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[#6282 open access status in the Graph] Result.Instance.accessRight defined with dedicated data type that includes the open access color.

This commit is contained in:
Claudio Atzori 2021-01-12 15:36:38 +01:00
parent bbe1a7c69a
commit d525785497
18 changed files with 217 additions and 99 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

40
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java
View File

@ -84,7 +84,7 @@ public class CleaningFunctions {
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
}
} else if (value instanceof Relation) {
// nothing to clean here
@ -152,12 +152,14 @@ public class CleaningFunctions {
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r
.setResourcetype(
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
}
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
i
.setAccessright(
accessRight(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
}
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
@ -203,6 +205,7 @@ public class CleaningFunctions {
p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
return p;
})
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.collect(
Collectors
.toMap(
@ -248,35 +251,18 @@ public class CleaningFunctions {
}
}
private static AccessRight accessRight(String classid, String classname, String scheme) {
return OafMapperUtils
.accessRight(
classid, classname, scheme, scheme);
}
private static Qualifier qualifier(String classid, String classname, String scheme) {
return OafMapperUtils
.qualifier(
classid, classname, scheme, scheme);
}
/**
* Utility method that filter PID values on a per-type basis.
* @param pid the PID whose value will be checked.
* @return true the PID containing the normalised value.
*/
private static boolean filterPid(StructuredProperty pid) {
String value = Optional
.ofNullable(pid.getValue())
.map(s -> StringUtils.replaceAll(s, "\\s", ""))
.orElse("");
if (StringUtils.isBlank(value)) {
return false;
}
switch (pid.getQualifier().getClassid()) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.startsWith("10.");
default:
return true;
}
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
@ -291,7 +277,7 @@ public class CleaningFunctions {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_PREFIX_REGEX, "10."));
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX_REGEX, ""));
break;
}
return pid;

23
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java
View File

@ -105,6 +105,29 @@ public class OafMapperUtils {
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final String schemename) {
return accessRight(classid, classname, schemeid, schemename, null);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final String schemename,
final OAStatus oaStatus) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(classid);
accessRight.setClassname(classname);
accessRight.setSchemeid(schemeid);
accessRight.setSchemename(schemename);
accessRight.setOaStatus(oaStatus);
return accessRight;
}
public static Qualifier qualifier(
final String classid,
final String classname,

5
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/LicenseComparator.java → dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/AccessRightComparator.java
View File

@ -3,12 +3,13 @@ package eu.dnetlib.dhp.schema.common;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class LicenseComparator implements Comparator<Qualifier> {
public class AccessRightComparator<T extends Qualifier> implements Comparator<T> {
@Override
public int compare(Qualifier left, Qualifier right) {
public int compare(T left, T right) {
if (left == null && right == null)
return 0;

3
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -20,7 +20,8 @@ public class ModelConstants {
public static final String DNET_ACCESS_MODES = "dnet:access_modes";
public static final String DNET_LANGUAGES = "dnet:languages";
public static final String DNET_PID_TYPES = "dnet:pid_types";
public static final String DNET_DATA_CITE_DATE = "dnet:dataCite_date";
public static final String DNET_DATACITE_DATE = "dnet:dataCite_date";
public static final String DNET_DATACITE_TITLE = "dnet:dataCite_title";
public static final String DNET_DATA_CITE_RESOURCE = "dnet:dataCite_resource";
public static final String DNET_PROVENANCE_ACTIONS = "dnet:provenanceActions";
public static final String DNET_COUNTRY_TYPE = "dnet:countries";

48
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/AccessRight.java Normal file
View File

