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dnet-hadoop
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-Renamed RelationInverse into RelationLabel. 

-Removed findRelation from ModelSupport
-code formatted
This commit is contained in:
Sandro La Bruzzo 2023-04-28 11:44:28 +02:00
parent 8c9a77d7eb
commit f8f4b9a018
17 changed files with 502 additions and 660 deletions
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38
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java
View File

@ -9,13 +9,13 @@ import java.util.concurrent.TimeUnit;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import org.jetbrains.annotations.NotNull;
import com.google.gson.Gson;
import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList;
import okhttp3.*;
import org.jetbrains.annotations.NotNull;
public class ZenodoAPIClient implements Serializable {
@ -80,7 +80,7 @@ public class ZenodoAPIClient implements Serializable {
int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
@ -115,7 +115,7 @@ public class ZenodoAPIClient implements Serializable {
}
int responseCode = conn.getResponseCode();
if(! checkOKStatus(responseCode)){
if (!checkOKStatus(responseCode)) {
throw new IOException("Unexpected code " + responseCode + getBody(conn));
}
@ -126,7 +126,7 @@ public class ZenodoAPIClient implements Serializable {
private String getBody(HttpURLConnection conn) throws IOException {
String body = "{}";
try (BufferedReader br = new BufferedReader(
new InputStreamReader(conn.getInputStream(), "utf-8"))) {
new InputStreamReader(conn.getInputStream(), "utf-8"))) {
StringBuilder response = new StringBuilder();
String responseLine = null;
while ((responseLine = br.readLine()) != null) {
@ -155,7 +155,6 @@ public class ZenodoAPIClient implements Serializable {
conn.setDoOutput(true);
conn.setRequestMethod("PUT");
try (OutputStream os = conn.getOutputStream()) {
byte[] input = metadata.getBytes("utf-8");
os.write(input, 0, input.length);
@ -164,19 +163,18 @@ public class ZenodoAPIClient implements Serializable {
final int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + getBody(conn));
return responseCode;
}
private boolean checkOKStatus(int responseCode) {
private boolean checkOKStatus(int responseCode) {
if(HttpURLConnection.HTTP_OK != responseCode ||
HttpURLConnection.HTTP_CREATED != responseCode)
return true ;
if (HttpURLConnection.HTTP_OK != responseCode ||
HttpURLConnection.HTTP_CREATED != responseCode)
return true;
return false;
}
@ -233,7 +231,6 @@ public class ZenodoAPIClient implements Serializable {
conn.setDoOutput(true);
conn.setRequestMethod("POST");
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
@ -245,7 +242,7 @@ public class ZenodoAPIClient implements Serializable {
int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
@ -290,13 +287,12 @@ public class ZenodoAPIClient implements Serializable {
int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
bucket = zenodoModel.getLinks().getBucket();
return responseCode;
}
@ -331,22 +327,16 @@ public class ZenodoAPIClient implements Serializable {
conn.setDoOutput(true);
conn.setRequestMethod("GET");
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
return body;
}
private String getBucket(String inputUurl) throws IOException {
@ -363,15 +353,13 @@ public class ZenodoAPIClient implements Serializable {
int responseCode = conn.getResponseCode();
conn.disconnect();
if(!checkOKStatus(responseCode))
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
return zenodoModel.getLinks().getBucket();
}
}

1
dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
View File

@ -86,7 +86,6 @@ public class ModelConstants {
public static final Qualifier PROVENANCE_ACTION_SET_QUALIFIER = qualifier(
SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, DNET_PROVENANCE_ACTIONS);
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";

