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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 2021-12-13 15:01:47 +01:00
parent b113586207 b70ecccea0
commit 936578aaf1
8 changed files with 244 additions and 9 deletions
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8
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn);
}
}
// add the term names as synonyms
vocs.vocs.values().forEach(voc -> {
voc.getTerms().values().forEach(term -> {
voc.addSynonym(term.getName().toLowerCase(), term.getId());
});
});
return vocs;
}

36
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -16,6 +16,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
@ -131,7 +133,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return true;
}
public static <T extends Oaf> T cleanup(T value) {
public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
@ -250,6 +252,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
if (r instanceof Publication) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Dataset) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Software) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof OtherResearchProduct) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
}
}
if (Objects.nonNull(i.getPid())) {
i.setPid(processPidCleaning(i.getPid()));
}

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

@ -88,7 +88,7 @@ public class CleanGraphSparkJob {
readTableFromPath(spark, inputPath, clazz)
.map((MapFunction<T, T>) GraphCleaningFunctions::fixVocabularyNames, Encoders.bean(clazz))
.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
.map((MapFunction<T, T>) GraphCleaningFunctions::cleanup, Encoders.bean(clazz))
.map((MapFunction<T, T>) value -> GraphCleaningFunctions.cleanup(value, vocs), Encoders.bean(clazz))
.filter((FilterFunction<T>) GraphCleaningFunctions::filter)
.write()
.mode(SaveMode.Overwrite)

19
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
View File

@ -151,6 +151,12 @@ public class GraphCleaningFunctionsTest {
assertEquals("0018", p_out.getInstance().get(0).getInstancetype().getClassid());
assertEquals("Annotation", p_out.getInstance().get(0).getInstancetype().getClassname());
assertEquals("0027", p_out.getInstance().get(1).getInstancetype().getClassid());
assertEquals("Model", p_out.getInstance().get(1).getInstancetype().getClassname());
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassid());
assertEquals("xyz", p_out.getInstance().get(2).getInstancetype().getClassname());
assertEquals("CLOSED", p_out.getInstance().get(0).getAccessright().getClassid());
assertEquals("Closed Access", p_out.getInstance().get(0).getAccessright().getClassname());
@ -164,7 +170,7 @@ public class GraphCleaningFunctionsTest {
List<Instance> poi = p_out.getInstance();
assertNotNull(poi);
assertEquals(1, poi.size());
assertEquals(3, poi.size());
final Instance poii = poi.get(0);
assertNotNull(poii);
@ -192,7 +198,7 @@ public class GraphCleaningFunctionsTest {
assertEquals(5, p_out.getTitle().size());
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
assertEquals(3, p_cleaned.getTitle().size());
@ -211,9 +217,12 @@ public class GraphCleaningFunctionsTest {
assertEquals("1970-10-07", p_cleaned.getDateofacceptance().getValue());
assertEquals("0038", p_cleaned.getInstance().get(2).getInstancetype().getClassid());
assertEquals("Other literature type", p_cleaned.getInstance().get(2).getInstancetype().getClassname());
final List<Instance> pci = p_cleaned.getInstance();
assertNotNull(pci);
assertEquals(1, pci.size());
assertEquals(3, pci.size());
final Instance pcii = pci.get(0);
assertNotNull(pcii);
@ -281,7 +290,7 @@ public class GraphCleaningFunctionsTest {
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
}
@ -292,7 +301,7 @@ public class GraphCleaningFunctionsTest {
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json"));
Publication p_in = MAPPER.readValue(json, Publication.class);
Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out);
Publication cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));

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

@ -708,7 +708,7 @@ class MappersTest {
assertEquals(1, p.getTitle().size());
assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
final Publication p_cleaned = cleanup(fixVocabularyNames(p));
final Publication p_cleaned = cleanup(fixVocabularyNames(p), vocs);
assertNotNull(p_cleaned.getTitle());
assertFalse(p_cleaned.getTitle().isEmpty());

172
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -403,6 +403,178 @@
"http://juuli.fi/Record/0275158616",
"http://dx.doi.org/10.1007/s109090161569x"
]
},
{
"pid": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1002/s21010127267xy"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1008/abcd"
}
],
"alternateIdentifier": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1007/s109090161569x"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1009/qwerty"
}
],
"accessright": {
"classid": "CLOSED",
"classname": "CLOSED",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"collectedfrom": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"dateofacceptance": {
"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"
},
"value": "2016-01-01"
},
"distributionlocation": "",
"hostedby": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"instancetype": {
"classid": "Model",
"classname": "Model",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
},
"url": [
"http://dx.doi.org/10.1002/s21010127267xy"
]
},
{
"pid": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1002/s21010127267xy"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1008/abcd"
}
],
"alternateIdentifier": [
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1007/s109090161569x"
},
{
"dataInfo": null,
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1009/qwerty"
}
],
"accessright": {
"classid": "CLOSED",
"classname": "CLOSED",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"collectedfrom": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"dateofacceptance": {
"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"
},
"value": "2016-01-01"
},
"distributionlocation": "",
"hostedby": {
"key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747",
"value": "VIRTA"
},
"instancetype": {
"classid": "xyz",
"classname": "xyz",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
},
"url": [
"http://dx.doi.org/10.1002/t32121238378t"
]
}
],
"journal": {

12
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -1212,6 +1212,17 @@ public class XmlRecordFactory implements Serializable {
"processingchargecurrency", instance.getProcessingchargecurrency()));
}
if (instance.getLicense() != null) {
fields
.addAll(
instance
.getLicense()
.stream()
.filter(d -> isNotBlank(d))
.map(d -> XmlSerializationUtils.asXmlElement("license", d))
.collect(Collectors.toList()));
}
children
.add(
templateFactory
@ -1282,6 +1293,7 @@ public class XmlRecordFactory implements Serializable {
.collect(Collectors.groupingBy(ImmutablePair::getLeft))
.values()
.stream()
.filter(Objects::nonNull)
.map(this::mergeInstances);
}

2
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
View File

@ -541,7 +541,7 @@
},
"trust": ""
},
"value": ""
"value": "CC-BY"
},
"url": [
"http://dx.doi.org/10.1109/TED.2018.2853550"