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mergin with branch beta

This commit is contained in:
Miriam Baglioni 2022-08-08 12:30:31 +02:00
parent 5968ec018d d85ba3c1a9
commit 390013a4b2
194 changed files with 2674 additions and 13199 deletions
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58
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -419,4 +419,62 @@ public class OafMapperUtils {
m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo)));
return m;
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
return getRelation(
source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(),
entity.getLastupdatetimestamp(), validationDate, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp) {
return getRelation(
source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp,
final String validationDate,
final List<KeyValue> properties) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setCollectedfrom(collectedfrom);
rel.setDataInfo(dataInfo);
rel.setLastupdatetimestamp(lastupdatetimestamp);
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
rel.setProperties(properties);
return rel;
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
View File

@ -118,7 +118,7 @@ public class CollectorWorker extends ReportingJob {
return new RestCollectorPlugin(clientParams);
case file:
return new FileCollectorPlugin(fileSystem);
case fileGZip:
case fileGzip:
return new FileGZipCollectorPlugin(fileSystem);
case other:
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException;
public interface CollectorPlugin {
enum NAME {
oai, other, rest_json2xml, file, fileGZip;
oai, other, rest_json2xml, file, fileGzip;
public enum OTHER_NAME {
mdstore_mongodb_dump, mdstore_mongodb

23
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java
View File

@ -17,6 +17,9 @@ public class PMArticle implements Serializable {
* the Pubmed Identifier
*/
private String pmid;
private String pmcId;
/**
* the DOI
*/
@ -122,7 +125,7 @@ public class PMArticle implements Serializable {
/**
* The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element.
* Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles.
* Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles.
* The NLM journal title abbreviation is exported in the <MedlineTA> element.
*
* @return the pubmed Journal Extracted
@ -140,10 +143,11 @@ public class PMArticle implements Serializable {
}
/**
* English-language abstracts are taken directly from the published article.
* If the article does not have a published abstract, the National Library of Medicine does not create one,
* thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
* labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
* <ArticleTitle> contains the entire title of the journal article. <ArticleTitle> is always in English;
* those titles originally published in a non-English language and translated for <ArticleTitle> are enclosed in square brackets.
* All titles end with a period unless another punctuation mark such as a question mark or bracket is present.
* Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl).
* Corporate/collective authors may appear at the end of <ArticleTitle> for citations up to about the year 2000.
*
* @return the extracted pubmed Title
*/
@ -250,4 +254,13 @@ public class PMArticle implements Serializable {
public List<PMGrant> getGrants() {
return grants;
}
public String getPmcId() {
return pmcId;
}
public PMArticle setPmcId(String pmcId) {
this.pmcId = pmcId;
return this;
}
}

5
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
View File

@ -584,7 +584,12 @@ object DataciteToOAFTransformation {
JField("awardUri", JString(awardUri)) <- fundingReferences
} yield awardUri
val oid = result.getId
result.setId(IdentifierFactory.createIdentifier(result))
if (!result.getId.equalsIgnoreCase(oid)) {
result.setOriginalId((oid :: List(doi)).asJava)
}
var relations: List[Relation] =
awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null)

1
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala
View File

@ -98,6 +98,7 @@ class PMParser(xml: XMLEventReader) extends Iterator[PMArticle] {
case "PMID" => currentArticle.setPmid(text.trim)
case "ArticleId" =>
if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim)
case "Language" => currentArticle.setLanguage(text.trim)
case "ISSN" => currentJournal.setIssn(text.trim)
case "GrantID" => currentGrant.setGrantID(text.trim)

50
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
View File

@ -4,9 +4,12 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
import eu.dnetlib.dhp.schema.oaf._
import collection.JavaConverters._
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import collection.JavaConverters._
import java.util.regex.Pattern
import scala.collection.mutable.ListBuffer
/**
*/
@ -14,6 +17,9 @@ object PubMedToOaf {
val SUBJ_CLASS = "keywords"
val OAI_HEADER = "oai:pubmedcentral.nih.gov:"
val OLD_PMC_PREFIX = "od_______267::"
val urlMap = Map(
"pmid" -> "https://pubmed.ncbi.nlm.nih.gov/",
"doi" -> "https://dx.doi.org/"
@ -50,6 +56,15 @@ object PubMedToOaf {
null
}
def createOriginalOpenaireId(article: PMArticle): String = {
if (StringUtils.isNotEmpty(article.getPmcId)) {
val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC", "")}")
s"$OLD_PMC_PREFIX$md5"
} else
null
}
/** Create an instance of class extends Result
* starting from OAF instanceType value
*
@ -122,16 +137,27 @@ object PubMedToOaf {
return null
// MAP PMID into pid with classid = classname = pmid
val pidList: List[StructuredProperty] = List(
OafMapperUtils.structuredProperty(
article.getPmid,
PidType.pmid.toString,
PidType.pmid.toString,
val pidList = ListBuffer[StructuredProperty]()
pidList += OafMapperUtils.structuredProperty(
article.getPmid,
PidType.pmid.toString,
PidType.pmid.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
dataInfo
)
if (StringUtils.isNotBlank(article.getPmcId)) {
pidList += OafMapperUtils.structuredProperty(
article.getPmcId,
PidType.pmc.toString,
PidType.pmc.toString,
ModelConstants.DNET_PID_TYPES,
ModelConstants.DNET_PID_TYPES,
dataInfo
)
)
}
if (pidList == null)
return null
@ -186,6 +212,7 @@ object PubMedToOaf {
val urlLists: List[String] = pidList
.map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
.filter(t => t._1.nonEmpty)
.toList
.map(t => t._1 + t._2)
if (urlLists != null)
pubmedInstance.setUrl(urlLists.asJava)
@ -262,7 +289,14 @@ object PubMedToOaf {
if (authors != null && authors.nonEmpty)
result.setAuthor(authors.asJava)
result.setOriginalId(pidList.map(s => s.getValue).asJava)
if (StringUtils.isNotEmpty(article.getPmcId)) {
val originalIDS = ListBuffer[String]()
originalIDS += createOriginalOpenaireId(article)
pidList.map(s => s.getValue).foreach(p => originalIDS += p)
result.setOriginalId(originalIDS.asJava)
} else
result.setOriginalId(pidList.map(s => s.getValue).asJava)
result.setId(article.getPmid)

22
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJobTest.java
View File

@ -2,6 +2,7 @@
package eu.dnetlib.dhp.actionmanager.ror;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.io.FileInputStream;
import java.util.List;
@ -38,25 +39,20 @@ class GenerateRorActionSetJobTest {
.readValue(IOUtils.toString(getClass().getResourceAsStream("ror_org.json")), RorOrganization.class);
final List<AtomicAction<? extends Oaf>> aas = GenerateRorActionSetJob.convertRorOrg(r);
Assertions.assertEquals(3, aas.size());
Assertions.assertEquals(1, aas.size());
assertEquals(Organization.class, aas.get(0).getClazz());
assertEquals(Relation.class, aas.get(1).getClazz());
assertEquals(Relation.class, aas.get(2).getClazz());
final Organization o = (Organization) aas.get(0).getPayload();
final Relation r1 = (Relation) aas.get(1).getPayload();
final Relation r2 = (Relation) aas.get(2).getPayload();
assertEquals(o.getId(), r1.getSource());
assertEquals(r1.getSource(), r2.getTarget());
assertEquals(r2.getSource(), r1.getTarget());
assertEquals(ModelConstants.IS_PARENT_OF, r1.getRelClass());
assertEquals(ModelConstants.IS_CHILD_OF, r2.getRelClass());
assertNotNull(o);
assertNotNull(o.getCountry());
assertEquals("AU", o.getCountry().getClassid());
assertNotNull(o.getLegalname());
assertEquals("Mount Stromlo Observatory", o.getLegalname().getValue());
System.out.println(mapper.writeValueAsString(o));
System.out.println(mapper.writeValueAsString(r1));
System.out.println(mapper.writeValueAsString(r2));
}
@Test

