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Merge branch 'beta' of https://code-repo.d4science.org/D-Net/dnet-hadoop into beta

This commit is contained in:
Miriam Baglioni 2021-12-03 12:36:08 +01:00
parent 87eedad898 0fa0ce33d6
commit f430688ff7
12 changed files with 3100 additions and 62 deletions
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2
.gitignore vendored
View File

@ -3,8 +3,6 @@
*.iws
*.ipr
*.iml
*.ipr
*.iws
*~
.vscode
.metals

16
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -86,6 +86,22 @@ public class GraphCleaningFunctions extends CleaningFunctions {
}
public static <T extends Oaf> boolean filter(T value) {
if (Boolean.TRUE
.equals(
Optional
.ofNullable(value)
.map(
o -> Optional
.ofNullable(o.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getInvisible())
.orElse(true))
.orElse(true))
.orElse(true))) {
return false;
}
if (value instanceof Datasource) {
// nothing to evaluate here
} else if (value instanceof Project) {

1
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala
View File

@ -18,6 +18,7 @@ import java.text.SimpleDateFormat
import java.util.Locale
import scala.io.Source
import org.junit.jupiter.api.Assertions._
@ExtendWith(Array(classOf[MockitoExtension]))
class DataciteToOAFTest extends AbstractVocabularyTest{

47
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
View File

@ -74,6 +74,53 @@ public class GraphCleaningFunctionsTest {
}
}
@Test
void testFilter_false() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(false, GraphCleaningFunctions.filter(p_in));
}
@Test
void testFilter_true() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(true, GraphCleaningFunctions.filter(p_in));
}
@Test
void testFilter_missing_invisible() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_missing_invisible.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Publication);
assertEquals(true, GraphCleaningFunctions.filter(p_in));
}
@Test
void testCleaning() throws Exception {

958
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_invisible.json Normal file
View File

@ -0,0 +1,958 @@
{
"author": [
{
"affiliation": [
],
"fullname": "Brien, Tom",
"name": "Tom",
"pid": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "ORCID12",
"classname": "ORCID12",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "0000-0001-9613-6639"
},
{
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"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "ORCID12",
"classname": "ORCID12",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "https://orcid.org/0000-0001-9613-6639"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:entityregistry",
"classname": "sysimport:crosswalk:entityregistry",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "orcid",
"classname": "ORCID12",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "0000-0001-9613-6639"
}
],
"rank": 1,
"surname": "Brien"
},
{
"affiliation": [
],
"fullname": "Ade, Peter",
"name": "Peter",
"pid": [
{
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},
"trust": "0.9"
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},
"value": "qwerty"
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},
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{
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"pid": null,
"rank": 3,
"surname": "Barry"
},
{
"affiliation": [
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"fullname": "Dunscombe, Chris J.",
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"rank": 4,
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{
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"surname": "Sudiwala"
},
{
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}
],
"accessright": {
"classid": "CLOSED",
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},
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},
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},
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},
{
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"invisible": false,
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},
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},
"qualifier": {
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},
"value": "lens antennas"
},
{
"dataInfo": {
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"invisible": false,
"provenanceaction": {
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},
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},
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},
{
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},
"trust": "0.9"
},
"qualifier": {
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},
"value": "strained silicon"
},
{
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},
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"qualifier": {
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"value": "cold electron bolometers"
},
{
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},
"trust": "0.9"
},
"qualifier": {
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},
"value": "doped silicon"
},
{
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},
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},
"qualifier": {
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},
"value": "measure noise"
},
{
"dataInfo": {
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"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
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},
"trust": "0.9"
},
"qualifier": {
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},
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},
{
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},
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"invisible": false,
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},
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},
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},
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},
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"value": "optical response"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"value": "photon noise"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"value": "silicon absorbers"
}
],
"title": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "Optical response of strained- and unstrained-silicon cold-electron bolometers test"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "test test 123 test"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "omic"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "main title",
"classname": "main title",
"schemeid": "dnet:dataCite_title",
"schemename": "dnet:dataCite_title"
},
"value": "-"
}
]
}

158
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/XmlInstance.java Normal file
View File