44
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java
View File

@ -2,16 +2,12 @@
package eu.dnetlib.dhp.schema.oaf.common;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.text.ParseException;
import java.util.Date;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.*;
import java.util.function.Function;
import org.apache.commons.codec.binary.Hex;
@ -96,26 +92,6 @@ public class ModelSupport {
idPrefixEntity.put("50", "result");
}
private static void set(Map<String, RelationInverse> relationInverseMap, String relType, String subRelType,
String relClass, String inverseRelClass) {
relationInverseMap
.put(
rel(relType, subRelType, relClass), new RelationInverse()
.setInverseRelClass(inverseRelClass)
.setRelClass(relClass)
.setRelType(relType)
.setSubReltype(subRelType));
if (!relClass.equals(inverseRelClass)) {
relationInverseMap
.put(
rel(relType, subRelType, inverseRelClass), new RelationInverse()
.setInverseRelClass(relClass)
.setRelClass(inverseRelClass)
.setRelType(relType)
.setSubReltype(subRelType));
}
}
/**
* Helper method: combines the relation attributes
* @param relType
@ -127,6 +103,24 @@ public class ModelSupport {
return String.format("%s_%s_%s", relType, subRelType, relClass);
}
/**
* Helper method: deserialize the relation attributes serialized with rel
* @param relType
* @param subRelType
* @param relClass
* @return
*/
public static RelationLabel unRel(String deserialization) {
final String[] s = deserialization.split("_");
if (s!= null && s.length==3) {
final Relation.RELTYPE currentRelType = Relation.RELTYPE.valueOf(s[0]);
final Relation.SUBRELTYPE currentSubRelType = Relation.SUBRELTYPE.valueOf(s[1]);
final Relation.RELCLASS currentRelClass = Relation.RELCLASS.valueOf(s[2]);
return new RelationLabel(currentRelClass, currentRelType, currentSubRelType);
}
throw new IllegalArgumentException("Invalid relationship format for "+ deserialization);
}
private static final String schemeTemplate = "dnet:%s_%s_relations";
public static final String DATE_FORMAT = "yyyy-MM-dd";

46
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/RelationInverse.java
View File

@ -1,46 +0,0 @@
package eu.dnetlib.dhp.schema.oaf.common;
public class RelationInverse {
private String relClass;
private String inverseRelClass;
private String relType;
private String subReltype;
public String getRelType() {
return relType;
}
public RelationInverse setRelType(String relType) {
this.relType = relType;
return this;
}
public String getSubReltype() {
return subReltype;
}
public RelationInverse setSubReltype(String subReltype) {
this.subReltype = subReltype;
return this;
}
public String getRelClass() {
return relClass;
}
public RelationInverse setRelClass(String relClass) {
this.relClass = relClass;
return this;
}
public String getInverseRelClass() {
return inverseRelClass;
}
public RelationInverse setInverseRelClass(String inverseRelClass) {
this.inverseRelClass = inverseRelClass;
return this;
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/RelationLabel.java Normal file
View File

@ -0,0 +1,33 @@
package eu.dnetlib.dhp.schema.oaf.common;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class RelationLabel {
private final Relation.RELCLASS relClass;
private final Relation.RELTYPE relType;
private final Relation.SUBRELTYPE subReltype;
public RelationLabel(Relation.RELCLASS relClass, Relation.RELTYPE relType, Relation.SUBRELTYPE subReltype) {
this.relClass = relClass;
this.relType = relType;
this.subReltype = subReltype;
}
public RelationLabel inverse() {
return new RelationLabel(relClass.getInverse(), relType, subReltype);
}
public Relation.RELTYPE getRelType() {
return relType;
}
public Relation.SUBRELTYPE getSubReltype() {
return subReltype;
}
public Relation.RELCLASS getRelClass() {
return relClass;
}
}