257
dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml
View File

@ -195,7 +195,9 @@
<Title>Biochemical and biophysical research communications</Title>
<ISOAbbreviation>Biochem Biophys Res Commun</ISOAbbreviation>
</Journal>
<ArticleTitle>Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution.</ArticleTitle>
<ArticleTitle>Delineation of the intimate details of the backbone conformation of pyridine nucleotide
coenzymes in aqueous solution.
</ArticleTitle>
<Pagination>
<MedlinePgn>1173-9</MedlinePgn>
</Pagination>
@ -473,7 +475,9 @@
<Title>Biochemical and biophysical research communications</Title>
<ISOAbbreviation>Biochem Biophys Res Commun</ISOAbbreviation>
</Journal>
<ArticleTitle>Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake.</ArticleTitle>
<ArticleTitle>Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and
inhibition of their uptake.
</ArticleTitle>
<Pagination>
<MedlinePgn>1338-43</MedlinePgn>
</Pagination>
@ -657,7 +661,8 @@
<Title>Biochemical and biophysical research communications</Title>
<ISOAbbreviation>Biochem Biophys Res Commun</ISOAbbreviation>
</Journal>
<ArticleTitle>Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.</ArticleTitle>
<ArticleTitle>Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin.
</ArticleTitle>
<Pagination>
<MedlinePgn>1349-56</MedlinePgn>
</Pagination>
@ -1627,7 +1632,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal amidase-esterase.</ArticleTitle>
<ArticleTitle>Comparison between procaine and isocarboxazid metabolism in vitro by a liver microsomal
amidase-esterase.
</ArticleTitle>
<Pagination>
<MedlinePgn>1517-21</MedlinePgn>
</Pagination>
@ -2030,7 +2037,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Radiochemical assay of glutathione S-epoxide transferase and its enhancement by phenobarbital in rat liver in vivo.</ArticleTitle>
<ArticleTitle>Radiochemical assay of glutathione S-epoxide transferase and its enhancement by
phenobarbital in rat liver in vivo.
</ArticleTitle>
<Pagination>
<MedlinePgn>1569-72</MedlinePgn>
</Pagination>
@ -2350,7 +2359,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists.</ArticleTitle>
<ArticleTitle>Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled
beta-adrenergic antagonists.
</ArticleTitle>
<Pagination>
<MedlinePgn>1651-8</MedlinePgn>
</Pagination>
@ -2598,7 +2609,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP concentration and on incorporation of 32Pi into ATP in rat fat cells.</ArticleTitle>
<ArticleTitle>The effect of adrenaline and of alpha- and beta-adrenergic blocking agents on ATP
concentration and on incorporation of 32Pi into ATP in rat fat cells.
</ArticleTitle>
<Pagination>
<MedlinePgn>1659-62</MedlinePgn>
</Pagination>
@ -2851,7 +2864,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the presence of valinomycin.</ArticleTitle>
<ArticleTitle>Action of propranolol on mitochondrial functions--effects on energized ion fluxes in the
presence of valinomycin.
</ArticleTitle>
<Pagination>
<MedlinePgn>1701-5</MedlinePgn>
</Pagination>
@ -3265,7 +3280,8 @@
</Chemical>
<Chemical>
<RegistryNumber>EC 2.6.1.16</RegistryNumber>
<NameOfSubstance UI="D005945">Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)</NameOfSubstance>
<NameOfSubstance UI="D005945">Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)
</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>EC 2.7.-</RegistryNumber>
@ -3324,7 +3340,9 @@
<DescriptorName UI="D005944" MajorTopicYN="N">Glucosamine</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D005945" MajorTopicYN="N">Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)</DescriptorName>
<DescriptorName UI="D005945" MajorTopicYN="N">Glutamine-Fructose-6-Phosphate Transaminase
(Isomerizing)
</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
@ -3463,7 +3481,8 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines.</ArticleTitle>
<ArticleTitle>Inhibition of aldehyde reductase by acidic metabolites of the biogenic amines.
</ArticleTitle>
<Pagination>
<MedlinePgn>1731-3</MedlinePgn>
</Pagination>
@ -3696,7 +3715,9 @@
<Title>Biochemical pharmacology</Title>
<ISOAbbreviation>Biochem Pharmacol</ISOAbbreviation>
</Journal>
<ArticleTitle>Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat.</ArticleTitle>
<ArticleTitle>Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central
catecholaminergic neurons of the rat.
</ArticleTitle>
<Pagination>
<MedlinePgn>1739-42</MedlinePgn>
</Pagination>
@ -4602,12 +4623,19 @@
<Title>Arzneimittel-Forschung</Title>
<ISOAbbreviation>Arzneimittelforschung</ISOAbbreviation>
</Journal>
<ArticleTitle>[Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)].</ArticleTitle>
<ArticleTitle>[Biochemical studies on camomile components/III. In vitro studies about the antipeptic
activity of (--)-alpha-bisabolol (author's transl)].
</ArticleTitle>
<Pagination>
<MedlinePgn>1352-4</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>(--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost.</AbstractText>
<AbstractText>(--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not
caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50
percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol
only occurs in case of direct contact. In case of a previous contact with the substrate, the
inhibiting effect is lost.
</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
@ -4626,7 +4654,9 @@
<PublicationType UI="D004740">English Abstract</PublicationType>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<VernacularTitle>Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols</VernacularTitle>
<VernacularTitle>Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die
antipeptische Wirkung des (-)-alpha-Bisabolols
</VernacularTitle>
</Article>
<MedlineJournalInfo>
<Country>Germany</Country>
@ -4753,12 +4783,37 @@
<Title>Arzneimittel-Forschung</Title>
<ISOAbbreviation>Arzneimittelforschung</ISOAbbreviation>
</Journal>
<ArticleTitle>[Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities].</ArticleTitle>
<ArticleTitle>[Demonstration of tumor inhibiting properties of a strongly immunostimulating
low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS
carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a
N-(2-cyanoethylene)-urea. Novel prophylactic possibilities].
</ArticleTitle>
<Pagination>
<MedlinePgn>1369-79</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising.</AbstractText>
<AbstractText>A report is given on the recent discovery of outstanding immunological properties in
BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS
carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent
LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40
percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under
otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development
of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent
LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent.
(Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.)
However this comparison is characterized by the fact that both substances exhibit two quite
different (complementary) mechanisms of action. Leucocyte counts made after application of the
said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with
ifosfamide, the known suppression in the post-therapeutic interval usually found with standard
cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow
conclusions on the immunity status. Since IF can be taken as one of the most efficient
cancerostatics--there is no other chemotherapeutic known up to now that has a more significant
effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally,
the total amount of leucocytes and lymphocytes as well as their time behaviour was determined
from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained
numerical values clearly show that further research work on the prophylactic use of this
substance seems to be necessary and very promising.
</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
@ -4778,7 +4833,11 @@
<PublicationType UI="D004740">English Abstract</PublicationType>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
<VernacularTitle>Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten</VernacularTitle>
<VernacularTitle>Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung
kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid.
Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen
N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten
</VernacularTitle>
</Article>
<MedlineJournalInfo>
<Country>Germany</Country>
@ -5016,7 +5075,20 @@
<MedlinePgn>1400-3</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism.</AbstractText>
<AbstractText>The distribution of blood flow to the subendocardial, medium and subepicardial layers
of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic
(B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C).
Regional myocardial blood flow was determined by means of the particle distribution method. In
normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a
significantly higher flow rate compared with the subepicardial layers. In hypoxia induced
vasodilation this transmural gradient of flow was persistent. In contrast a marked
redistribution of regional flow was observed under pharmacologically induced vasodilation. The
transmural gradient decreased. In contrast to some findings these experiments demonstrate that a
considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by
drugs. The differences observed for the intramural distribution pattern of flow under hypoxia
and drug induced vasodilation support the hypothesis that this pattern reflects corresponding
gradients of regional myocardial metabolism.
</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
@ -5185,4 +5257,151 @@
</ReferenceList>
</PubmedData>
</PubmedArticle>
<PubmedArticle>
<MedlineCitation Status="MEDLINE" Owner="NLM">
<PMID Version="1">4917185</PMID>
<DateCompleted>
<Year>1970</Year>
<Month>10</Month>
<Day>27</Day>
</DateCompleted>
<DateRevised>
<Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Print">
<Journal>
<ISSN IssnType="Print">0003-6919</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>19</Volume>
<Issue>6</Issue>
<PubDate>
<Year>1970</Year>
<Month>Jun</Month>
</PubDate>
</JournalIssue>
<Title>Applied microbiology</Title>
<ISOAbbreviation>Appl Microbiol</ISOAbbreviation>
</Journal>
<ArticleTitle>Bactericidal activity of a broad-spectrum illumination source.</ArticleTitle>
<Pagination>
<MedlinePgn>1013-4</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>Several hours of exposure to Vita-Lite lamps, which have a unique spectral
distribution, give significant killing of cells of Staphylococcus aureus.
</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Himmelfarb</LastName>
<ForeName>P</ForeName>
<Initials>P</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Scott</LastName>
<ForeName>A</ForeName>
<Initials>A</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Thayer</LastName>
<ForeName>P S</ForeName>
<Initials>PS</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType UI="D016428">Journal Article</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>Appl Microbiol</MedlineTA>
<NlmUniqueID>7605802</NlmUniqueID>
<ISSNLinking>0003-6919</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D001431" MajorTopicYN="N">Bacteriological Techniques</DescriptorName>
<QualifierName UI="Q000295" MajorTopicYN="Y">instrumentation</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D008027" MajorTopicYN="Y">Light</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D011830" MajorTopicYN="N">Radiation Effects</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D012706" MajorTopicYN="N">Serratia marcescens</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="N">growth &amp; development</QualifierName>
<QualifierName UI="Q000528" MajorTopicYN="Y">radiation effects</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013210" MajorTopicYN="N">Staphylococcus</DescriptorName>
<QualifierName UI="Q000254" MajorTopicYN="N">growth &amp; development</QualifierName>
<QualifierName UI="Q000528" MajorTopicYN="Y">radiation effects</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D013242" MajorTopicYN="N">Sterilization</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>1970</Year>
<Month>6</Month>
<Day>1</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>1970</Year>
<Month>6</Month>
<Day>1</Day>
<Hour>0</Hour>
<Minute>1</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="entrez">
<Year>1970</Year>
<Month>6</Month>
<Day>1</Day>
<Hour>0</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">4917185</ArticleId>
<ArticleId IdType="pmc">PMC376844</ArticleId>
</ArticleIdList>
<ReferenceList>
<Reference>
<Citation>Photochem Photobiol. 1969 Jan;9(1):99-102</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">4889809</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Endocrinology. 1969 Dec;85(6):1218-21</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">5347623</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Arch Mikrobiol. 1956;24(1):60-79</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">13327987</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>J Bacteriol. 1941 Sep;42(3):353-66</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">16560457</ArticleId>
</ArticleIdList>
</Reference>
</ReferenceList>
</PubmedData>
</PubmedArticle>
</PubmedArticleSet>