@ -0,0 +1,158 @@
package eu.dnetlib.dhp.oa.provision.model;
import java.util.Set;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import scala.Serializable;
public class XmlInstance implements Serializable {
public static final AccessRight UNKNOWN_ACCESS_RIGHT;
static {
UNKNOWN_ACCESS_RIGHT = new AccessRight();
UNKNOWN_ACCESS_RIGHT.setClassid(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setClassname(ModelConstants.UNKNOWN);
UNKNOWN_ACCESS_RIGHT.setSchemeid(ModelConstants.DNET_ACCESS_MODES);
UNKNOWN_ACCESS_RIGHT.setSchemename(ModelConstants.DNET_ACCESS_MODES);
}
private String url;
private AccessRight accessright;
private Set<KeyValue> collectedfrom = Sets.newHashSet();
private Set<KeyValue> hostedby = Sets.newHashSet();
private Set<Qualifier> instancetype = Sets.newHashSet();
private Set<String> license = Sets.newHashSet();
// other research products specifc
private Set<String> distributionlocation = Sets.newHashSet();
private Set<StructuredProperty> pid = Sets.newHashSet();
private Set<StructuredProperty> alternateIdentifier = Sets.newHashSet();
private Set<String> dateofacceptance = Sets.newHashSet();
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results
private String processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results
private String processingchargecurrency;
private Set<Qualifier> refereed = Sets.newHashSet();; // peer-review status
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public AccessRight getAccessright() {
return accessright;
}
public void setAccessright(AccessRight accessright) {
this.accessright = accessright;
}
public Set<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(Set<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public Set<KeyValue> getHostedby() {
return hostedby;
}
public void setHostedby(Set<KeyValue> hostedby) {
this.hostedby = hostedby;
}
public Set<Qualifier> getInstancetype() {
return instancetype;
}
public void setInstancetype(Set<Qualifier> instancetype) {
this.instancetype = instancetype;
}
public Set<String> getLicense() {
return license;
}
public void setLicense(Set<String> license) {
this.license = license;
}
public Set<String> getDistributionlocation() {
return distributionlocation;
}
public void setDistributionlocation(Set<String> distributionlocation) {
this.distributionlocation = distributionlocation;
}
public Set<StructuredProperty> getPid() {
return pid;
}
public void setPid(Set<StructuredProperty> pid) {
this.pid = pid;
}
public Set<StructuredProperty> getAlternateIdentifier() {
return alternateIdentifier;
}
public void setAlternateIdentifier(Set<StructuredProperty> alternateIdentifier) {
this.alternateIdentifier = alternateIdentifier;
}
public Set<String> getDateofacceptance() {
return dateofacceptance;
}
public void setDateofacceptance(Set<String> dateofacceptance) {
this.dateofacceptance = dateofacceptance;
}
public String getProcessingchargeamount() {
return processingchargeamount;
}
public void setProcessingchargeamount(String processingchargeamount) {
this.processingchargeamount = processingchargeamount;
}
public String getProcessingchargecurrency() {
return processingchargecurrency;
}
public void setProcessingchargecurrency(String processingchargecurrency) {
this.processingchargecurrency = processingchargecurrency;
}
public Set<Qualifier> getRefereed() {
return refereed;
}
public void setRefereed(Set<Qualifier> refereed) {
this.refereed = refereed;
}
}

13
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java
View File

@ -8,11 +8,16 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import javax.swing.text.html.Option;
import org.apache.commons.lang3.StringUtils;
import org.stringtemplate.v4.ST;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
@ -94,13 +99,15 @@ public class TemplateFactory {
}
public String getInstance(
final String resultId, final List<String> instancemetadata, final List<String> webresources) {
final List<String> instancemetadata, final String url) {
return getTemplate(resources.getInstance())
.add("instanceId", escapeXml(removePrefix(resultId)))
.add("metadata", instancemetadata)
.add(
"webresources",
(webresources != null ? webresources : new ArrayList<String>())
Optional
.ofNullable(url)
.map(u -> Lists.newArrayList(url))
.orElse(Lists.newArrayList())
.stream()
.filter(StringUtils::isNotBlank)
.map(this::getWebResource)