778
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -18,443 +18,443 @@ import eu.dnetlib.dhp.schema.oaf.common.AccessRightComparator;
public class OafMapperUtils {
private OafMapperUtils() {
}
private OafMapperUtils() {
}
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
kv.setKey(k);
kv.setValue(v);
return kv;
}
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
kv.setKey(k);
kv.setValue(v);
return kv;
}
public static List<KeyValue> listKeyValues(final String... s) {
if (s.length % 2 > 0) {
throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)");
}
public static List<KeyValue> listKeyValues(final String... s) {
if (s.length % 2 > 0) {
throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)");
}
final List<KeyValue> list = new ArrayList<>();
for (int i = 0; i < s.length; i += 2) {
list.add(keyValue(s[i], s[i + 1]));
}
return list;
}
final List<KeyValue> list = new ArrayList<>();
for (int i = 0; i < s.length; i += 2) {
list.add(keyValue(s[i], s[i + 1]));
}
return list;
}
public static <T> List<T> listValues(Array values) throws SQLException {
if (Objects.isNull(values)) {
return null;
}
return Arrays
.stream((T[]) values.getArray())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
public static <T> List<T> listValues(Array values) throws SQLException {
if (Objects.isNull(values)) {
return null;
}
return Arrays
.stream((T[]) values.getArray())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
public static Qualifier unknown(final String schemeid) {
return qualifier(UNKNOWN, "Unknown", schemeid);
}
public static Qualifier unknown(final String schemeid) {
return qualifier(UNKNOWN, "Unknown", schemeid);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid) {
return accessRight(classid, classname, schemeid, null);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid) {
return accessRight(classid, classname, schemeid, null);
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final OpenAccessRoute openAccessRoute) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(classid);
accessRight.setClassname(classname);
accessRight.setSchemeid(schemeid);
accessRight.setOpenAccessRoute(openAccessRoute);
return accessRight;
}
public static AccessRight accessRight(
final String classid,
final String classname,
final String schemeid,
final OpenAccessRoute openAccessRoute) {
final AccessRight accessRight = new AccessRight();
accessRight.setClassid(classid);
accessRight.setClassname(classname);
accessRight.setSchemeid(schemeid);
accessRight.setOpenAccessRoute(openAccessRoute);
return accessRight;
}
public static Qualifier qualifier(
final String classid,
final String classname,
final String schemeid) {
final Qualifier q = new Qualifier();
q.setClassid(classid);
q.setClassname(classname);
q.setSchemeid(schemeid);
return q;
}
public static Qualifier qualifier(
final String classid,
final String classname,
final String schemeid) {
final Qualifier q = new Qualifier();
q.setClassid(classid);
q.setClassname(classname);
q.setSchemeid(schemeid);
return q;
}
public static Qualifier qualifier(final Qualifier qualifier) {
final Qualifier q = new Qualifier();
q.setClassid(qualifier.getClassid());
q.setClassname(qualifier.getClassname());
q.setSchemeid(qualifier.getSchemeid());
return q;
}
public static Qualifier qualifier(final Qualifier qualifier) {
final Qualifier q = new Qualifier();
q.setClassid(qualifier.getClassid());
q.setClassname(qualifier.getClassname());
q.setSchemeid(qualifier.getSchemeid());
return q;
}
public static Subject subject(
final String value,
final String classid,
final String classname,
final String schemeid,
final DataInfo dataInfo) {
public static Subject subject(
final String value,
final String classid,
final String classname,
final String schemeid,
final DataInfo dataInfo) {
return subject(value, qualifier(classid, classname, schemeid), dataInfo);
}
return subject(value, qualifier(classid, classname, schemeid), dataInfo);
}
public static StructuredProperty structuredProperty(
final String value,
final String classid,
final String classname,
final String schemeid) {
public static StructuredProperty structuredProperty(
final String value,
final String classid,
final String classname,
final String schemeid) {
return structuredProperty(value, qualifier(classid, classname, schemeid));
}
return structuredProperty(value, qualifier(classid, classname, schemeid));
}
public static Subject subject(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final Subject s = new Subject();
s.setValue(value);
s.setQualifier(qualifier);
s.setDataInfo(dataInfo);
return s;
}
public static Subject subject(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final Subject s = new Subject();
s.setValue(value);
s.setQualifier(qualifier);
s.setDataInfo(dataInfo);
return s;
}
public static StructuredProperty structuredProperty(
final String value,
final Qualifier qualifier) {
if (value == null) {
return null;
}
final StructuredProperty sp = new StructuredProperty();
sp.setValue(value);
sp.setQualifier(qualifier);
return sp;
}
public static StructuredProperty structuredProperty(
final String value,
final Qualifier qualifier) {
if (value == null) {
return null;
}
final StructuredProperty sp = new StructuredProperty();
sp.setValue(value);
sp.setQualifier(qualifier);
return sp;
}
public static Publisher publisher(final String name) {
final Publisher p = new Publisher();
p.setName(name);
return p;
}
public static Publisher publisher(final String name) {
final Publisher p = new Publisher();
p.setName(name);
return p;
}
public static License license(final String url) {
final License l = new License();
l.setUrl(url);
return l;
}
public static License license(final String url) {
final License l = new License();
l.setUrl(url);
return l;
}
public static AuthorPid authorPid(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final AuthorPid ap = new AuthorPid();
ap.setValue(value);
ap.setQualifier(qualifier);
ap.setDataInfo(dataInfo);
return ap;
}
public static AuthorPid authorPid(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final AuthorPid ap = new AuthorPid();
ap.setValue(value);
ap.setQualifier(qualifier);
ap.setDataInfo(dataInfo);
return ap;