@ -0,0 +1,48 @@
package eu.dnetlib.dhp.schema.oaf;
import java.util.Optional;
/**
* This class models the access rights of research products.
*/
public class AccessRight extends Qualifier {
private OAStatus oaStatus;
public OAStatus getOaStatus() {
return oaStatus;
}
public void setOaStatus(OAStatus oaStatus) {
this.oaStatus = oaStatus;
}
public String toComparableString() {
String s = super.toComparableString();
return Optional
.ofNullable(getOaStatus())
.map(x -> s + "::" + x.toString())
.orElse(s);
}
@Override
public int hashCode() {
return toComparableString().hashCode();
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
Qualifier other = (Qualifier) obj;
return toComparableString().equals(other.toComparableString());
}
}

6
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java
View File

@ -8,7 +8,7 @@ public class Instance implements Serializable {
private Field<String> license;
private Qualifier accessright;
private AccessRight accessright;
private Qualifier instancetype;
@ -41,11 +41,11 @@ public class Instance implements Serializable {
this.license = license;
}
public Qualifier getAccessright() {
public AccessRight getAccessright() {
return accessright;
}
public void setAccessright(Qualifier accessright) {
public void setAccessright(AccessRight accessright) {
this.accessright = accessright;
}

13
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/OAStatus.java Normal file
View File

@ -0,0 +1,13 @@
package eu.dnetlib.dhp.schema.oaf;
/**
* This Enum models the OpenAccess status, currently including only the values from Unpaywall
*
* https://support.unpaywall.org/support/solutions/articles/44001777288-what-do-the-types-of-oa-status-green-gold-hybrid-and-bronze-mean-
*/
public enum OAStatus {
gold, green, hybrid, bronze
}

5
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java
View File

@ -2,12 +2,11 @@
package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
public class Result extends OafEntity implements Serializable {
@ -248,7 +247,7 @@ public class Result extends OafEntity implements Serializable {
instance = mergeLists(instance, r.getInstance());
if (r.getBestaccessright() != null
&& new LicenseComparator().compare(r.getBestaccessright(), bestaccessright) < 0)
&& new AccessRightComparator().compare(r.getBestaccessright(), bestaccessright) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0)

11
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/OafUtils.scala
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dhp.schema.scholexplorer
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Field, KeyValue, Qualifier, StructuredProperty}
object OafUtils {
@ -39,6 +39,15 @@ object OafUtils {
q
}
def createAccessRight(classId: String, className: String, schemeId: String, schemeName: String): AccessRight = {
val accessRight: AccessRight = new AccessRight
accessRight.setClassid(classId)
accessRight.setClassname(className)
accessRight.setSchemeid(schemeId)
accessRight.setSchemename(schemeName)
accessRight
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]

13
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/migration/ProtoConverter.java
View File

@ -82,7 +82,7 @@ public class ProtoConverter implements Serializable {
private static Instance convertInstance(ResultProtos.Result.Instance ri) {
final Instance i = new Instance();
i.setAccessright(mapQualifier(ri.getAccessright()));
i.setAccessright(mapAccessRight(ri.getAccessright()));
i.setCollectedfrom(mapKV(ri.getCollectedfrom()));
i.setDateofacceptance(mapStringField(ri.getDateofacceptance()));
i.setDistributionlocation(ri.getDistributionlocation());
@ -510,7 +510,7 @@ public class ProtoConverter implements Serializable {
.map(i -> i.getAccessright())
.min(new LicenseComparator());
final Qualifier rights = min.isPresent() ? mapQualifier(min.get()) : new Qualifier();
final Qualifier rights = min.isPresent() ? mapAccessRight(min.get()) : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
@ -579,6 +579,15 @@ public class ProtoConverter implements Serializable {
return qualifier;
}
public static AccessRight mapAccessRight(FieldTypeProtos.Qualifier q) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(q.getClassid());
accessRight.setClassname(q.getClassname());
accessRight.setSchemeid(q.getSchemeid());
accessRight.setSchemename(q.getSchemename());
return accessRight;
}
public static Country mapQualifierAsCountry(FieldTypeProtos.Qualifier q) {
final Country c = new Country();
c.setClassid(q.getClassid());