13
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala
View File

@ -2,11 +2,14 @@ package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature}
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import org.apache.commons.io.FileUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.functions.{col, count}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{AfterEach, BeforeEach, Test}
@ -70,17 +73,15 @@ class DataciteToOAFTest extends AbstractVocabularyTest {
assertEquals(100, nativeSize)
spark.read.load(targetPath).printSchema();
val result: Dataset[Oaf] = spark.read.load(targetPath).as[Oaf]
val result: Dataset[String] =
spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING)
result
.map(s => s.getClass.getSimpleName)
.groupBy(col("value").alias("class"))
.agg(count("value").alias("Total"))
.show(false)
val t = spark.read.load(targetPath).count()
val t = spark.read.text(targetPath).as[String].count()
assertTrue(t > 0)

30
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala Normal file
View File

@ -0,0 +1,30 @@
package eu.dnetlib.dhp.datacite
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
object DataciteUtilityTest {
def convertToOAF(input: String): String = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val isRelation: String = (json \\ "source").extractOrElse("NULL")
if (isRelation != "NULL") {
return "Relation"
}
val iType: List[String] = for {
JObject(instance) <- json \\ "instance"
JField("instancetype", JObject(instancetype)) <- instance
JField("classname", JString(classname)) <- instancetype
} yield classname
val l: String = iType.head.toLowerCase()
l
}
}

95
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
View File

@ -2,9 +2,10 @@ package eu.dnetlib.dhp.sx.bio
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.schema.oaf.utils.PidType
import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result}
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf}
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
@ -16,6 +17,7 @@ import org.mockito.junit.jupiter.MockitoExtension
import java.io.{BufferedReader, InputStream, InputStreamReader}
import java.util.zip.GZIPInputStream
import scala.collection.JavaConverters._
import scala.collection.mutable.ListBuffer
import scala.io.Source
import scala.xml.pull.XMLEventReader
@ -74,6 +76,95 @@ class BioScholixTest extends AbstractVocabularyTest {
}
private def checkPMArticle(article: PMArticle): Unit = {
assertNotNull(article.getPmid)
assertNotNull(article.getTitle)
assertNotNull(article.getAuthors)
article.getAuthors.asScala.foreach { a =>
assertNotNull(a)
assertNotNull(a.getFullName)
}
}
@Test
def testParsingPubmedXML(): Unit = {
val xml = new XMLEventReader(
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
)
val parser = new PMParser(xml)
parser.foreach(checkPMArticle)
}
private def checkPubmedPublication(o: Oaf): Unit = {
assertTrue(o.isInstanceOf[Publication])
val p: Publication = o.asInstanceOf[Publication]
assertNotNull(p.getId)
assertNotNull(p.getTitle)
p.getTitle.asScala.foreach(t => assertNotNull(t.getValue))
p.getAuthor.asScala.foreach(a => assertNotNull(a.getFullname))
assertNotNull(p.getInstance())
p.getInstance().asScala.foreach { i =>
assertNotNull(i.getCollectedfrom)
assertNotNull(i.getPid)
assertNotNull(i.getInstancetype)
}
assertNotNull(p.getOriginalId)
p.getOriginalId.asScala.foreach(oId => assertNotNull(oId))
val hasPMC = p
.getInstance()
.asScala
.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString)))
if (hasPMC) {
assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::")))
}
}
@Test
def testPubmedOriginalID(): Unit = {
val article: PMArticle = new PMArticle
article.setPmid("1234")
article.setTitle("a Title")
// VERIFY PUBLICATION IS NOT NULL
article.getPublicationTypes.add(new PMSubject("article", null, null))
var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication]
assertNotNull(publication)
assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId)
// VERIFY PUBLICATION ID DOES NOT CHANGE ALSO IF SETTING PMC IDENTIFIER
article.setPmcId("PMC1517292")
publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication]
assertNotNull(publication)
assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId)
// VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS
val oldOpenaireID = "od_______267::0000072375bc0e68fa09d4e6b7658248"
val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID))
assertTrue(hasOldOpenAIREID)
}
@Test
def testPubmedMapping(): Unit = {
val xml = new XMLEventReader(
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
)
val parser = new PMParser(xml)
val results = ListBuffer[Oaf]()
parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies))
results.foreach(checkPubmedPublication)
}
@Test
def testPDBToOAF(): Unit = {

4
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo_datetime.json
View File

@ -1443,7 +1443,7 @@
17
]
],
"date-time": "2021-05-17T15:08:12Z",
"date-time": "3021-05-17T15:08:12Z",
"timestamp": 1621264092000
},
"score": 1.0,
@ -1461,7 +1461,7 @@
22
]
],
"date-time": "2021-05-17T15:08:12Z"
"date-time": "3021-05-17T15:08:12Z"
},
"references-count": 83,
"journal-issue": {

29
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/DatasourceMaster.java Normal file
View File

@ -0,0 +1,29 @@
package eu.dnetlib.dhp.bulktag.eosc;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
public class DatasourceMaster implements Serializable {
private String datasource;
private String master;
public String getDatasource() {
return datasource;
}
public void setDatasource(String datasource) {
this.datasource = datasource;
}
public String getMaster() {
return master;
}
public void setMaster(String master) {
this.master = master;
}
}

136
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/ReadMasterDatasourceFromDB.java Normal file
View File

@ -0,0 +1,136 @@
package eu.dnetlib.dhp.bulktag.eosc;
import java.io.BufferedWriter;
import java.io.Closeable;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.StandardCharsets;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.Arrays;
import java.util.List;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.common.RelationInverse;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class ReadMasterDatasourceFromDB implements Closeable {
private final DbClient dbClient;
private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class);
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " +
"(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " +
"FULL JOIN " +
"(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " +
"ON dso.id = d.duplicate";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
ReadMasterDatasourceFromDB.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json")));
parser.parseArgument(args);
final String dbUrl = parser.get("postgresUrl");
final String dbUser = parser.get("postgresUser");
final String dbPassword = parser.get("postgresPassword");
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("hdfsNameNode");
try (
final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
dbPassword)) {
log.info("Processing datasources...");
rmd.execute(QUERY, rmd::datasourceMasterMap);
}
}
public void execute(final String sql, final Function<ResultSet, DatasourceMaster> producer) {
dbClient.processResults(sql, rs -> writeMap(producer.apply(rs)));
}
public DatasourceMaster datasourceMasterMap(ResultSet rs) {
try {
DatasourceMaster dm = new DatasourceMaster();
String datasource = rs.getString("datasource");
dm.setDatasource(datasource);
String master = rs.getString("master");
if (StringUtils.isNotBlank(master))
dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true));
else
dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true));
return dm;
} catch (final SQLException e) {
throw new RuntimeException(e);
}
}
@Override
public void close() throws IOException {
dbClient.close();
writer.close();
}
public ReadMasterDatasourceFromDB(
final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
throws IOException {
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fsDataOutputStream = fileSystem.append(hdfsWritePath);
} else {
fsDataOutputStream = fileSystem.create(hdfsWritePath);
}
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
}
protected void writeMap(final DatasourceMaster dm) {
try {
writer.write(OBJECT_MAPPER.writeValueAsString(dm));
writer.newLine();
} catch (final IOException e) {
throw new RuntimeException(e);
}
}
}

170
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscBulkTag.java Normal file
View File