}
public static AuthorPid authorPid(
final String value,
final String classid,
final String schemeid,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final AuthorPid ap = new AuthorPid();
ap.setValue(value);
ap.setQualifier(qualifier(classid, classid, schemeid));
ap.setDataInfo(dataInfo);
return ap;
}
public static AuthorPid authorPid(
final String value,
final String classid,
final String schemeid,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final AuthorPid ap = new AuthorPid();
ap.setValue(value);
ap.setQualifier(qualifier(classid, classid, schemeid));
ap.setDataInfo(dataInfo);
return ap;
}
public static ExtraInfo extraInfo(
final String name,
final String value,
final String typology,
final String provenance,
final String trust) {
final ExtraInfo info = new ExtraInfo();
info.setName(name);
info.setValue(value);
info.setTypology(typology);
info.setProvenance(provenance);
info.setTrust(trust);
return info;
}
public static ExtraInfo extraInfo(
final String name,
final String value,
final String typology,
final String provenance,
final String trust) {
final ExtraInfo info = new ExtraInfo();
info.setName(name);
info.setValue(value);
info.setTypology(typology);
info.setProvenance(provenance);
info.setTrust(trust);
return info;
}
public static OAIProvenance oaiIProvenance(
final String identifier,
final String baseURL,
final String metadataNamespace,
final Boolean altered,
final String datestamp,
final String harvestDate) {
public static OAIProvenance oaiIProvenance(
final String identifier,
final String baseURL,
final String metadataNamespace,
final Boolean altered,
final String datestamp,
final String harvestDate) {
final OriginDescription desc = new OriginDescription();
desc.setIdentifier(identifier);
desc.setBaseURL(baseURL);
desc.setMetadataNamespace(metadataNamespace);
desc.setAltered(altered);
desc.setDatestamp(datestamp);
desc.setHarvestDate(harvestDate);
final OriginDescription desc = new OriginDescription();
desc.setIdentifier(identifier);
desc.setBaseURL(baseURL);
desc.setMetadataNamespace(metadataNamespace);
desc.setAltered(altered);
desc.setDatestamp(datestamp);
desc.setHarvestDate(harvestDate);
final OAIProvenance p = new OAIProvenance();
p.setOriginDescription(desc);
final OAIProvenance p = new OAIProvenance();
p.setOriginDescription(desc);
return p;
}
return p;
}
public static Journal journal(
final String name,
final String issnPrinted,
final String issnOnline,
final String issnLinking) {
public static Journal journal(
final String name,
final String issnPrinted,
final String issnOnline,
final String issnLinking) {
return hasIssn(issnPrinted, issnOnline, issnLinking) ? journal(
name,
issnPrinted,
issnOnline,
issnLinking,
null,
null,
null,
null,
null,
null,
null) : null;
}
return hasIssn(issnPrinted, issnOnline, issnLinking) ? journal(
name,
issnPrinted,
issnOnline,
issnLinking,
null,
null,
null,
null,
null,
null,
null) : null;
}
public static Journal journal(
final String name,
final String issnPrinted,
final String issnOnline,
final String issnLinking,
final String ep,
final String iss,
final String sp,
final String vol,
final String edition,
final String conferenceplace,
final String conferencedate) {
public static Journal journal(
final String name,
final String issnPrinted,
final String issnOnline,
final String issnLinking,
final String ep,
final String iss,
final String sp,
final String vol,
final String edition,
final String conferenceplace,
final String conferencedate) {
if (StringUtils.isNotBlank(name) || hasIssn(issnPrinted, issnOnline, issnLinking)) {
final Journal j = new Journal();
j.setName(name);
j.setIssnPrinted(issnPrinted);
j.setIssnOnline(issnOnline);
j.setIssnLinking(issnLinking);
j.setEp(ep);
j.setIss(iss);
j.setSp(sp);
j.setVol(vol);
j.setEdition(edition);
j.setConferenceplace(conferenceplace);
j.setConferencedate(conferencedate);
return j;
} else {
return null;
}
}
if (StringUtils.isNotBlank(name) || hasIssn(issnPrinted, issnOnline, issnLinking)) {
final Journal j = new Journal();
j.setName(name);
j.setIssnPrinted(issnPrinted);
j.setIssnOnline(issnOnline);
j.setIssnLinking(issnLinking);
j.setEp(ep);
j.setIss(iss);
j.setSp(sp);
j.setVol(vol);
j.setEdition(edition);
j.setConferenceplace(conferenceplace);
j.setConferencedate(conferencedate);
return j;
} else {
return null;
}
}
private static boolean hasIssn(String issnPrinted, String issnOnline, String issnLinking) {
return StringUtils.isNotBlank(issnPrinted)
|| StringUtils.isNotBlank(issnOnline)
|| StringUtils.isNotBlank(issnLinking);
}
private static boolean hasIssn(String issnPrinted, String issnOnline, String issnLinking) {
return StringUtils.isNotBlank(issnPrinted)
|| StringUtils.isNotBlank(issnOnline)
|| StringUtils.isNotBlank(issnLinking);
}
public static DataInfo dataInfo(
final float trust,
final String inferenceprovenance,
final boolean inferred,
final Qualifier provenanceaction) {
final DataInfo d = new DataInfo();
d.setTrust(trust);
d.setInferenceprovenance(inferenceprovenance);
d.setInferred(inferred);
d.setProvenanceaction(provenanceaction);
return d;
}
public static DataInfo dataInfo(
final float trust,
final String inferenceprovenance,
final boolean inferred,
final Qualifier provenanceaction) {
final DataInfo d = new DataInfo();
d.setTrust(trust);
d.setInferenceprovenance(inferenceprovenance);
d.setInferred(inferred);
d.setProvenanceaction(provenanceaction);
return d;
}
public static EntityDataInfo dataInfo(
final boolean invisible,
final boolean deletedbyinference,
final float trust,
final String inferenceprovenance,
final boolean inferred,
final Qualifier provenanceaction) {
final EntityDataInfo d = new EntityDataInfo();
d.setTrust(trust);
d.setInvisible(invisible);
d.setDeletedbyinference(deletedbyinference);
d.setInferenceprovenance(inferenceprovenance);
d.setInferred(inferred);
d.setProvenanceaction(provenanceaction);
return d;
}
public static EntityDataInfo dataInfo(
final boolean invisible,
final boolean deletedbyinference,
final float trust,
final String inferenceprovenance,
final boolean inferred,
final Qualifier provenanceaction) {
final EntityDataInfo d = new EntityDataInfo();
d.setTrust(trust);
d.setInvisible(invisible);