36
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -1,10 +1,11 @@
package eu.dnetlib.doiboost
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
@ -125,13 +126,12 @@ object DoiBoostMappingUtil {
}
def getOpenAccessQualifier():Qualifier = {
createQualifier("OPEN","Open Access","dnet:access_modes", "dnet:access_modes")
def getOpenAccessQualifier():AccessRight = {
OafUtils.createAccessRight("OPEN","Open Access","dnet:access_modes", "dnet:access_modes")
}
def getRestrictedQualifier():Qualifier = {
createQualifier("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes")
def getRestrictedQualifier():AccessRight = {
OafUtils.createAccessRight("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes")
}
@ -260,7 +260,7 @@ object DoiBoostMappingUtil {
di.setInferred(false)
di.setInvisible(false)
di.setTrust(trust)
di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di.setProvenanceaction(OafUtils.createQualifier("sysimport:actionset", "dnet:provenanceActions"))
di
}
@ -268,7 +268,7 @@ object DoiBoostMappingUtil {
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setQualifier(OafUtils.createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp
@ -278,7 +278,7 @@ object DoiBoostMappingUtil {
def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
sp.setQualifier(OafUtils.createQualifier(classId,className, schemeId, schemeName))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
@ -287,7 +287,7 @@ object DoiBoostMappingUtil {
def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setQualifier(OafUtils.createQualifier(classId, schemeId))
sp.setValue(value)
sp
@ -297,7 +297,7 @@ object DoiBoostMappingUtil {
def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setQualifier(OafUtils.createQualifier(classId, schemeId))
sp.setValue(value)
sp.setDataInfo(dataInfo)
sp
@ -350,20 +350,6 @@ object DoiBoostMappingUtil {
}
def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = {
val q = new Qualifier
q.setClassid(clsName)
q.setClassname(clsValue)
q.setSchemeid(schName)
q.setSchemename(schValue)
q
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch, sch)
}
def asField[T](value: T): Field[T] = {
val tmp = new Field[T]
tmp.setValue(value)

8
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -15,6 +15,8 @@ import scala.collection.JavaConverters._
import scala.collection.mutable
import scala.util.matching.Regex
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils;
case class CrossrefDT(doi: String, json:String, timestamp: Long) {}
case class mappingAffiliation(name: String) {}
@ -179,14 +181,14 @@ case object Crossref2Oaf {
if(has_review != JNothing) {
instance.setRefereed(
createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels"))
OafUtils.createQualifier("0001", "peerReviewed", "dnet:review_levels", "dnet:review_levels"))
}
instance.setAccessright(getRestrictedQualifier())
result.setInstance(List(instance).asJava)
instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
result.setResourcetype(createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource"))
instance.setInstancetype(OafUtils.createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
result.setResourcetype(OafUtils.createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource"))
instance.setCollectedfrom(createCrossrefCollectedFrom())
if (StringUtils.isNotBlank(issuedDate)) {