@ -0,0 +1,170 @@
package eu.dnetlib.dhp.bulktag.eosc;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import javax.print.attribute.DocAttributeSet;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
import eu.dnetlib.dhp.bulktag.community.*;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
public class SparkEoscBulkTag implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkEoscBulkTag.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String workingPath = parser.get("workingPath");
log.info("workingPath: {}", workingPath);
String datasourceMapPath = parser.get("datasourceMapPath");
log.info("datasourceMapPath: {}", datasourceMapPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
CommunityConfiguration cc;
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
removeOutputDir(spark, workingPath);
execBulkTag(spark, inputPath, workingPath, datasourceMapPath, resultClazz);
});
}
private static <R extends Result> void execBulkTag(
SparkSession spark,
String inputPath,
String workingPath,
String datasourceMapPath,
Class<R> resultClazz) {
List<String> hostedByList = readPath(spark, datasourceMapPath, DatasourceMaster.class)
.map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING())
.collectAsList();
readPath(spark, inputPath, resultClazz)
.map(patchResult(), Encoders.bean(resultClazz))
.filter(Objects::nonNull)
.map(
(MapFunction<R, R>) value -> enrich(value, hostedByList),
Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingPath);
readPath(spark, workingPath, resultClazz)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(inputPath);
}
private static <R extends Result> R enrich(R value, List<String> hostedByList) {
if (value
.getInstance()
.stream()
.anyMatch(
i -> (hostedByList.contains(i.getHostedby().getKey())) ||
(value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0))
&&
!value.getContext().stream().anyMatch(c -> c.getId().equals("eosc"))) {
Context context = new Context();
context.setId("eosc");
context
.setDataInfo(
Arrays
.asList(
OafMapperUtils
.dataInfo(
false, BULKTAG_DATA_INFO_TYPE, true, false,
OafMapperUtils
.qualifier(
CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE,
DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS),
TAGGING_TRUST)));
value.getContext().add(context);
}
return value;
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
private static <R extends Result> MapFunction<R, R> patchResult() {
return r -> {
if (r.getDataInfo().getDeletedbyinference() == null) {
r.getDataInfo().setDeletedbyinference(false);
}
if (r.getContext() == null) {
r.setContext(new ArrayList<>());
}
return r;
};
}
}

132
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java → dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/eosc/SparkEoscTag.java
View File

@ -1,13 +1,10 @@
package eu.dnetlib.dhp.bulktag;
package eu.dnetlib.dhp.bulktag.eosc;
import static eu.dnetlib.dhp.PropagationConstant.readPath;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
@ -21,35 +18,15 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class SparkEoscTag {
private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static final Qualifier EOSC_QUALIFIER = OafMapperUtils
.qualifier(
"EOSC",
"European Open Science Cloud",
ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES);
public static final DataInfo EOSC_DATAINFO = OafMapperUtils
.dataInfo(
false, "propagation", true, false,
OafMapperUtils
.qualifier(
"propagation:subject", "Inferred by OpenAIRE",
ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
"0.9");
public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils
.structuredProperty(
"EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO);
public final static StructuredProperty EOSC_GALAXY = OafMapperUtils
.structuredProperty(
"EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO);
public final static StructuredProperty EOSC_TWITTER = OafMapperUtils
.structuredProperty(
"EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO);
public static final String EOSC_GALAXY_WORKFLOW = "EOSC::Galaxy Workflow";
public static final String EOSC_TWITTER_DATA = "EOSC::Twitter Data";
public static final String EOSC_JUPYTER_NOTEBOOK = "EOSC::Jupyter Notebook";
public static final String COMPLIES_WITH = "compliesWith";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
@ -84,29 +61,35 @@ public class SparkEoscTag {
});
}
public static EoscIfGuidelines newInstance(String code, String label, String url, String semantics) {
EoscIfGuidelines eig = new EoscIfGuidelines();
eig.setCode(code);
eig.setLabel(label);
eig.setUrl(url);
eig.setSemanticRelation(semantics);
return eig;
}
private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) {
readPath(spark, inputPath + "/software", Software.class)
.map((MapFunction<Software, Software>) s -> {
List<StructuredProperty> sbject;
if (!Optional.ofNullable(s.getSubject()).isPresent())
s.setSubject(new ArrayList<>());
sbject = s.getSubject();
if (containsCriteriaNotebook(s)) {
sbject.add(EOSC_NOTEBOOK);
if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) {
sbject = sbject.stream().map(sb -> {
if (sb.getValue().equals("EOSC Jupyter Notebook")) {
return null;
}
return sb;
}).filter(Objects::nonNull).collect(Collectors.toList());
s.setSubject(sbject);
}
if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent())
s.setEoscifguidelines(new ArrayList<>());
addEIG(
s.getEoscifguidelines(), EOSC_JUPYTER_NOTEBOOK, EOSC_JUPYTER_NOTEBOOK, "",
COMPLIES_WITH);
}
if (containsCriteriaGalaxy(s)) {
sbject.add(EOSC_GALAXY);
if (!Optional.ofNullable(s.getEoscifguidelines()).isPresent())
s.setEoscifguidelines(new ArrayList<>());
addEIG(
s.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "", COMPLIES_WITH);
}
return s;
}, Encoders.bean(Software.class))
@ -123,15 +106,17 @@ public class SparkEoscTag {
readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class)
.map((MapFunction<OtherResearchProduct, OtherResearchProduct>) orp -> {
List<StructuredProperty> sbject;
if (!Optional.ofNullable(orp.getSubject()).isPresent())
orp.setSubject(new ArrayList<>());
sbject = orp.getSubject();
if (!Optional.ofNullable(orp.getEoscifguidelines()).isPresent())
orp.setEoscifguidelines(new ArrayList<>());
if (containsCriteriaGalaxy(orp)) {
sbject.add(EOSC_GALAXY);
addEIG(
orp.getEoscifguidelines(), EOSC_GALAXY_WORKFLOW, EOSC_GALAXY_WORKFLOW, "",
COMPLIES_WITH);
}
if (containscriteriaTwitter(orp)) {
sbject.add(EOSC_TWITTER);
addEIG(orp.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
return orp;
}, Encoders.bean(OtherResearchProduct.class))
@ -148,12 +133,11 @@ public class SparkEoscTag {
readPath(spark, inputPath + "/dataset", Dataset.class)
.map((MapFunction<Dataset, Dataset>) d -> {
List<StructuredProperty> sbject;
if (!Optional.ofNullable(d.getSubject()).isPresent())
d.setSubject(new ArrayList<>());
sbject = d.getSubject();
if (!Optional.ofNullable(d.getEoscifguidelines()).isPresent())
d.setEoscifguidelines(new ArrayList<>());
if (containscriteriaTwitter(d)) {
sbject.add(EOSC_TWITTER);
addEIG(d.getEoscifguidelines(), EOSC_TWITTER_DATA, EOSC_TWITTER_DATA, "", COMPLIES_WITH);
}
return d;
}, Encoders.bean(Dataset.class))
@ -169,6 +153,12 @@ public class SparkEoscTag {
.json(inputPath + "/dataset");
}
private static void addEIG(List<EoscIfGuidelines> eoscifguidelines, String code, String label, String url,
String sem) {
if (!eoscifguidelines.stream().anyMatch(eig -> eig.getCode().equals(code)))
eoscifguidelines.add(newInstance(code, label, url, sem));
}
private static boolean containscriteriaTwitter(Result r) {
Set<String> words = getWordsSP(r.getTitle());
words.addAll(getWordsF(r.getDescription()));
@ -177,10 +167,12 @@ public class SparkEoscTag {
(words.contains("data") || words.contains("dataset")))
return true;
if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) &&
r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data")))
return true;
return false;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data")))
.orElse(false);
}
private static boolean containsCriteriaGalaxy(Result r) {
@ -190,13 +182,17 @@ public class SparkEoscTag {
words.contains("workflow"))
return true;
if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) &&
r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow")))
return true;
return false;
return Optional
.ofNullable(r.getSubject())
.map(
s -> s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) &&
s.stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow")))
.orElse(false);
}
private static boolean containsCriteriaNotebook(Software s) {
if (!Optional.ofNullable(s.getSubject()).isPresent())
return false;
if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter")))
return true;
if (s
@ -212,13 +208,6 @@ public class SparkEoscTag {
return false;
}
private static Set<String> getSubjects(List<StructuredProperty> s) {
Set<String> subjects = new HashSet<>();
s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" "))));
s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase()));
return subjects;
}
private static Set<String> getWordsSP(List<StructuredProperty> elem) {
Set<String> words = new HashSet<>();
Optional
@ -242,10 +231,7 @@ public class SparkEoscTag {
t -> words
.addAll(
Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))));
// elem
// .forEach(
// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))));
return words;
return words;
}
}

32
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/datasourcemaster_parameters.json Normal file
View File

