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mergin with branch beta

This commit is contained in:
Miriam Baglioni 2021-08-13 10:31:35 +02:00
parent 32fd75691f dc8b05b39e
commit f4ec81c92c
6 changed files with 125 additions and 74 deletions
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4
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -231,9 +231,7 @@ object DoiBoostMappingUtil {
var hb = new KeyValue
if (item != null) {
hb.setValue(item.officialname)
hb.setKey(generateDSId(item.id))
//TODO replace with the one above as soon as the new HBM will be used
//hb.setKey(item.id)
hb.setKey(item.id)
if (item.openAccess) {
i.setAccessright(getOpenAccessQualifier())
i.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)

82
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
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@ -28,10 +28,7 @@ import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.Document;
import org.dom4j.DocumentFactory;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.dom4j.*;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
@ -112,43 +109,40 @@ public abstract class AbstractMdRecordToOafMapper {
this.forceOriginalId = false;
}
public List<Oaf> processMdRecord(final String xml) {
try {
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
public List<Oaf> processMdRecord(final String xml) throws DocumentException {
final Document doc = DocumentHelper
.parseText(
xml
.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
final KeyValue collectedFrom = getProvenanceDatasource(
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
final Document doc = DocumentHelper
.parseText(
xml
.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3)
.replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3));
if (collectedFrom == null) {
return Lists.newArrayList();
}
final KeyValue collectedFrom = getProvenanceDatasource(
doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
if (hostedBy == null) {
return Lists.newArrayList();
}
final DataInfo info = prepareDataInfo(doc, invisible);
final long lastUpdateTimestamp = new Date().getTime();
final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
final String type = getResultType(doc, instances);
return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
} catch (final Exception e) {
throw new RuntimeException(e);
if (collectedFrom == null) {
return Lists.newArrayList();
}
final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
? collectedFrom
: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
if (hostedBy == null) {
return Lists.newArrayList();
}
final DataInfo info = prepareDataInfo(doc, invisible);
final long lastUpdateTimestamp = new Date().getTime();
final List<Instance> instances = prepareInstances(doc, info, collectedFrom, hostedBy);
final String type = getResultType(doc, instances);
return createOafs(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
}
protected String getResultType(final Document doc, final List<Instance> instances) {
@ -499,22 +493,6 @@ public abstract class AbstractMdRecordToOafMapper {
return vocs.getTermAsQualifier(schemeId, classId);
}
protected List<StructuredProperty> prepareListStructProps(
final Node node,
final String xpath,
final String xpathClassId,
final String schemeId,
final DataInfo info) {
final List<StructuredProperty> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
final String classId = n.valueOf(xpathClassId).trim();
res.add(structuredProperty(n.getText(), prepareQualifier(classId, schemeId), info));
}
return res;
}
protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
final Node node,
final String xpath,

3
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -17,6 +17,7 @@ import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -158,7 +159,7 @@ public class GenerateEntitiesApplication {
final String id,
final String s,
final boolean shouldHashId,
final VocabularyGroup vocs) {
final VocabularyGroup vocs) throws DocumentException {
final String type = StringUtils.substringAfter(id, ":");
switch (type.toLowerCase()) {

6
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
View File

@ -9,6 +9,7 @@ import java.io.IOException;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.dom4j.DocumentException;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -44,7 +45,7 @@ class GenerateEntitiesApplicationTest {
}
@Test
void testMergeResult() throws IOException {
void testMergeResult() throws IOException, DocumentException {
Result publication = getResult("oaf_record.xml", Publication.class);
Result dataset = getResult("odf_dataset.xml", Dataset.class);
Result software = getResult("odf_software.xml", Software.class);
@ -76,7 +77,8 @@ class GenerateEntitiesApplicationTest {
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, DocumentException {
final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName));
return new OdfToOafMapper(vocs, false, true)
.processMdRecord(xml)