44
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java
View File

@ -18,6 +18,7 @@ import com.google.gson.*;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.scholexplorer.OafUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility;
import eu.dnetlib.doiboost.orcidnodoi.util.Pair;
@ -102,8 +103,6 @@ public class PublicationToOaf implements Serializable {
}
}
public static final String PID_TYPES = "dnet:pid_types";
public Oaf generatePublicationActionsFromJson(final String json) {
try {
if (parsedPublications != null) {
@ -138,8 +137,8 @@ public class PublicationToOaf implements Serializable {
mapQualifier(
"sysimport:actionset:orcidworks-no-doi",
"sysimport:actionset:orcidworks-no-doi",
"dnet:provenanceActions",
"dnet:provenanceActions"));
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS));
publication.setDataInfo(dataInfo);
publication.setLastupdatetimestamp(new Date().getTime());
@ -159,7 +158,9 @@ public class PublicationToOaf implements Serializable {
publication
.getExternalReference()
.add(
convertExtRef(extId, classid, classname, "dnet:pid_types", "dnet:pid_types"));
convertExtRef(
extId, classid, classname, ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES));
}
});
@ -182,7 +183,8 @@ public class PublicationToOaf implements Serializable {
}
return null;
}
Qualifier q = mapQualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
Qualifier q = mapQualifier(
"main title", "main title", ModelConstants.DNET_DATACITE_TITLE, ModelConstants.DNET_DATACITE_TITLE);
publication
.setTitle(
titles
@ -214,7 +216,10 @@ public class PublicationToOaf implements Serializable {
final String type = getStringValue(rootElement, "type");
String cobjValue = "";
if (StringUtils.isNotBlank(type)) {
publication.setResourcetype(mapQualifier(type, type, "dnet:dataCite_resource", "dnet:dataCite_resource"));
publication
.setResourcetype(
mapQualifier(
type, type, ModelConstants.DNET_DATA_CITE_RESOURCE, ModelConstants.DNET_DATA_CITE_RESOURCE));
final String typeValue = typologiesMapping.get(type).get("value");
cobjValue = typologiesMapping.get(type).get("cobj");
@ -239,12 +244,21 @@ public class PublicationToOaf implements Serializable {
instance.setCollectedfrom(createCollectedFrom());
// Adding accessright
instance.setAccessright(mapQualifier("UNKNOWN", "UNKNOWN", "dnet:access_modes", "dnet:access_modes"));
instance
.setAccessright(
OafUtils
.createAccessRight(
ModelConstants.UNKNOWN,
ModelConstants.UNKNOWN,
ModelConstants.DNET_ACCESS_MODES,
ModelConstants.DNET_ACCESS_MODES));
// Adding type
instance
.setInstancetype(
mapQualifier(cobjValue, typeValue, "dnet:publication_resource", "dnet:publication_resource"));
mapQualifier(
cobjValue, typeValue, ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
publication.setInstance(Arrays.asList(instance));
} else {
@ -266,7 +280,10 @@ public class PublicationToOaf implements Serializable {
}
String classValue = getDefaultResulttype(cobjValue);
publication
.setResulttype(mapQualifier(classValue, classValue, "dnet:result_typologies", "dnet:result_typologies"));
.setResulttype(
mapQualifier(
classValue, classValue, ModelConstants.DNET_RESULT_TYPOLOGIES,
ModelConstants.DNET_RESULT_TYPOLOGIES));
if (enrichedPublications != null) {
enrichedPublications.add(1);
}
@ -373,7 +390,8 @@ public class PublicationToOaf implements Serializable {
if (addToDateOfAcceptance) {
publication.setDateofacceptance(mapStringField(pubDate, null));
}
Qualifier q = mapQualifier(dictionaryKey, dictionaryKey, "dnet:dataCite_date", "dnet:dataCite_date");
Qualifier q = mapQualifier(
dictionaryKey, dictionaryKey, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE);
publication
.setRelevantdate(
Arrays
@ -535,8 +553,8 @@ public class PublicationToOaf implements Serializable {
mapQualifier(
"sysimport:crosswalk:entityregistry",
"Harvested",
"dnet:provenanceActions",
"dnet:provenanceActions"));
ModelConstants.DNET_PROVENANCE_ACTIONS,
ModelConstants.DNET_PROVENANCE_ACTIONS));
sp.setDataInfo(dataInfo);
return sp;
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java
View File

@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
@ -22,6 +23,7 @@ public class CleaningRuleMap extends HashMap<Class, SerializableConsumer<Object>
public static CleaningRuleMap create(VocabularyGroup vocabularies) {
CleaningRuleMap mapping = new CleaningRuleMap();
mapping.put(Qualifier.class, o -> cleanQualifier(vocabularies, (Qualifier) o));
mapping.put(AccessRight.class, o -> cleanQualifier(vocabularies, (AccessRight) o));
mapping.put(Country.class, o -> {
final Country c = (Country) o;
if (StringUtils.isBlank(c.getSchemeid())) {

