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refactoring: CleaningFunctions and OafMapperUtils moved in dhp-commong

This commit is contained in:
Claudio Atzori 2020-11-03 12:19:46 +01:00
parent 8471888ad3
commit 86d6fbe95b
14 changed files with 203 additions and 228 deletions
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56
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java → dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/CleaningFunctions.java
View File

@ -1,8 +1,9 @@
package eu.dnetlib.dhp.oa.graph.clean; package eu.dnetlib.dhp.schema.oaf;
import java.util.LinkedHashMap; import java.util.LinkedHashMap;
import java.util.Objects; import java.util.Objects;
import java.util.Optional;
import java.util.function.Function; import java.util.function.Function;
import java.util.stream.Collectors; import java.util.stream.Collectors;
@ -10,13 +11,13 @@ import org.apache.commons.lang3.StringUtils;
import com.clearspring.analytics.util.Lists; import com.clearspring.analytics.util.Lists;
import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class CleaningFunctions { public class CleaningFunctions {
public static final String DOI_URL_PREFIX = "^http(s?):\\/\\/(dx\\.)?doi\\.org\\/";
public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/"; public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
public static final String NONE = "none"; public static final String NONE = "none";
@ -72,7 +73,7 @@ public class CleaningFunctions {
return value; return value;
} }
protected static <T extends Oaf> T fixDefaults(T value) { public static <T extends Oaf> T fixDefaults(T value) {
if (value instanceof Datasource) { if (value instanceof Datasource) {
// nothing to clean here // nothing to clean here
} else if (value instanceof Project) { } else if (value instanceof Project) {
@ -109,20 +110,17 @@ public class CleaningFunctions {
} }
if (Objects.nonNull(r.getPid())) { if (Objects.nonNull(r.getPid())) {
r r
.setPid( .setPid(
r r
.getPid() .getPid()
.stream() .stream()
.filter(Objects::nonNull) .filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue()))) .filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
.filter(sp -> NONE.equalsIgnoreCase(sp.getValue())) .filter(sp -> NONE.equalsIgnoreCase(sp.getValue()))
.filter(sp -> Objects.nonNull(sp.getQualifier())) .filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid())) .filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(sp -> { .map(CleaningFunctions::normalizePidValue)
sp.setValue(StringUtils.trim(sp.getValue())); .collect(Collectors.toList()));
return sp;
})
.collect(Collectors.toList()));
} }
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) { if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r r
@ -143,7 +141,7 @@ public class CleaningFunctions {
} }
} }
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) { if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance()); Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance());
if (Objects.isNull(bestaccessrights)) { if (Objects.isNull(bestaccessrights)) {
r r
.setBestaccessright( .setBestaccessright(
@ -219,4 +217,24 @@ public class CleaningFunctions {
classid, classname, scheme, scheme); classid, classname, scheme, scheme);
} }
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
String value = Optional
.ofNullable(pid.getValue())
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pid.getQualifier().getClassid()) {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX, ""));
break;
}
return pid;
}
} }

53
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/OafMapperUtils.java → dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/OafMapperUtils.java
View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.oa.graph.raw.common; package eu.dnetlib.dhp.schema.oaf;
import java.util.ArrayList; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.util.Arrays; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
import java.util.List;
import java.util.Map; import java.util.*;
import java.util.Objects;
import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function; import java.util.function.Function;
import java.util.function.Predicate; import java.util.function.Predicate;
@ -13,15 +12,7 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.common.LicenseComparator;
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
import eu.dnetlib.dhp.schema.oaf.OriginDescription;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
public class OafMapperUtils { public class OafMapperUtils {
@ -270,4 +261,36 @@ public class OafMapperUtils {
final Map<Object, Boolean> seen = new ConcurrentHashMap<>(); final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null; return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
} }
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<Qualifier> min = instanceList
.stream()
.map(i -> i.getAccessright())
.min(new LicenseComparator());
final Qualifier rights = min.isPresent() ? min.get() : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
}
if (StringUtils.isBlank(rights.getClassname())
|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
rights.setClassname(NOT_AVAILABLE);
}
if (StringUtils.isBlank(rights.getSchemeid())) {
rights.setSchemeid(DNET_ACCESS_MODES);
}
if (StringUtils.isBlank(rights.getSchemename())) {
rights.setSchemename(DNET_ACCESS_MODES);
}
return rights;
}
return null;
}
} }