43
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -13,6 +13,7 @@ import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.dom4j.DocumentException;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
@ -48,7 +49,7 @@ class MappersTest {
}
@Test
void testPublication() throws IOException {
void testPublication() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
@ -145,7 +146,7 @@ class MappersTest {
}
@Test
void testPublication_PubMed() throws IOException {
void testPublication_PubMed() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record_pubmed.xml")));
@ -217,7 +218,7 @@ class MappersTest {
}
@Test
void testPublicationInvisible() throws IOException {
void testPublicationInvisible() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
@ -233,7 +234,17 @@ class MappersTest {
}
@Test
void testDataset() throws IOException {
void testOdfFwfEBookLibrary() throws IOException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_fwfebooklibrary.xml")));
assertThrows(
IllegalArgumentException.class,
() -> new OdfToOafMapper(vocs, false, true).processMdRecord(xml));
}
@Test
void testDataset() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_dataset.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@ -346,7 +357,7 @@ class MappersTest {
}
@Test
void testOdfBielefeld() throws IOException {
void testOdfBielefeld() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_bielefeld.xml")));
@ -394,7 +405,7 @@ class MappersTest {
}
@Test
void testOpentrial() throws IOException {
void testOpentrial() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_opentrial.xml")));
@ -511,7 +522,7 @@ class MappersTest {
}
@Test
void testSoftware() throws IOException {
void testSoftware() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_software.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@ -530,7 +541,7 @@ class MappersTest {
}
@Test
void testClaimDedup() throws IOException {
void testClaimDedup() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_dedup.xml")));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@ -544,7 +555,7 @@ class MappersTest {
}
@Test
void testNakala() throws IOException {
void testNakala() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_nakala.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@ -572,7 +583,7 @@ class MappersTest {
}
@Test
void testEnermaps() throws IOException {
void testEnermaps() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("enermaps.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@ -597,7 +608,7 @@ class MappersTest {
}
@Test
void testClaimFromCrossref() throws IOException {
void testClaimFromCrossref() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_crossref.xml")));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@ -614,7 +625,7 @@ class MappersTest {
}
@Test
void testODFRecord() throws IOException {
void testODFRecord() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
@ -628,7 +639,7 @@ class MappersTest {
}
@Test
void testTextGrid() throws IOException {
void testTextGrid() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("textgrid.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@ -662,7 +673,7 @@ class MappersTest {
}
@Test
void testBologna() throws IOException {
void testBologna() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf-bologna.xml")));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@ -679,7 +690,7 @@ class MappersTest {
}
@Test
void testJairo() throws IOException {
void testJairo() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_jairo.xml")));
final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@ -703,7 +714,7 @@ class MappersTest {
}
@Test
void testOdfFromHdfs() throws IOException {
void testOdfFromHdfs() throws IOException, DocumentException {
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_from_hdfs.xml")));

61
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_fwfebooklibrary.xml Normal file
View File