@ -0,0 +1,32 @@
[
{
"paramName": "p",
"paramLongName": "hdfsPath",
"paramDescription": "the path where storing the sequential file",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "hdfsNameNode",
"paramDescription": "the name node on hdfs",
"paramRequired": true
},
{
"paramName": "pgurl",
"paramLongName": "postgresUrl",
"paramDescription": "postgres url, example: jdbc:postgresql://localhost:5432/testdb",
"paramRequired": true
},
{
"paramName": "pguser",
"paramLongName": "postgresUser",
"paramDescription": "postgres user",
"paramRequired": false
},
{
"paramName": "pgpasswd",
"paramLongName": "postgresPassword",
"paramDescription": "postgres password",
"paramRequired": false
}
]

25
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json → dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eosc_bulkTag_parameters.json
View File

@ -1,4 +1,5 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
@ -6,8 +7,20 @@
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramName": "dmp",
"paramLongName":"datasourceMapPath",
"paramDescription": "the path where the association datasource master has been stored",
"paramRequired": true
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName": "wp",
"paramLongName": "workingPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
@ -16,12 +29,6 @@
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "pl",
"paramLongName": "projectListPath",
"paramDescription": "the path of the association result projectlist",
"paramRequired": true
}
]
]

141
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml
View File

@ -16,6 +16,21 @@
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>postgresURL</name>
<description>the url of the postgress server to query</description>
</property>
<property>
<name>postgresUser</name>
<description>the username to access the postgres db</description>
</property>
<property>
<name>postgresPassword</name>
<description>the postgres password</description>
</property>
</parameters>
<global>
@ -211,7 +226,7 @@
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.SparkEoscTag</class>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
@ -226,10 +241,132 @@
<arg>--sourcePath</arg><arg>${outputPath}</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscTag</arg>
</spark>
<ok to="End"/>
<ok to="eosc_get_datasource_master"/>
<error to="Kill"/>
</action>
<action name="eosc_get_datasource_master">
<java>
<main-class>eu.dnetlib.dhp.bulktag.eosc.ReadMasterDatasourceFromDB</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/datasourcemaster</arg>
<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
<arg>--postgresUrl</arg><arg>${postgresURL}</arg>
<arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
</java>
<ok to="fork_eosc_context_tag"/>
<error to="Kill"/>
</action>
<fork name="fork_eosc_context_tag">
<path start="eosc_context_tag_publication"/>
<path start="eosc_context_tag_dataset"/>
<path start="eosc_context_tag_otherresearchproduct"/>
<path start="eosc_context_tag_software"/>
</fork>
<action name="eosc_context_tag_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/publication</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/dataset</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/software</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<action name="eosc_context_tag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>EOSC_tagging</name>
<class>eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
</spark>
<ok to="wait_eosc_context_tag"/>
<error to="Kill"/>
</action>
<join name="wait_eosc_context_tag" to="End"/>
<end name="End"/>
</workflow-app>

162
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCContextTaggingTest.java Normal file
View File

@ -0,0 +1,162 @@
package eu.dnetlib.dhp.bulktag;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* @author miriam.baglioni
* @Date 22/07/22
*/
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscBulkTag;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
//"50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea" has instance hostedby eosc
//"50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1" has instance hostedby eosc
//"50|475c1990cbb2::449f28eefccf9f70c04ad70d61e041c7" has two instance one hostedby eosc
//"50|475c1990cbb2::3894c94123e96df8a21249957cf160cb" has EoscTag
public class EOSCContextTaggingTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(EOSCContextTaggingTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(EOSCContextTaggingTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(EOSCContextTaggingTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(EOSCTagJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void EoscContextTagTest() throws Exception {
spark
.read()
.textFile(getClass().getResource("/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json").getPath())
.map(
(MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class),
Encoders.bean(Dataset.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(workingDir.toString() + "/input/dataset");
SparkEoscBulkTag
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
workingDir.toString() + "/input/dataset",
"-workingPath", workingDir.toString() + "/working/dataset",
"-datasourceMapPath",
getClass()
.getResource("/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster")
.getPath(),
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
Assertions
.assertEquals(
4,
tmp
.filter(
s -> s.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::0fecfb874d9395aa69d2f4d7cd1acbea")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3185cd5d8a2b0a06bb9b23ef11748eb1")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
d -> d.getId().equals("50|475c1990cbb2::3894c94123e96df8a21249957cf160cb")
&&
d.getContext().stream().anyMatch(c -> c.getId().equals("eosc")))
.count());
}
}

215
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java
View File

@ -1,21 +1,17 @@
package eu.dnetlib.dhp.bulktag;
import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
@ -27,6 +23,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.bulktag.eosc.SparkEoscTag;
import eu.dnetlib.dhp.schema.oaf.*;
public class EOSCTagJobTest {
@ -126,10 +123,23 @@ public class EOSCTagJobTest {
.assertEquals(
4,
tmp
.filter(s -> s.getEoscifguidelines() != null)
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertEquals(
1, tmp
@ -140,6 +150,16 @@ public class EOSCTagJobTest {
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
@ -166,16 +186,24 @@ public class EOSCTagJobTest {
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11"))
.collect()
.get(0)
.getEoscifguidelines() == null);
Assertions
.assertEquals(
9, tmp
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
@ -183,6 +211,23 @@ public class EOSCTagJobTest {
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
@ -201,17 +246,24 @@ public class EOSCTagJobTest {
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589"))
.collect()
.get(0)
.getEoscifguidelines() == null);
Assertions
.assertEquals(
9, tmp
8, tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
@ -219,14 +271,31 @@ public class EOSCTagJobTest {
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions
.assertEquals(
1,
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
List<StructuredProperty> subjects = tmp
.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244"))
.collect()
.get(0)
.getSubject();
Assertions.assertEquals(8, subjects.size());
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
Assertions.assertEquals(7, subjects.size());
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation")));
Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire")));
@ -250,6 +319,17 @@ public class EOSCTagJobTest {
.filter(
ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
.filter(
ds -> ds
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
@ -264,7 +344,22 @@ public class EOSCTagJobTest {
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
orp -> orp
.getSubject()
.stream()
.anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook")))
.count());
Assertions
.assertEquals(
0, sc
.textFile(workingDir.toString() + "/input/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class))
.filter(
orp -> orp
.getSubject()
.stream()
.anyMatch(eig -> eig.getValue().equals("EOSC::Jupyter Notebook")))
.count());
// spark.stop();
@ -326,22 +421,41 @@ public class EOSCTagJobTest {
Assertions
.assertEquals(
1,
0,
tmp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines() != null)
.count());
Assertions
.assertEquals(
1,
tmp
.filter(
s -> s.getEoscifguidelines() != null)
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
2, tmp
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
.assertFalse(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
@ -350,6 +464,24 @@ public class EOSCTagJobTest {
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
tmp
.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
5, tmp
@ -385,22 +517,34 @@ public class EOSCTagJobTest {
Assertions
.assertEquals(
1,
0,
orp
.filter(
s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow")))
.count());
orp.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o)));
Assertions
.assertEquals(
3, orp
1, orp
.filter(o -> o.getEoscifguidelines() != null)
.filter(
o -> o
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Galaxy Workflow")))
.count());
Assertions
.assertEquals(
2, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getSubject()
.size());
Assertions
.assertTrue(
.assertFalse(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
@ -408,6 +552,23 @@ public class EOSCTagJobTest {
.getSubject()
.stream()
.anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
1, orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.size());
Assertions
.assertTrue(
orp
.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07"))
.collect()
.get(0)
.getEoscifguidelines()
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Galaxy Workflow")));
Assertions
.assertEquals(
@ -516,10 +677,20 @@ public class EOSCTagJobTest {
Assertions
.assertEquals(
3,
0,
orp
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.count());
Assertions
.assertEquals(
3,
orp
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
JavaRDD<Dataset> dats = sc
.textFile(workingDir.toString() + "/input/dataset")
@ -531,7 +702,11 @@ public class EOSCTagJobTest {
.assertEquals(
3,
dats
.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data")))
.filter(
s -> s
.getEoscifguidelines()
.stream()
.anyMatch(eig -> eig.getCode().equals("EOSC::Twitter Data")))
.count());
}

10
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json Normal file
View File

File diff suppressed because one or more lines are too long

318
dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/eosc/datasourceMasterAssociation/datasourceMaster Normal file
View File