d.setDeletedbyinference(deletedbyinference);
d.setInferenceprovenance(inferenceprovenance);
d.setInferred(inferred);
d.setProvenanceaction(provenanceaction);
return d;
}
public static String asString(final Object o) {
return o == null ? "" : o.toString();
}
public static String asString(final Object o) {
return o == null ? "" : o.toString();
}
public static <T> Predicate<T> distinctByKey(
final Function<? super T, ?> keyExtractor) {
final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
}
public static <T> Predicate<T> distinctByKey(
final Function<? super T, ?> keyExtractor) {
final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
}
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<AccessRight> min = instanceList
.stream()
.map(Instance::getAccessright)
.min(new AccessRightComparator<>());
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<AccessRight> min = instanceList
.stream()
.map(Instance::getAccessright)
.min(new AccessRightComparator<>());
final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new);
final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new);
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.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);
}
return rights;
}
return null;
}
return rights;
}
return null;
}
public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) {
Measure m = new Measure();
m.setId(id);
m.setUnit(Arrays.asList(unit(key, value, dataInfo)));
return m;
}
public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) {
Measure m = new Measure();
m.setId(id);
m.setUnit(Arrays.asList(unit(key, value, dataInfo)));
return m;
}
public static MeasureUnit unit(String key, String value, DataInfo dataInfo) {
MeasureUnit unit = new MeasureUnit();
unit.setKey(key);
unit.setValue(value);
unit.setDataInfo(dataInfo);
return unit;
}
public static MeasureUnit unit(String key, String value, DataInfo dataInfo) {
MeasureUnit unit = new MeasureUnit();
unit.setKey(key);
unit.setValue(value);
unit.setDataInfo(dataInfo);
return unit;
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final Entity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final Entity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final Entity entity,
final String validationDate) {
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final Entity entity,
final String validationDate) {
final List<Provenance> provenance = getProvenance(
entity.getCollectedfrom(), fromEntityDataInfo(entity.getDataInfo()));
return getRelation(
source, target, relType, subRelType, relClass, provenance, validationDate, null);
}
final List<Provenance> provenance = getProvenance(
entity.getCollectedfrom(), fromEntityDataInfo(entity.getDataInfo()));
return getRelation(
source, target, relType, subRelType, relClass, provenance, validationDate, null);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance) {
return getRelation(
source, target, relType, subRelType, relClass, provenance, null, null);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance) {
return getRelation(
source, target, relType, subRelType, relClass, provenance, null, null);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance,
final List<KeyValue> properties) {
return getRelation(
source, target, relType, subRelType, relClass, provenance, null, properties);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance,
final List<KeyValue> properties) {
return getRelation(
source, target, relType, subRelType, relClass, provenance, null, properties);
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance,
final String validationDate,
final List<KeyValue> properties) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setProvenance(provenance);
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
rel.setProperties(properties);
return rel;
}
public static Relation getRelation(final String source,
final String target,
final Relation.RELTYPE relType,
final Relation.SUBRELTYPE subRelType,
final Relation.RELCLASS relClass,
final List<Provenance> provenance,
final String validationDate,
final List<KeyValue> properties) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setProvenance(provenance);
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
rel.setProperties(properties);
return rel;
}
public static List<Provenance> getProvenance(final List<KeyValue> collectedfrom, final DataInfo dataInfo) {
return collectedfrom
.stream()
.map(cf -> getProvenance(cf, dataInfo))
.collect(Collectors.toList());
}
public static List<Provenance> getProvenance(final List<KeyValue> collectedfrom, final DataInfo dataInfo) {
return collectedfrom
.stream()
.map(cf -> getProvenance(cf, dataInfo))
.collect(Collectors.toList());
}
public static Provenance getProvenance(final KeyValue collectedfrom, final DataInfo dataInfo) {
final Provenance prov = new Provenance();
prov.setCollectedfrom(collectedfrom);
prov.setDataInfo(dataInfo);
return prov;
}
public static Provenance getProvenance(final KeyValue collectedfrom, final DataInfo dataInfo) {
final Provenance prov = new Provenance();
prov.setCollectedfrom(collectedfrom);
prov.setDataInfo(dataInfo);
return prov;
}
public static String getProvenance(DataInfo dataInfo) {
return Optional
.ofNullable(dataInfo)
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
}
public static String getProvenance(DataInfo dataInfo) {
return Optional
.ofNullable(dataInfo)
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
}
public static DataInfo fromEntityDataInfo(EntityDataInfo entityDataInfo) {
DataInfo dataInfo = new DataInfo();
dataInfo.setTrust(entityDataInfo.getTrust());
dataInfo.setInferenceprovenance(entityDataInfo.getInferenceprovenance());
dataInfo.setInferred(entityDataInfo.getInferred());
dataInfo.setProvenanceaction(entityDataInfo.getProvenanceaction());
return dataInfo;
}
public static DataInfo fromEntityDataInfo(EntityDataInfo entityDataInfo) {
DataInfo dataInfo = new DataInfo();
dataInfo.setTrust(entityDataInfo.getTrust());
dataInfo.setInferenceprovenance(entityDataInfo.getInferenceprovenance());
dataInfo.setInferred(entityDataInfo.getInferred());
dataInfo.setProvenanceaction(entityDataInfo.getProvenanceaction());
return dataInfo;
}
}