@ -0,0 +1,61 @@
<?xml version="1.0" encoding="UTF-8"?>
<record xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
xmlns:oaf="http://namespace.openaire.eu/oaf"
xmlns:datacite="http://datacite.org/schema/kernel-4"
xmlns:dri="http://www.driver-repository.eu/namespace/dri"
xmlns:xs="http://www.w3.org/2001/XMLSchema"
xmlns:dr="http://www.driver-repository.eu/namespace/dr"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<header xmlns="http://www.openarchives.org/OAI/2.0/">
<identifier>oai:e-book.fwf.ac.at:o:116</identifier>
<datestamp>2020-04-08T13:25:21.742Z</datestamp>
<setSpec>text</setSpec>
<dr:dateOfTransformation>2021-08-12T00:16:55.365Z</dr:dateOfTransformation>
</header>
<metadata>
<datacite:resource>
<datacite:alternateIdentifiers>
<datacite:alternateIdentifier alternateIdentifierType="ISBN">978-3-205-77704-5</datacite:alternateIdentifier>
<datacite:alternateIdentifier alternateIdentifierType="URL">https://e-book.fwf.ac.at/o:116</datacite:alternateIdentifier>
</datacite:alternateIdentifiers>
<datacite:relatedIdentifiers/>
<datacite:description descriptionType="Abstract">Although small and not particularly peoples both Chechens and Palestinians became famous for suicide bomber attacks in recent years. This can - partly - be explained by the unrecognised collective traumas of the past. Both Chechens and Palestinians experienced collective traumas in the 1940ties. The entire Chechen population wad deported by Josef Stalin to Kasakhstan, Kirgysia and Sibiria in February 1944 under the pretext of collaboration with the Third Reich. Those who survived were allowed to return in 1957 to Chechenya. Half of the Palestinian Arab population was expelled from Palestine in 1947/48, when fighting erupted between Jews and Arabs. The refugees were never allowed to return. The memory of the deportation/expulsion was kept alive. The founding traumas contributed to the development of Chechen and Palestinian nationalism. Chechens and Palestinians till today suffer from their collective traumas, which stayed unrecognised and therefore create psychological and political problems for the following generations - and for their adverseries. The phenomenon of the "closed circle of violence" created a phobic collective behaviour, which led for example Chechens to the illusionary declaration of independence in 1991. It also led to the individual overreaction of young Chechens or Palestinians, who became living bombs. The collective Trauma, if untreated, poses a threat to any peaceful political solution.</datacite:description>
<datacite:description descriptionType="Abstract">1. Einleitung Ausgehend von der Fragestellung, warum gerade bei Tschetschenen und Palästinensern der Selbstmordterrorismus in den letzten Jahren so populär geworden ist, analysiert die Autorin die Geschichte dieser beiden Völker. Einer der Gründe ist bisher wenig beachtet worden. Der Einfluss eines kollektiven Traumas, das als solches nicht anerkannt, behandelt und auch nicht einer politischen Lösung zugeführt wurde. 2. Geschichte der Palästinenser und Tschetschenen Im Zuge der Errichtung Israels im Unabhängigkeitskrieg 1948 verlor die Hälfte des palästinensischen Volkes - 750.000 Menschen - ihre Heimat. Unter der Führung von Jassir Arafat kämpften sie in den Jahrzehnten danach - mit Gewalt und am Verhandlungstisch - um einen eigenen Staat. Das Recht auf Rückkehr spielte dabei immer eine besondere Rolle. Die "Nakbah", die als Katastrophe empfundene Vertreibung 1948, wurde dabei Bezugs- und Angelpunkt mehrer Generationen von Flüchtlingen. Die Weigerung Israels, die Mitverantwortung für die Vertreibung der Palästinenser zu übernehmen und das kollektive Trauma der Palästinenser anzuerkennen - aus Angst vor einer Infragestellung des eigenen Staates - ist einer der Gründe, warum der Nahostkonflikt bisher nicht gelöst werden konnte. Auch die Tschetschenen durften jahrzehntelang über die Deportation ihres Volkes nicht einmal sprechen. Hatte Josef Stallin sie erst unter dem Vorwand der Kollaboration mit Nazi-Deutschland deportiert, waren sie zwar nach seinem Tod in die Heimat zurückgekehrt, lebten dort aber jahrzehntelang weiterhin als "unzuverlässiges Volk". Das kollektive Trauma der Deportation konnte nur mündlich überliefert werden. Mit dem Zusammenbruch der Sowjetunion brach der ungelöste Konflikt zwischen Tschetschenien und Russland sofort auf, das Land ging in blutigen Kriegen unter. 3. Zusammenfassung Die kollektive Erinnerung ist in den vergangenen Jahrzehnten zu einem zentralen Forschungsthema geworden. Der vorsichtige Einsatz von in der Individualpsychologie gewonnenen Erkenntnissen in der Behandlung von kollektiven Traumata, um zu einer politischen Lösung zu kommen, ist eine Chance. Das Studium historischer Fakten in Kombination mit den Erkenntnissen der Psychologie und Psychiatrie bietet die Basis für eine politische Lösung. Die vorliegende Arbeit zeigt, dass kollektive Traumata, die nicht behandelt werden, immer wieder, auch Generationen später, zu kollektiven Reaktionen führen können, die auf den ersten Blick irrational erscheinen. Die vielleicht radikalste Form des politischen Widerstandes, das Selbstmordattentat, ist dafür ein Beispiel.</datacite:description>
<datacite:language>deu/ger</datacite:language>
<datacite:publisher>Böhlau</datacite:publisher>
<datacite:format>application/pdf</datacite:format>
<datacite:titles>
<datacite:title xml:lang="de">Trauma und Terror: Zum palästinensischen und tschetschenischen Nationalismus</datacite:title>
</datacite:titles>
<datacite:creators>
<datacite:creator>
<datacite:creatorName nameType="Personal">Szyszkowitz, Tessa</datacite:creatorName>
<datacite:givenName>Tessa</datacite:givenName>
<datacite:familyName>Szyszkowitz</datacite:familyName>
</datacite:creator>
</datacite:creators>
<datacite:subjects>
<datacite:subject xml:lang="en">Trauma, Terror, Palestinians, Suicide attacks, Recognition, Chechens</datacite:subject>
<datacite:subject xml:lang="en">ÖFOS 2002, Contemporary history</datacite:subject>
<datacite:subject xml:lang="en">BIC Standard Subject Categories, Postwar 20th century history, from c 1945 to c 2000 (HBLW3)</datacite:subject>
<datacite:subject xml:lang="de">ÖFOS 2002, Zeitgeschichte</datacite:subject>
</datacite:subjects>
<datacite:sizes>
<datacite:size>14.02 MB</datacite:size>
</datacite:sizes>
<datacite:dates>
<datacite:date dateType="Issued">2007</datacite:date>
</datacite:dates>
</datacite:resource>
<dr:CobjCategory type="literature">literature</dr:CobjCategory>
<oaf:dateAccepted>2007-01-01</oaf:dateAccepted>
<oaf:accessrights>http://creativecommons.org/licenses/by-nc-nd/3.0/at/</oaf:accessrights>
<oaf:license>http://creativecommons.org/licenses/by-nc-nd/3.0/at/</oaf:license>
<oaf:language>deu/ger</oaf:language>
<oaf:projectid>fwf_________::D 3929</oaf:projectid>
<oaf:hostedBy name="FWF-E-Book-Library" id="opendoar____::2639"/>
<oaf:collectedFrom name="FWF-E-Book-Library" id="opendoar____::2639"/>
<oaf:fulltext>https://fedora.e-book.fwf.ac.at/fedora/get/o:116/bdef:Content/download</oaf:fulltext>
</metadata>
</record>