64
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/ResultTypeComparator.java
View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.util.Comparator; import java.util.Comparator;
@ -6,44 +7,43 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
public class ResultTypeComparator implements Comparator<Result> { public class ResultTypeComparator implements Comparator<Result> {
@Override @Override
public int compare(Result left, Result right) { public int compare(Result left, Result right) {
if (left == null && right == null) if (left == null && right == null)
return 0; return 0;
if (left == null) if (left == null)
return 1; return 1;
if (right == null) if (right == null)
return -1; return -1;
String lClass = left.getResulttype().getClassid(); String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid(); String rClass = right.getResulttype().getClassid();
if (lClass.equals(rClass)) if (lClass.equals(rClass))
return 0; return 0;
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1; return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID)) if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1; return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1; return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID)) if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1; return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1; return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID)) if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1; return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1; return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID)) if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1; return 1;
// Else (but unlikely), lexicographical ordering will do. // Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass); return lClass.compareTo(rClass);
} }
} }

31
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
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@ -7,6 +7,7 @@ import java.util.Optional;
import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.StringUtils;
import eu.dnetlib.dhp.schema.oaf.CleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.dhp.utils.DHPUtils;
@ -16,8 +17,6 @@ import eu.dnetlib.dhp.utils.DHPUtils;
*/ */
public class IdentifierFactory implements Serializable { public class IdentifierFactory implements Serializable {
public static final String DOI_URL_PREFIX = "^http(s?):\\/\\/(dx\\.)?doi\\.org\\/";
public static final String ID_SEPARATOR = "::"; public static final String ID_SEPARATOR = "::";
public static final String ID_PREFIX_SEPARATOR = "|"; public static final String ID_PREFIX_SEPARATOR = "|";
public final static String ID_REGEX = "^[0-9][0-9]\\" + ID_PREFIX_SEPARATOR + ".{12}" + ID_SEPARATOR public final static String ID_REGEX = "^[0-9][0-9]\\" + ID_PREFIX_SEPARATOR + ".{12}" + ID_SEPARATOR
@ -50,29 +49,9 @@ public class IdentifierFactory implements Serializable {
protected static boolean pidFilter(StructuredProperty s) { protected static boolean pidFilter(StructuredProperty s) {
return Objects.nonNull(s.getQualifier()) && return Objects.nonNull(s.getQualifier()) &&
PidType.isValid(s.getQualifier().getClassid()) && PidType.isValid(s.getQualifier().getClassid()) &&
StringUtils.isNotBlank(StringUtils.trim(s.getValue())) && StringUtils.isNotBlank(StringUtils.trim(s.getValue())) &&
!NONE.equals(StringUtils.trim(StringUtils.lowerCase(s.getValue()))); !NONE.equals(StringUtils.trim(StringUtils.lowerCase(s.getValue())));
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
String value = Optional
.ofNullable(pid.getValue())
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pid.getQualifier().getClassid()) {
// TODO add cleaning for more PID types as needed
case "doi":
pid.setValue(value.toLowerCase().replaceAll(DOI_URL_PREFIX, ""));
break;
}
return pid;
} }
private static String verifyIdSyntax(String s) { private static String verifyIdSyntax(String s) {
@ -89,7 +68,7 @@ public class IdentifierFactory implements Serializable {
.append(ID_PREFIX_SEPARATOR) .append(ID_PREFIX_SEPARATOR)
.append(createPrefix(s.getQualifier().getClassid())) .append(createPrefix(s.getQualifier().getClassid()))
.append(ID_SEPARATOR) .append(ID_SEPARATOR)
.append(DHPUtils.md5(normalizePidValue(s).getValue())) .append(DHPUtils.md5(CleaningFunctions.normalizePidValue(s).getValue()))
.toString(); .toString();
} }