59
dhp-common/src/main/java/eu/dnetlib/dhp/schema/sx/OafUtils.scala
View File

@ -1,59 +0,0 @@
package eu.dnetlib.dhp.schema.sx
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
object OafUtils {
def generateKeyValue(key: String, value: String): KeyValue = {
val kv: KeyValue = new KeyValue()
kv.setKey(key)
kv.setValue(value)
kv
}
def generateDataInfo(trust: Float = 0.9f, invisible: Boolean = false): DataInfo = {
val di = new DataInfo
di.setInferred(false)
di.setTrust(trust)
di.setProvenanceaction(createQualifier(ModelConstants.SYSIMPORT_ACTIONSET, ModelConstants.DNET_PROVENANCE_ACTIONS))
di
}
def createQualifier(cls: String, sch: String): Qualifier = {
createQualifier(cls, cls, sch)
}
def createQualifier(classId: String, className: String, schemeId: String): Qualifier = {
val q: Qualifier = new Qualifier
q.setClassid(classId)
q.setClassname(className)
q.setSchemeid(schemeId)
q
}
def createAccessRight(classId: String, className: String, schemeId: String): AccessRight = {
val accessRight: AccessRight = new AccessRight
accessRight.setClassid(classId)
accessRight.setClassname(className)
accessRight.setSchemeid(schemeId)
accessRight
}
def createSP(value: String, classId: String,className:String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId,className, schemeId))
sp.setValue(value)
sp
}
def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
val sp = new StructuredProperty
sp.setQualifier(createQualifier(classId, schemeId))
sp.setValue(value)
sp
}
}

25
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java
View File

@ -1,25 +0,0 @@
package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable;
public class RelInfo implements Serializable {
private String original;
private String inverse;
public String getOriginal() {
return original;
}
public void setOriginal(String original) {
this.original = original;
}
public String getInverse() {
return inverse;
}
public void setInverse(String inverse) {
this.inverse = inverse;
}
}

20
dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java
View File

@ -1,20 +0,0 @@
package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable;
import java.util.HashMap;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
public static RelationMapper load() throws Exception {
final String json = IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class);
}
}