@ -0,0 +1,318 @@
{"datasource":"eosc________::100percentit::100percentit.100_percent_it_trusted_cloud","master":"10|eosc________::7ef2576047f040612b983a27347471fc"}
{"datasource":"eosc________::altec::altec.space-vis_adn_service","master":"10|eosc________::2946c48bbcc514ad76bbbf727d5d8fbc"}
{"datasource":"eosc________::astron::astron.","master":"10|eosc________::acb262d4bfdeb6aa9b463a4a6d0d662a"}
{"datasource":"eosc________::athena::athena.atmo-flud","master":"10|eosc________::ac448975e1d7f8b0266c8bb3b3992029"}
{"datasource":"eosc________::athena::athena.uw-map","master":"10|eosc________::5f2a401cf8ce9dc22a3776cea519b594"}
{"datasource":"eosc________::athena::athena.verbal_aggression_analyser_va_analyser","master":"10|eosc________::8b26233e89a50e3754972b1341130494"}
{"datasource":"eosc________::authenix::authenix.authenix","master":"10|eosc________::3cd84764da5728473593a580efb29a40"}
{"datasource":"eosc________::bineo::bineo.cos4bio","master":"10|eosc________::903e0526a6e56eeaf0e4561aa862ecb8"}
{"datasource":"eosc________::blue-cloud::blue-cloud.phytoplankton_eovs","master":"10|eosc________::c2438d79b48baf817956f3856877b3b8"}
{"datasource":"eosc________::bsc-es::bsc-es.bdrc_-_barcelona_dust_regional_center","master":"10|eosc________::756664ca614118315840eb8e985e4377"}
{"datasource":"eosc________::bsc-es::bsc-es.openebench","master":"10|eosc________::69ed72b873b803feed5ba6ae47548419"}
{"datasource":"eosc________::capsh::capsh.dissemin","master":"10|eosc________::e81587742e4107ce83723df17c27cb40"}
{"datasource":"eosc________::carlzeissm::carlzeissm.aper","master":"10|eosc________::f3beb9ee5ee293b723e2edd6f990fde3"}
{"datasource":"eosc________::ccsd::ccsd.episciences","master":"10|eosc________::e1e9de0dbf4bce79c49338d7cf9327e2"}
{"datasource":"eosc________::cds::cds.simbad_simbad_astronomical_database_provides_basic_data_cross-identifications_bibliography_and_measurements_for_astronomical_objects_outside_the_solar_system","master":"10|eosc________::a1e41e71453ac32161f4ac3f5c0e0421"}
{"datasource":"eosc________::centerdata::centerdata.surveycodingsorg","master":"10|eosc________::72db73ab253727c889905da50f506d10"}
{"datasource":"eosc________::cesga::cesga.finisterrae","master":"10|eosc________::6af4303d93f72744cc4c3c815ed2c9a0"}
{"datasource":"eosc________::cesnet::cesnet.metacentrum_cloud","master":"10|eosc________::cebfaa2d0b93502d56a8fbeb6b66cfbe"}
{"datasource":"eosc________::cesnet::cesnet.object_based_storage","master":"10|eosc________::1c5b55339bb86ff997a256d42d7be4b0"}
{"datasource":"eosc________::cesnet::cesnet.umsa_-_untargeted_mass_spectrometry_data_analysis","master":"10|eosc________::d928868211759352cb1604713e0347ec"}
{"datasource":"eosc________::cessda-eric::cessda-eric.cessda_data_catalogue","master":"10|fairsharing_::936824c0191953647ec609b4f49bc964"}
{"datasource":"eosc________::cessda-eric::cessda-eric.data_management_expert_guide_dmeg","master":"10|eosc________::22c14aaf31fc64424fa97adffe6380b9"}
{"datasource":"eosc________::cessda-eric::cessda-eric.elsst__european_language_social_science_thesaurus","master":"10|eosc________::5b30e057381cf0200dc2cdc7b562f570"}
{"datasource":"eosc________::cines::cines.etdr","master":"10|eosc________::3b7f7d6aafb0154025330183d59ce670"}
{"datasource":"eosc________::clarin-eric::clarin-eric.language_resource_switchboard","master":"10|eosc________::3531aa80dbe2b1018133b510a933de40"}
{"datasource":"eosc________::clarin-eric::clarin-eric.virtual_collection_registry","master":"10|eosc________::454e4f7f9f53d9dacf9dc3ba27902f16"}
{"datasource":"eosc________::clarin-eric::clarin-eric.virtual_language_observatory","master":"10|eosc________::4db0c877190783461728c6714cb66cbc"}
{"datasource":"eosc________::cloudferro::cloudferro.data_collections_catalog","master":"10|eosc________::eba1540eb9e87231fdf366eb23d16c3a"}
{"datasource":"eosc________::cloudferro::cloudferro.data_related_services_-_eo_browser","master":"10|eosc________::c24ebda20485c08293b72561ee3c634b"}
{"datasource":"eosc________::cloudferro::cloudferro.data_related_services_-_eo_finder","master":"10|eosc________::3d68186239b6c0f0d677ff55d9b549d1"}
{"datasource":"eosc________::cloudferro::cloudferro.infrastructure","master":"10|eosc________::ac7e3c0151fa3f11d3a7739dddaa3416"}
{"datasource":"eosc________::cmcc::cmcc.enes_data_space","master":"10|eosc________::2925e4df4147819e5b5d2f886f40e3a2"}
{"datasource":"eosc________::cnb-csic::cnb-csic.3dbionotes-ws_web_application_to_annotate_biochemical_and_biomedical_information_onto_structural_models","master":"10|eosc________::77fe0a66415f2440ab60d47dcee678a5"}
{"datasource":"eosc________::cnb-csic::cnb-csic.scipioncloud","master":"10|eosc________::7f09b7fee99363813f24aca9ebdecf61"}
{"datasource":"eosc________::cnr-iia::cnr-iia.geo_dab","master":"10|eosc________::108b0148352c15ee1ce935699e09add3"}
{"datasource":"eosc________::collabwith::collabwith.collabwith_marketplace","master":"10|eosc________::894a0ffa7768b228c1b46793670c85e6"}
{"datasource":"eosc________::coronis_computing_sl::coronis_computing_sl.uw-mos","master":"10|eosc________::9cbf0a75d817e291771b8bce6440f5f4"}
{"datasource":"eosc________::coronis_computing_sl::coronis_computing_sl.vd-maps","master":"10|eosc________::b5af1514b39d8e021554a73076a694d9"}
{"datasource":"eosc________::creaf::creaf.nimmbus_geospatial_user_feedback","master":"10|eosc________::86c325db16448760b3390dda7e46631a"}
{"datasource":"eosc________::creatis::creatis.virtual_imaging_platform","master":"10|eosc________::01a45ac2677f89414af91e651735846d"}
{"datasource":"eosc________::cs_group::cs_group.ai4geo_engine","master":"10|eosc________::c61211295d27e5e08f4c64f3e3098294"}
{"datasource":"eosc________::csc-fi::csc-fi.chipster","master":"10|eosc________::61549f785a2c93939be011b0453a6981"}
{"datasource":"eosc________::csc-fi::csc-fi.cpouta","master":"10|eosc________::d71c843b4e00eff17db07bf9d10769f9"}
{"datasource":"eosc________::csc-fi::csc-fi.csc_epouta","master":"10|eosc________::4493bd6a93e5b8465fda8cf7ab2dfdea"}
{"datasource":"eosc________::csc-fi::csc-fi.rahti_container_cloud","master":"10|eosc________::cc60eb9fc76f9598ee581eff0792573b"}
{"datasource":"eosc________::cscs::cscs.object_storage","master":"10|eosc________::3da6a817fe85ef43f7d97ef07e467d45"}
{"datasource":"eosc________::csi_piemonte::csi_piemonte.nivola2","master":"10|eosc________::ac6483be3e556c8652b8595680795983"}
{"datasource":"eosc________::csic::csic.csic_cloud_infrastructure","master":"10|eosc________::05ea2eb193382e22f32b32fbe9a4d961"}
{"datasource":"eosc________::cyberbotics::cyberbotics.robotbenchmark","master":"10|eosc________::27ee094c68b7a758ca2915aca6215a1d"}
{"datasource":"eosc________::d4science::d4science.alien_and_invasive_species_vre","master":"10|eosc________::b5cff6d55dcf6c20e78a0f1f847b3005"}
{"datasource":"eosc________::d4science::d4science.rprototypinglab_virtual_research_environment","master":"10|eosc________::8073ab0dbb22dc3b9f17627a7b25903f"}
{"datasource":"eosc________::d4science::d4science.visual_media_service_vre","master":"10|eosc________::eabf459f53c2bfe6247f006fcc0f4db7"}
{"datasource":"eosc________::dariah_eric::dariah_eric.dariah-campus","master":"10|eosc________::9c63075d6642a2d269776c2b90c2f976"}
{"datasource":"eosc________::dariah_eric::dariah_eric.ssh_open_marketplace","master":"10|eosc________::91fe494a3c21805febb03353152f1212"}
{"datasource":"eosc________::datacite::datacite.datacite_doi_registration_service","master":"10|eosc________::c146a470f01ee7ded3b55acda9362e7f"}
{"datasource":"eosc________::dcc-uk::dcc-uk.dmponline","master":"10|eosc________::fe480090e0739dab86b24a11177eeffd"}
{"datasource":"eosc________::denbi::denbi.cloud","master":"10|eosc________::59399e560967488c0ae0329e0d37f5b4"}
{"datasource":"eosc________::desy::desy.pan_data","master":"10|eosc________::52008fe404bf2e939140109162f9233f"}
{"datasource":"eosc________::desy::desy.pan_faas","master":"10|eosc________::026939c4b12d7d71e2b05bc5acde804e"}
{"datasource":"eosc________::desy::desy.pan_gitlab","master":"10|eosc________::f13cefc9f3207cb82f3285b05f190f78"}
{"datasource":"eosc________::desy::desy.pan_notebook","master":"10|eosc________::500fe61cce6562797cd43797aab12be5"}
{"datasource":"eosc________::digitalglobe::digitalglobe.earthwatch","master":"10|eosc________::020d905260267066c1926f526bb86f30"}
{"datasource":"eosc________::dkrz::dkrz.enes_climate_analytics_service","master":"10|eosc________::1d7a1fea6694d15d9e67f08e1e77082b"}
{"datasource":"eosc________::doabf::doabf.operas_certification","master":"10|eosc________::79b9748edeffb872a28660a9d238dcec"}
{"datasource":"eosc________::ds-wizard::ds-wizard.data_stewardship_wizard","master":"10|eosc________::fc6bad963e15e218efc62c7befd122af"}
{"datasource":"eosc________::egi-fed::egi-fed.check-in","master":"10|eosc________::baa3c497b9499b3d8c87ea8d2b37a44f"}
{"datasource":"eosc________::egi-fed::egi-fed.cloud_compute","master":"10|eosc________::b1179384a336d409fc909fe3711d3d1f"}
{"datasource":"eosc________::egi-fed::egi-fed.cloud_container_compute","master":"10|eosc________::a66bb1ac56a3bcf2c24b0ef85ed2bdfc"}
{"datasource":"eosc________::egi-fed::egi-fed.data_transfer","master":"10|eosc________::6c0bf38e885c42161b88093517f6cd3e"}
{"datasource":"eosc________::egi-fed::egi-fed.egi_datahub","master":"10|eosc________::5a260dae80795584ac08df133adb1fad"}
{"datasource":"eosc________::egi-fed::egi-fed.fitsm_training","master":"10|eosc________::927b4455c0a21692d2a9f634bccd8309"}
{"datasource":"eosc________::egi-fed::egi-fed.high-throughput_compute","master":"10|eosc________::e27ec11ac7b7d6ffbbce668b7d1f81d5"}
{"datasource":"eosc________::egi-fed::egi-fed.iso_27001_training","master":"10|eosc________::98a6655b6421166c5c29baa2f5815de3"}
{"datasource":"eosc________::egi-fed::egi-fed.notebook","master":"10|eosc________::1d37909a6a31147a09ee9f2e579a6706"}
{"datasource":"eosc________::egi-fed::egi-fed.online_storage","master":"10|eosc________::d8b94284582d3e2185a782ae2ba42186"}
{"datasource":"eosc________::egi-fed::egi-fed.training_infrastructure","master":"10|eosc________::38cdb8e44638f2e561c466f0dd26cf96"}
{"datasource":"eosc________::egi-fed::egi-fed.workload_manager","master":"10|eosc________::ff515071cd88afb40599edcb6637f47e"}
{"datasource":"eosc________::ehri::ehri.begrenzte_flucht","master":"10|eosc________::01d1445605fc1d25e6a7f21ba995d724"}
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@ -1,11 +1,11 @@
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8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextSparkJob.java
View File