24
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -4,7 +4,13 @@ package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
import java.util.*;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
@ -15,7 +21,7 @@ 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.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
@ -418,6 +424,20 @@ public abstract class AbstractMdRecordToOafMapper {
}
protected AccessRight prepareAccessRight(final Node node, final String xpath, final String schemeId) {
Qualifier qualifier = prepareQualifier(node.valueOf(xpath).trim(), schemeId);
AccessRight accessRight = new AccessRight();
accessRight.setClassid(qualifier.getClassid());
accessRight.setClassname(qualifier.getClassname());
accessRight.setSchemeid(qualifier.getSchemeid());
accessRight.setSchemename(qualifier.getSchemename());
// TODO set the OAStatus
// accessRight.setOaStatus(...);
return accessRight;
}
protected Qualifier prepareQualifier(final Node node, final String xpath, final String schemeId) {
return prepareQualifier(node.valueOf(xpath).trim(), schemeId);
}

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -128,7 +128,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
.setAccessright(prepareAccessRight(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
instance

27
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
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@ -102,10 +102,11 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE));
instance.setCollectedfrom(collectedfrom);
instance.setHostedby(hostedby);
instance.setPid(prepareResultPids(doc, info));
instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
instance
.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
.setAccessright(prepareAccessRight(doc, "//oaf:accessrights", DNET_ACCESS_MODES));
instance.setLicense(field(doc.valueOf("//oaf:license"), info));
instance.setRefereed(prepareQualifier(doc, "//oaf:refereed", DNET_REVIEW_LEVELS));
instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
@ -150,14 +151,20 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
for (final Object o : doc.selectNodes("//datacite:date")) {
final String dateType = ((Node) o).valueOf("@dateType");
if (StringUtils.isBlank(dateType)
&& !dateType.equalsIgnoreCase("Accepted")
&& !dateType.equalsIgnoreCase("Issued")
&& !dateType.equalsIgnoreCase("Updated")
&& !dateType.equalsIgnoreCase("Available")) {
|| (!dateType.equalsIgnoreCase("Accepted")
&& !dateType.equalsIgnoreCase("Issued")
&& !dateType.equalsIgnoreCase("Updated")
&& !dateType.equalsIgnoreCase("Available"))) {
res
.add(
structuredProperty(
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATACITE_DATE, DNET_DATACITE_DATE,
info));
} else {
res
.add(
structuredProperty(
((Node) o).getText(), dateType, dateType, DNET_DATACITE_DATE, DNET_DATACITE_DATE,
info));
}
}
@ -186,13 +193,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@Override
protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo 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());
return prepareListFields(doc, "//datacite:description[@descriptionType='Abstract']", info);
}
@Override

6
dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala
View File

@ -258,7 +258,7 @@ object DLIToOAF {
result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue))
result.setPublisher(inputPublication.getPublisher)
result.setSource(inputPublication.getSource)
result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
result.setBestaccessright(createAccessRight("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue)
if (dois.isEmpty)
@ -337,7 +337,7 @@ object DLIToOAF {
result.setDateofacceptance(asField(d.getRelevantdate.get(0).getValue))
result.setPublisher(d.getPublisher)
result.setSource(d.getSource)
result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
result.setBestaccessright(createAccessRight("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
val instance_urls = if (fpids.head.length < 5) s"https://www.rcsb.org/structure/${fpids.head}" else s"https://dx.doi.org/${fpids.head}"
@ -373,7 +373,7 @@ object DLIToOAF {
if (originalInstance != null && originalInstance.getHostedby != null)
i.setHostedby(originalInstance.getHostedby)
i.setAccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
i.setAccessright(createAccessRight("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
i.setDateofacceptance(doa)
i