11
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupportTest.java
View File

@ -36,15 +36,4 @@ public class ModelSupportTest {
}
}
@Nested
class InverseRelation {
@Test
void findRelations() {
assertNotNull(ModelSupport.findRelation("isMetadataFor"));
assertNotNull(ModelSupport.findRelation("ismetadatafor"));
assertNotNull(ModelSupport.findRelation("ISMETADATAFOR"));
assertNotNull(ModelSupport.findRelation("isRelatedTo"));
}
}
}

16
dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java
View File

@ -1,16 +0,0 @@
package eu.dnetlib.scholexplorer.relation;
import static org.junit.jupiter.api.Assertions.assertFalse;
import org.junit.jupiter.api.Test;
class RelationMapperTest {
@Test
void testLoadRels() throws Exception {
RelationMapper relationMapper = RelationMapper.load();
assertFalse(relationMapper.isEmpty());
}
}

11
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala
View File

@ -2,7 +2,7 @@ package eu.dnetlib.dhp.datacite
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
import eu.dnetlib.dhp.schema.oaf.{DataInfo, EntityDataInfo, KeyValue}
import eu.dnetlib.dhp.schema.oaf.{DataInfo, EntityDataInfo, KeyValue, Relation}
import java.io.InputStream
import java.time.format.DateTimeFormatter
@ -66,12 +66,13 @@ class DataciteModelConstants extends Serializable {}
object DataciteModelConstants {
val REL_TYPE_VALUE: String = "resultResult"
val REL_TYPE_VALUE =Relation.RELTYPE.resultResult
val DATE_RELATION_KEY = "RelationDate"
val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter"
val DOI_CLASS = "doi"
val SUBJ_CLASS = "keywords"
val DATACITE_NAME = "Datacite"
val PMID = "pmid"
val ARXIV = "arxiv"
val dataInfo: EntityDataInfo = dataciteDataInfo(0.9f)
val relDataInfo = OafMapperUtils.fromEntityDataInfo(dataInfo);
@ -138,4 +139,8 @@ object DataciteModelConstants {
Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
)
def validIdentifiersInRelation(relatedIdentifierType:String):Boolean = {
relatedIdentifierType.equalsIgnoreCase(ModelConstants.DOI) || relatedIdentifierType.equalsIgnoreCase(PMID) ||
relatedIdentifierType.equalsIgnoreCase(ARXIV)
}
}

44
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
View File

@ -100,7 +100,7 @@ object DataciteToOAFTransformation {
}
/** This utility method indicates whether the embargo date has been reached
* @param embargo_end_date
* @param embargo_end_date the end date of embargo
* @return True if the embargo date has been reached, false otherwise
*/
def embargo_end(embargo_end_date: String): Boolean = {
@ -345,8 +345,8 @@ object DataciteToOAFTransformation {
// DOI is mapped on a PID inside a Instance object
val doi_q = OafMapperUtils.qualifier(
"doi",
"doi",
ModelConstants.DOI,
ModelConstants.DOI,
ModelConstants.DNET_PID_TYPES
)
val pid = OafMapperUtils.structuredProperty(doi, doi_q)
@ -615,44 +615,52 @@ object DataciteToOAFTransformation {
List(result)
}
//TODO @CLAUDIO we need to define relation in which verse
/**
* This function generate unresolved relation from the original Datacite document
* @param rels the related identifier section on the document
* @param id the source record Identifier
* @param date the date of collection
* @return a List of OAF relation
*/
private def generateRelations(
rels: List[RelatedIdentifierType],
id: String,
date: String
): List[Relation] = {
// TODO We need to check how to generate realtions
// in the previous implementation we create all Bidirection Relations
// related to a DOI pid or arxiv,
val bidirectionalRels: List[Relation] = rels
.filter(r =>
Relation.RELCLASS.exists(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
Relation.RELCLASS.exists(r.relationType) && validIdentifiersInRelation(r.relatedIdentifierType)
)
.map(r => {
val subRelType = subRelTypeMapping(r.relationType).relType
val subRelType = Relation.SUBRELTYPE.valueOf(r.relationType)
val target = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
relation(id, target, subRelType, r.relationType, date)
relation(id, target, subRelType, Relation.RELCLASS.valueOf(r.relationType), date)
})
val citationRels: List[Relation] = rels
.filter(r =>
(r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv")) &&
.filter(r =>validIdentifiersInRelation(r.relatedIdentifierType) &&
(r.relationType.toLowerCase.contains("cite") || r.relationType.toLowerCase.contains("reference"))
)
.map(r => {
r.relationType match {
case ModelConstants.CITES | ModelConstants.REFERENCES =>
case Relation.RELCLASS.Cites.toString | Relation.RELCLASS.References.toString =>
val target = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
relation(id, target, ModelConstants.CITATION, ModelConstants.CITES, date)
case ModelConstants.IS_CITED_BY | ModelConstants.IS_REFERENCED_BY =>
relation(id, target, Relation.SUBRELTYPE.citation, Relation.RELCLASS.Cites, date)
case Relation.RELCLASS.IsCitedBy.toString | Relation.RELCLASS.IsReferencedBy.toString =>
val source = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
relation(source, id, ModelConstants.CITATION, ModelConstants.CITES, date)
relation(source, id, Relation.SUBRELTYPE.citation, Relation.RELCLASS.Cites, date)
}
})
citationRels ::: bidirectionalRels
}
def relation(source: String, target: String, subRelType: String, relClass: String, date: String): Relation = {
def relation(source: String, target: String, subRelType: Relation.SUBRELTYPE, relClass: Relation.RELCLASS, date: String): Relation = {
val rel = new Relation
rel.setProvenance(Lists.newArrayList(OafMapperUtils.getProvenance(DATACITE_COLLECTED_FROM, relDataInfo)))