193
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -10,6 +10,7 @@ import java.io.IOException;
import java.io.Serializable;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
@ -17,7 +18,10 @@ import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.function.Function;
import java.util.stream.Collector;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
@ -27,7 +31,11 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.solr.common.util.URLUtil;
import org.apache.spark.util.LongAccumulator;
import org.dom4j.Document;
import org.dom4j.DocumentException;
@ -49,25 +57,9 @@ import com.mycila.xmltool.XMLTag;
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.MainEntityType;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
import eu.dnetlib.dhp.schema.oaf.ExtraInfo;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.oa.provision.model.XmlInstance;
import eu.dnetlib.dhp.schema.common.*;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
public class XmlRecordFactory implements Serializable {
@ -1112,37 +1104,64 @@ public class XmlRecordFactory implements Serializable {
if (MainEntityType.result.toString().equals(ModelSupport.getMainType(entityType))) {
final List<Instance> instances = ((Result) entity).getInstance();
if (instances != null) {
for (final Instance instance : ((Result) entity).getInstance()) {
groupInstancesByUrl(((Result) entity).getInstance()).forEach(instance -> {
final List<String> fields = Lists.newArrayList();
if (instance.getAccessright() != null && !instance.getAccessright().isBlank()) {
fields
.add(XmlSerializationUtils.mapQualifier("accessright", instance.getAccessright()));
}
if (instance.getCollectedfrom() != null && kvNotBlank(instance.getCollectedfrom())) {
if (instance.getCollectedfrom() != null) {
fields
.add(XmlSerializationUtils.mapKeyValue("collectedfrom", instance.getCollectedfrom()));
.addAll(
instance
.getCollectedfrom()
.stream()
.filter(cf -> kvNotBlank(cf))
.map(cf -> XmlSerializationUtils.mapKeyValue("collectedfrom", cf))
.collect(Collectors.toList()));
}
if (instance.getHostedby() != null && kvNotBlank(instance.getHostedby())) {
fields.add(XmlSerializationUtils.mapKeyValue("hostedby", instance.getHostedby()));
}
if (instance.getDateofacceptance() != null
&& isNotBlank(instance.getDateofacceptance().getValue())) {
if (instance.getHostedby() != null) {
fields
.add(
XmlSerializationUtils
.asXmlElement("dateofacceptance", instance.getDateofacceptance().getValue()));
.addAll(
instance
.getHostedby()
.stream()
.filter(hb -> kvNotBlank(hb))
.map(hb -> XmlSerializationUtils.mapKeyValue("hostedby", hb))
.collect(Collectors.toList()));
}
if (instance.getInstancetype() != null && !instance.getInstancetype().isBlank()) {
if (instance.getDateofacceptance() != null) {
fields
.add(XmlSerializationUtils.mapQualifier("instancetype", instance.getInstancetype()));
.addAll(
instance
.getDateofacceptance()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("dateofacceptance", d))
.collect(Collectors.toList()));
}
if (isNotBlank(instance.getDistributionlocation())) {
if (instance.getInstancetype() != null) {
fields
.add(
XmlSerializationUtils
.asXmlElement("distributionlocation", instance.getDistributionlocation()));
.addAll(
instance
.getInstancetype()
.stream()
.filter(t -> !t.isBlank())
.map(t -> XmlSerializationUtils.mapQualifier("instancetype", t))
.collect(Collectors.toList()));
}
if (instance.getDistributionlocation() != null) {
fields
.addAll(
instance
.getDistributionlocation()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("distributionlocation", d))
.collect(Collectors.toList()));
}
if (instance.getPid() != null) {
fields
@ -1165,32 +1184,39 @@ public class XmlRecordFactory implements Serializable {
.collect(Collectors.toList()));
}
if (instance.getRefereed() != null && !instance.getRefereed().isBlank()) {
if (instance.getRefereed() != null) {
fields
.add(XmlSerializationUtils.mapQualifier("refereed", instance.getRefereed()));
.addAll(
instance
.getRefereed()
.stream()
.filter(Objects::nonNull)
.filter(r -> !r.isBlank())
.map(r -> XmlSerializationUtils.mapQualifier("refereed", r))
.collect(Collectors.toList()));
}
if (instance.getProcessingchargeamount() != null
&& isNotBlank(instance.getProcessingchargeamount().getValue())) {
&& isNotBlank(instance.getProcessingchargeamount())) {
fields
.add(
XmlSerializationUtils
.asXmlElement(
"processingchargeamount", instance.getProcessingchargeamount().getValue()));
"processingchargeamount", instance.getProcessingchargeamount()));
}
if (instance.getProcessingchargecurrency() != null
&& isNotBlank(instance.getProcessingchargecurrency().getValue())) {
&& isNotBlank(instance.getProcessingchargecurrency())) {
fields
.add(
XmlSerializationUtils
.asXmlElement(
"processingchargecurrency", instance.getProcessingchargecurrency().getValue()));
"processingchargecurrency", instance.getProcessingchargecurrency()));
}
children
.add(
templateFactory
.getInstance(instance.getHostedby().getKey(), fields, instance.getUrl()));
}
.getInstance(fields, instance.getUrl()));
});
}
final List<ExternalReference> ext = ((Result) entity).getExternalReference();
if (ext != null) {
@ -1234,6 +1260,85 @@ public class XmlRecordFactory implements Serializable {
return children;
}
private Stream<XmlInstance> groupInstancesByUrl(List<Instance> instance) {
return instance
.stream()
.map(i -> {
i
.setUrl(
i
.getUrl()
.stream()
.filter(this::isValidUrl)
.collect(Collectors.toList()));
return i;
})
.filter(
i -> Optional
.ofNullable(i.getUrl())
.map(u -> !u.isEmpty())
.orElse(false))
.map(this::pickByUrl)
.collect(Collectors.groupingBy(ImmutablePair::getLeft))
.values()
.stream()
.map(this::mergeInstances);
}
private boolean isValidUrl(String url) {
try {
new URL(url).toURI();
return true;
} catch (Exception e) {
return false;
}
}
private ImmutablePair<String, Instance> pickByUrl(Instance i) {
return new ImmutablePair<>(i.getUrl().get(0), i);
}
private XmlInstance mergeInstances(List<ImmutablePair<String, Instance>> instances) {
final XmlInstance instance = new XmlInstance();
instance.setUrl(instances.get(0).getLeft());
instance
.setAccessright(
instances
.stream()
.map(Pair::getValue)
.map(Instance::getAccessright)
.min(new AccessRightComparator<AccessRight>())
.orElse(XmlInstance.UNKNOWN_ACCESS_RIGHT));
instances.forEach(p -> {
final Instance i = p.getRight();
instance.getCollectedfrom().add(i.getCollectedfrom());
instance.getHostedby().add(i.getHostedby());
instance.getInstancetype().add(i.getInstancetype());
instance.getLicense().add(i.getLicense().getValue());
instance.getDistributionlocation().add(i.getDistributionlocation());
instance.getPid().addAll(i.getPid());
instance.getAlternateIdentifier().addAll(i.getAlternateIdentifier());
instance.getDateofacceptance().add(i.getDateofacceptance().getValue());
instance
.setProcessingchargeamount(
Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null));
instance
.setProcessingchargecurrency(
Optional.ofNullable(i.getProcessingchargecurrency()).map(c -> c.getValue()).orElse(null));
instance.getRefereed().add(i.getRefereed());
});
if (instance.getHostedby().size() > 1
&& instance.getHostedby().stream().anyMatch(hb -> ModelConstants.UNKNOWN_REPOSITORY.equals(hb))) {
instance.getHostedby().remove(ModelConstants.UNKNOWN_REPOSITORY);
}
return instance;
}
private boolean isDuplicate(final RelatedEntityWrapper link) {
return ModelConstants.DEDUP.equalsIgnoreCase(link.getRelation().getSubRelType());
}