7
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java
View File

@ -3,13 +3,9 @@ package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.BufferedInputStream;
import java.util.Objects;
import java.util.Optional; import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
@ -23,10 +19,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

36
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
import java.util.*; import java.util.*;
@ -282,7 +282,7 @@ public abstract class AbstractMdRecordToOafMapper {
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
r.setInstance(instances); r.setInstance(instances);
r.setBestaccessright(getBestAccessRights(instances)); r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances));
} }
protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info); protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
@ -367,38 +367,6 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info); protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
return getBestAccessRights(instanceList);
}
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
if (instanceList != null) {
final Optional<Qualifier> min = instanceList
.stream()
.map(i -> i.getAccessright())
.min(new LicenseComparator());
final Qualifier rights = min.isPresent() ? min.get() : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
}
if (StringUtils.isBlank(rights.getClassname())
|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
rights.setClassname(NOT_AVAILABLE);
}
if (StringUtils.isBlank(rights.getSchemeid())) {
rights.setSchemeid(DNET_ACCESS_MODES);
}
if (StringUtils.isBlank(rights.getSchemename())) {
rights.setSchemename(DNET_ACCESS_MODES);
}
return rights;
}
return null;
}
private Journal prepareJournal(final Document doc, final DataInfo info) { private Journal prepareJournal(final Document doc, final DataInfo info) {
final Node n = doc.selectSingleNode("//oaf:journal"); final Node n = doc.selectSingleNode("//oaf:journal");
if (n != null) { if (n != null) {

22
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -1,16 +1,6 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.asString;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.journal;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASOURCE_ORGANIZATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS; import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION; import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION;
@ -19,19 +9,25 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PARTICIPANT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PROVIDED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO; import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME; import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.PARTICIPATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES; import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROJECT_ORGANIZATION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVIDES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION; import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP; import static eu.dnetlib.dhp.schema.common.ModelConstants.RELATIONSHIP;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.io.Closeable; import java.io.Closeable;
import java.io.IOException; import java.io.IOException;

9
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -1,14 +1,13 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
@ -293,7 +292,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
return prepareListStructPropsWithValidQualifier( return prepareListStructPropsWithValidQualifier(
doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info) doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info)
.stream() .stream()
.map(IdentifierFactory::normalizePidValue) .map(CleaningFunctions::normalizePidValue)
.collect(Collectors.toList()); .collect(Collectors.toList());
} }

11
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
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@ -1,10 +1,10 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Arrays; import java.util.Arrays;
@ -17,11 +17,8 @@ import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.Node; import org.dom4j.Node;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
@ -382,7 +379,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
return res return res
.stream() .stream()
.map(IdentifierFactory::normalizePidValue) .map(CleaningFunctions::normalizePidValue)
.collect(Collectors.toList()); .collect(Collectors.toList());
} }

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/Vocabulary.java
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@ -10,6 +10,7 @@ import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class Vocabulary implements Serializable { public class Vocabulary implements Serializable {

1
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java
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@ -7,6 +7,7 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.Qualifier; import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java
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@ -7,8 +7,6 @@ import static org.mockito.Mockito.lenient;
import java.io.IOException; import java.io.IOException;
import java.util.List; import java.util.List;
import java.util.Set; import java.util.Set;
import java.util.function.Predicate;
import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;

