate(bestIds3, "50|defaultID"); System.out - .println("id list 2 = " + bestIds2.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList())); + .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())); + .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) { @@ -127,7 +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(); } @@ -140,23 +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/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": 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"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": 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"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", 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"provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "http://creativecommons.org/licenses/by-nc-nd/4.0/"}, "url": ["http://dx.doi.org/10.1016/j.nicl.2015.11.006"], "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, 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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. 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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. 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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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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. 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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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. 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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