22
dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java
View File

@ -14,7 +14,7 @@ import java.util.function.Consumer;
import java.util.function.Function;
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
@ -76,30 +76,22 @@ public class ReadBlacklistFromDB implements Closeable {
public List<Relation> processBlacklistEntry(ResultSet rs) {
try {
Relation direct = new Relation();
Relation inverse = new Relation();
String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type"));
String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type"));
String source_direct = source_prefix + "|" + rs.getString("source");
direct.setSource(source_direct);
inverse.setTarget(source_direct);
String target_direct = target_prefix + "|" + rs.getString("target");
direct.setTarget(target_direct);
inverse.setSource(target_direct);
String encoding = rs.getString("relationship");
RelationInverse ri = ModelSupport.findInverse(encoding);
direct.setRelClass(ri.getRelClass());
inverse.setRelClass(ri.getInverseRelClass());
direct.setRelType(ri.getRelType());
inverse.setRelType(ri.getRelType());
direct.setSubRelType(ri.getSubReltype());
inverse.setSubRelType(ri.getSubReltype());
return Arrays.asList(direct, inverse);
final RelationLabel directLabel = ModelSupport.unRel(encoding);
direct.setRelClass(directLabel.getRelClass());
direct.setRelType(directLabel.getRelType());
direct.setSubRelType(directLabel.getSubReltype());
return Arrays.asList(direct, direct.inverse());
} catch (final SQLException e) {
throw new RuntimeException(e);
}

4
dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java
View File

@ -5,7 +5,7 @@ import java.util.Arrays;
import java.util.List;
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
@ -25,7 +25,7 @@ public class BlacklistRelationTest {
"resultProject_outcome_isProducedBy");
rels.forEach(r -> {
RelationInverse inverse = ModelSupport.relationInverseMap.get(r);
RelationLabel inverse = ModelSupport.relationInverseMap.get(r);
Assertions.assertNotNull(inverse);
Assertions.assertNotNull(inverse.getRelType());
Assertions.assertNotNull(inverse.getSubReltype());

6
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -203,9 +203,9 @@ object SparkGenerateDoiBoost {
val r: Relation = new Relation
r.setSource(pub.getId)
r.setTarget(affId)
r.setRelType(ModelConstants.RESULT_ORGANIZATION)
r.setRelClass(ModelConstants.HAS_AUTHOR_INSTITUTION)
r.setSubRelType(ModelConstants.AFFILIATION)
r.setRelType(Relation.RELTYPE.resultOrganization)
r.setRelClass(Relation.RELCLASS.hasAuthorInstitution)
r.setSubRelType(Relation.SUBRELTYPE.affiliation)
r.setProvenance(OafMapperUtils.getProvenance(pub.getCollectedfrom, dataInfo))
List(r)

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -11,7 +11,7 @@ import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.Element;
@ -401,7 +401,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
protected List<Oaf> getRelations(final String reltype, final String entityId, final String otherId,
final Entity entity) {
final List<Oaf> res = new ArrayList<>();
RelationInverse rel = ModelSupport.findRelation(reltype);
RelationLabel rel = ModelSupport.findRelation(reltype);
if (rel != null) {
res
.add(