136
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
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@ -1,11 +1,13 @@
package eu.dnetlib.dhp.oa.graph.raw; package eu.dnetlib.dhp.oa.graph.raw;
import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; import static org.junit.jupiter.api.Assertions.assertEquals;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import static org.junit.jupiter.api.Assertions.assertTrue;
import eu.dnetlib.dhp.schema.common.ModelConstants; import static org.mockito.Mockito.lenient;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import java.io.IOException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import java.util.List;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -13,85 +15,85 @@ import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock; import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import java.io.IOException; import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest;
import java.util.List; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import static org.junit.jupiter.api.Assertions.assertEquals; import eu.dnetlib.dhp.schema.oaf.*;
import static org.junit.jupiter.api.Assertions.assertTrue; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import static org.mockito.Mockito.lenient; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class GenerateEntitiesApplicationTest { public class GenerateEntitiesApplicationTest {
@Mock @Mock
private ISLookUpService isLookUpService; private ISLookUpService isLookUpService;
@Mock @Mock
private VocabularyGroup vocs; private VocabularyGroup vocs;
@BeforeEach @BeforeEach
public void setUp() throws IOException, ISLookUpException { public void setUp() throws IOException, ISLookUpException {
lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs()); lenient().when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARIES_XQUERY)).thenReturn(vocs());
lenient() lenient()
.when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY)) .when(isLookUpService.quickSearchProfile(VocabularyGroup.VOCABULARY_SYNONYMS_XQUERY))
.thenReturn(synonyms()); .thenReturn(synonyms());
vocs = VocabularyGroup.loadVocsFromIS(isLookUpService); vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
} }
@Test @Test
public void testMergeResult() throws IOException { public void testMergeResult() throws IOException {
Result publication = getResult("oaf_record.xml", Publication.class); Result publication = getResult("oaf_record.xml", Publication.class);
Result dataset = getResult("odf_dataset.xml", Dataset.class); Result dataset = getResult("odf_dataset.xml", Dataset.class);
Result software = getResult("odf_software.xml", Software.class); Result software = getResult("odf_software.xml", Software.class);
Result orp = getResult("oaf_orp.xml", OtherResearchProduct.class); Result orp = getResult("oaf_orp.xml", OtherResearchProduct.class);
verifyMerge(publication, dataset, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(publication, dataset, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(dataset, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(dataset, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(publication, software, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(publication, software, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(software, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(software, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(publication, orp, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(publication, orp, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(orp, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID); verifyMerge(orp, publication, Publication.class, ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
verifyMerge(dataset, software, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); verifyMerge(dataset, software, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
verifyMerge(software, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); verifyMerge(software, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
verifyMerge(dataset, orp, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); verifyMerge(dataset, orp, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
verifyMerge(orp, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID); verifyMerge(orp, dataset, Dataset.class, ModelConstants.DATASET_RESULTTYPE_CLASSID);
verifyMerge(software, orp, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID); verifyMerge(software, orp, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID);
verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID); verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID);
} }
protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz, String resultType) { protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz,
final Result merge = GenerateEntitiesApplication.mergeResults(publication, dataset); String resultType) {
assertTrue(clazz.isAssignableFrom(merge.getClass())); final Result merge = GenerateEntitiesApplication.mergeResults(publication, dataset);
assertEquals(resultType, merge.getResulttype().getClassid()); assertTrue(clazz.isAssignableFrom(merge.getClass()));
} assertEquals(resultType, merge.getResulttype().getClassid());
}
protected <T extends Result> Result getResult(String xmlFileName, Class<T> clazz) throws IOException { protected <T extends Result> Result getResult(String xmlFileName, Class<T> clazz) throws IOException {
final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName)); final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName));
return new OdfToOafMapper(vocs, false) return new OdfToOafMapper(vocs, false)
.processMdRecord(xml) .processMdRecord(xml)
.stream() .stream()
.filter(s -> clazz.isAssignableFrom(s.getClass())) .filter(s -> clazz.isAssignableFrom(s.getClass()))
.map(s -> (Result) s) .map(s -> (Result) s)
.findFirst() .findFirst()
.get(); .get();
} }
private List<String> vocs() throws IOException {
return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt"));
}
private List<String> vocs() throws IOException { private List<String> synonyms() throws IOException {
return IOUtils return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); .readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
} }
private List<String> synonyms() throws IOException {
return IOUtils
.readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt"));
}
} }

2
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
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@ -27,10 +27,10 @@ import org.mockito.junit.jupiter.MockitoExtension;
import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafMapperUtils;
import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;