@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.graph.clean;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
@ -21,15 +20,8 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class CleanContextSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class);

58
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java
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@ -1,58 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.util.Map;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Constants {
protected static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
protected static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
public static final String INFERRED = "Inferred by OpenAIRE";
public static final String CABF2 = "c_abf2";
public static final String HARVESTED = "Harvested";
public static final String DEFAULT_TRUST = "0.9";
public static final String USER_CLAIM = "Linked by user";
public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/";
public static final String RESEARCH_COMMUNITY = "Research Community";
public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative";
static {
accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2);
accessRightsCoarMap.put("RESTRICTED", "c_16ec");
accessRightsCoarMap.put("OPEN SOURCE", CABF2);
accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb");
accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf");
}
static {
coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN);
coarCodeLabelMap.put("c_16ec", "RESTRICTED");
coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED);
coarCodeLabelMap.put("c_f1cf", "EMBARGO");
}
public enum DUMPTYPE {
COMPLETE("complete"), COMMUNITY("community"), FUNDER("funder");
private final String type;
DUMPTYPE(String type) {
this.type = type;
}
public String getType() {
return type;
}
}
}

107
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java
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package eu.dnetlib.dhp.oa.graph.dump;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* It fires the execution of the actual dump for result entities. If the dump is for RC/RI products its checks for each
* result its belongingess to at least one RC/RI before "asking" for its mapping.
*/
public class DumpProducts implements Serializable {
public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath,
Class<? extends OafEntity> inputClazz,
Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> outputClazz,
String dumpType) {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
execDump(
spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType);
});
}
public static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> void execDump(
SparkSession spark,
String inputPath,
String outputPath,
String communityMapPath,
Class<I> inputClazz,
Class<O> outputClazz,
String dumpType) {
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
Utils
.readPath(spark, inputPath, inputClazz)
.map((MapFunction<I, O>) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz))
.filter((FilterFunction<O>) value -> value != null)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> O execMap(I value,
CommunityMap communityMap,
String dumpType) throws NoAvailableEntityTypeException {
Optional<DataInfo> odInfo = Optional.ofNullable(value.getDataInfo());
if (odInfo.isPresent()) {
if (odInfo.get().getDeletedbyinference() || odInfo.get().getInvisible()) {
return null;
}
} else {
return null;
}
if (Constants.DUMPTYPE.COMMUNITY.getType().equals(dumpType)) {
Set<String> communities = communityMap.keySet();
Optional<List<Context>> inputContext = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext());
if (!inputContext.isPresent()) {
return null;
}
List<String> toDumpFor = inputContext.get().stream().map(c -> {
if (communities.contains(c.getId())) {
return c.getId();
}
if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) {
return c.getId().substring(0, c.getId().indexOf("::"));
}
return null;
}).filter(Objects::nonNull).collect(Collectors.toList());
if (toDumpFor.isEmpty()) {
return null;
}
}
return (O) ResultMapper.map(value, communityMap, dumpType);
}
}

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dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java
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package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.LocatedFileStatus;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.fs.RemoteIterator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.MakeTarArchive;
public class MakeTar implements Serializable {
private static final Logger log = LoggerFactory.getLogger(MakeTar.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
MakeTar.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String outputPath = parser.get("hdfsPath");
log.info("hdfsPath: {}", outputPath);
final String hdfsNameNode = parser.get("nameNode");
log.info("nameNode: {}", hdfsNameNode);
final String inputPath = parser.get("sourcePath");
log.info("input path : {}", inputPath);
final int gBperSplit = Optional
.ofNullable(parser.get("splitSize"))
.map(Integer::valueOf)
.orElse(10);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit);
}
public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
throws IOException {
RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
while (dirIterator.hasNext()) {
LocatedFileStatus fileStatus = dirIterator.next();
Path p = fileStatus.getPath();
String pathString = p.toString();
String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
}
}
}

74
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java
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package eu.dnetlib.dhp.oa.graph.dump;
import java.io.StringReader;
import java.util.List;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class QueryInformationSystem {
private ISLookUpService isLookUp;
private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and ($x//context/param[./@name = 'status']/text() = 'all') "
+
" return " +
"<community> " +
"{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" +
"</community>";
private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and $x//CONFIGURATION/context[./@id=%s] "
+
" return " +
"<community> " +
"{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" +
"</community>";
public CommunityMap getCommunityMap(boolean singleCommunity, String communityId)
throws ISLookUpException, DocumentException, SAXException {
if (singleCommunity)
return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'")));
return getMap(isLookUp.quickSearchProfile(XQUERY_ALL));
}
public ISLookUpService getIsLookUp() {
return isLookUp;
}
public void setIsLookUp(ISLookUpService isLookUpService) {
this.isLookUp = isLookUpService;
}
private CommunityMap getMap(List<String> communityMap) throws DocumentException, SAXException {
final CommunityMap map = new CommunityMap();
for (String xml : communityMap) {
final Document doc;
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
doc = reader.read(new StringReader(xml));
Element root = doc.getRootElement();
map.put(root.attribute("id").getValue(), root.attribute("label").getValue());
}
return map;
}
}