2
dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/template/instance.st
View File

@ -1,4 +1,4 @@
<instance id="$instanceId$">
<instance>
$metadata:{ it | $it$ }$
$webresources:{ it | $it$ }$
</instance>

22
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -12,7 +12,6 @@ import org.apache.commons.io.IOUtils;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
@ -54,18 +53,19 @@ public class XmlRecordFactoryTest {
System.out.println(doc.asXML());
Assertions.assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
Assertions.assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
Assertions.assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
Assertions.assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
assertEquals("0000-0001-9613-9956", doc.valueOf("//creator[@rank = '2']/@orcid"));
assertEquals("", doc.valueOf("//creator[@rank = '2']/@orcid_pending"));
Assertions.assertEquals("doi", doc.valueOf("//instance/pid/@classid"));
Assertions.assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()"));
assertEquals("doi", doc.valueOf("//instance/pid/@classid"));
assertEquals("10.1109/TED.2018.2853550", doc.valueOf("//instance/pid/text()"));
Assertions.assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
Assertions.assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
// TODO add assertions based of values extracted from the XML record
assertEquals("doi", doc.valueOf("//instance/alternateidentifier/@classid"));
assertEquals("10.5689/LIB.2018.2853550", doc.valueOf("//instance/alternateidentifier/text()"));
assertEquals(3, doc.selectNodes("//instance").size());
}
@Test
@ -96,7 +96,7 @@ public class XmlRecordFactoryTest {
final Document doc = new SAXReader().read(new StringReader(xml));
assertNotNull(doc);
System.out.println(doc.asXML());
Assertions.assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
assertEquals("2021-01-01", doc.valueOf("//validated/@date"));
}
@Test

793
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
View File

@ -412,9 +412,800 @@
"value": ""
},
"url": [
"http://juuli.fi/Record/0331473718",
"http://dx.doi.org/10.1109/TED.2018.2853550"
]
},
{
"pid": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1109/TED.2018.2853550"
}
],
"alternateIdentifier": [
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.5689/LIB.2018.2853550"
}
],
"accessright": {
"classid": "CLOSED",
"classname": "Closed Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"collectedfrom": {
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"key": "10|od______3456::b2b9ce8435390bcbfc05f3cae3948567",
"value": "A wonderful repository"
},
"dateofacceptance": {
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
"value": "2020-01-01"
},
"distributionlocation": "",
"hostedby": {
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
},
"trust": ""
},
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