672
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java
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package eu.dnetlib.dhp.oa.graph.dump;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.AccessRight;
import eu.dnetlib.dhp.schema.dump.oaf.Author;
import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.Measure;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.Result;
import eu.dnetlib.dhp.schema.dump.oaf.community.CfHbKeyValue;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Context;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.*;
public class ResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in, Map<String, String> communityMap, String dumpType) throws NoAvailableEntityTypeException {
Result out;
if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
out = new GraphResult();
} else {
out = new CommunityResult();
}
eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in;
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
if (ort.isPresent()) {
try {
addTypeSpecificInformation(out, input, ort);
Optional
.ofNullable(input.getAuthor())
.ifPresent(
ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
out
.setBestaccessright(
BestAccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
final List<String> contributorList = new ArrayList<>();
Optional
.ofNullable(input.getContributor())
.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
out.setContributor(contributorList);
Optional
.ofNullable(input.getCountry())
.ifPresent(
value -> out
.setCountry(
value
.stream()
.map(
c -> {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null;
}
ResultCountry country = new ResultCountry();
country.setCode(c.getClassid());
country.setLabel(c.getClassname());
Optional
.ofNullable(c.getDataInfo())
.ifPresent(
provenance -> country
.setProvenance(
Provenance
.newInstance(
provenance
.getProvenanceaction()
.getClassname(),
c.getDataInfo().getTrust())));
return country;
})
.filter(Objects::nonNull)
.collect(Collectors.toList())));
final List<String> coverageList = new ArrayList<>();
Optional
.ofNullable(input.getCoverage())
.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
out.setCoverage(coverageList);
out.setDateofcollection(input.getDateofcollection());
final List<String> descriptionList = new ArrayList<>();
Optional
.ofNullable(input.getDescription())
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
out.setDescription(descriptionList);
Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
if (oStr.isPresent()) {
out.setEmbargoenddate(oStr.get().getValue());
}
final List<String> formatList = new ArrayList<>();
Optional
.ofNullable(input.getFormat())
.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
out.setFormat(formatList);
out.setId(input.getId());
out.setOriginalId(new ArrayList<>());
Optional
.ofNullable(input.getOriginalId())
.ifPresent(
v -> out
.setOriginalId(
input
.getOriginalId()
.stream()
.filter(s -> !s.startsWith("50|"))
.collect(Collectors.toList())));
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
if (oInst.isPresent()) {
if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
((GraphResult) out)
.setInstance(
oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList()));
} else {
((CommunityResult) out)
.setInstance(
oInst
.get()
.stream()
.map(ResultMapper::getCommunityInstance)
.collect(Collectors.toList()));
}
}
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Language.newInstance(language.getClassid(), language.getClassname()));
}
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) {
out.setLastupdatetimestamp(oLong.get());
}
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
if (otitle.isPresent()) {
List<StructuredProperty> iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setMaintitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setSubtitle(iTitle.get(0).getValue());
}
}
Optional
.ofNullable(input.getPid())
.ifPresent(
value -> out
.setPid(
value
.stream()
.map(
p -> ResultPid
.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue());
}
oStr = Optional.ofNullable(input.getPublisher());
if (oStr.isPresent()) {
out.setPublisher(oStr.get().getValue());
}
Optional
.ofNullable(input.getSource())
.ifPresent(
value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList())));
List<Subject> subjectList = new ArrayList<>();
Optional
.ofNullable(input.getSubject())
.ifPresent(
value -> value
.forEach(s -> subjectList.add(getSubject(s))));
out.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid());
if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) {
((CommunityResult) out)
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> CfHbKeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
Set<String> communities = communityMap.keySet();
List<Context> contextList = Optional
.ofNullable(
input
.getContext())
.map(
value -> value
.stream()
.map(c -> {
String communityId = c.getId();
if (communityId.contains("::")) {
communityId = communityId.substring(0, communityId.indexOf("::"));
}
if (communities.contains(communityId)) {
Context context = new Context();
context.setCode(communityId);
context.setLabel(communityMap.get(communityId));
Optional<List<DataInfo>> dataInfo = Optional.ofNullable(c.getDataInfo());
if (dataInfo.isPresent()) {
List<Provenance> provenance = new ArrayList<>();
provenance
.addAll(
dataInfo
.get()
.stream()
.map(
di -> Optional
.ofNullable(di.getProvenanceaction())
.map(
provenanceaction -> Provenance
.newInstance(
provenanceaction.getClassname(),
di.getTrust()))
.orElse(null))
.filter(Objects::nonNull)
.collect(Collectors.toSet()));
try {
context.setProvenance(getUniqueProvenance(provenance));
} catch (NoAvailableEntityTypeException e) {
e.printStackTrace();
}
}
return context;
}
return null;
})
.filter(Objects::nonNull)
.collect(Collectors.toList()))
.orElse(new ArrayList<>());
if (!contextList.isEmpty()) {
Set<Integer> hashValue = new HashSet<>();
List<Context> remainigContext = new ArrayList<>();
contextList.forEach(c -> {
if (!hashValue.contains(c.hashCode())) {
remainigContext.add(c);
hashValue.add(c.hashCode());
}
});
((CommunityResult) out).setContext(remainigContext);
}
}
} catch (ClassCastException cce) {
return out;
}
}
return out;
}
private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input,
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort) throws NoAvailableEntityTypeException {
switch (ort.get().getClassid()) {
case "publication":
Optional<Journal> journal = Optional
.ofNullable(((Publication) input).getJournal());
if (journal.isPresent()) {
Journal j = journal.get();
Container c = new Container();
c.setConferencedate(j.getConferencedate());
c.setConferenceplace(j.getConferenceplace());
c.setEdition(j.getEdition());
c.setEp(j.getEp());
c.setIss(j.getIss());
c.setIssnLinking(j.getIssnLinking());
c.setIssnOnline(j.getIssnOnline());
c.setIssnPrinted(j.getIssnPrinted());
c.setName(j.getName());
c.setSp(j.getSp());
c.setVol(j.getVol());
out.setContainer(c);
out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
}
break;
case "dataset":
Dataset id = (Dataset) input;
Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue()));
Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
out
.setGeolocation(
Optional
.ofNullable(id.getGeolocation())
.map(
igl -> igl
.stream()
.filter(Objects::nonNull)
.map(gli -> {
GeoLocation gl = new GeoLocation();
gl.setBox(gli.getBox());
gl.setPlace(gli.getPlace());
gl.setPoint(gli.getPoint());
return gl;
})
.collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
break;
case "software":
Software is = (Software) input;
Optional
.ofNullable(is.getCodeRepositoryUrl())
.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
Optional
.ofNullable(is.getDocumentationUrl())
.ifPresent(
value -> out
.setDocumentationUrl(
value
.stream()
.map(Field::getValue)
.collect(Collectors.toList())));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break;
case "other":
OtherResearchProduct ir = (OtherResearchProduct) input;
out
.setContactgroup(
Optional
.ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break;
default:
throw new NoAvailableEntityTypeException();
}
}
private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
Instance instance = new Instance();
setCommonValue(i, instance);
return instance;
}
private static CommunityInstance getCommunityInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
setCommonValue(i, instance);
instance
.setCollectedfrom(
CfHbKeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
instance
.setHostedby(
CfHbKeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
return instance;
}
private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
Optional<eu.dnetlib.dhp.schema.oaf.AccessRight> opAr = Optional.ofNullable(i.getAccessright());
if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
instance
.setAccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
Optional<List<eu.dnetlib.dhp.schema.oaf.Measure>> mes = Optional.ofNullable(i.getMeasures());
if (mes.isPresent()) {
List<Measure> measure = new ArrayList<>();
mes
.get()
.forEach(
m -> m.getUnit().forEach(u -> measure.add(Measure.newInstance(m.getId(), u.getValue()))));
instance.setMeasures(measure);
}
if (opAr.get().getOpenAccessRoute() != null) {
switch (opAr.get().getOpenAccessRoute()) {
case hybrid:
instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid);
break;
case gold:
instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold);
break;
case green:
instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green);
break;
case bronze:
instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze);
break;
}
}
}
Optional
.ofNullable(i.getPid())
.ifPresent(
pid -> instance
.setPid(
pid
.stream()
.map(p -> ResultPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional
.ofNullable(i.getAlternateIdentifier())
.ifPresent(
ai -> instance
.setAlternateIdentifier(
ai
.stream()
.map(p -> AlternateIdentifier.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
Optional
.ofNullable(i.getLicense())
.ifPresent(value -> instance.setLicense(value.getValue()));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
Optional
.ofNullable(i.getRefereed())
.ifPresent(value -> instance.setRefereed(value.getClassname()));
Optional
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
Optional<Field<String>> oPca = Optional.ofNullable(i.getProcessingchargeamount());
Optional<Field<String>> oPcc = Optional.ofNullable(i.getProcessingchargecurrency());
if (oPca.isPresent() && oPcc.isPresent()) {
Field<String> pca = oPca.get();
Field<String> pcc = oPcc.get();
if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) {
APC apc = new APC();
apc.setCurrency(oPcc.get().getValue());
apc.setAmount(oPca.get().getValue());
instance.setArticleprocessingcharge(apc);
}
}
Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl);
}
private static List<Provenance> getUniqueProvenance(List<Provenance> provenance)
throws NoAvailableEntityTypeException {
Provenance iProv = new Provenance();
Provenance hProv = new Provenance();
Provenance lProv = new Provenance();
for (Provenance p : provenance) {
switch (p.getProvenance()) {
case Constants.HARVESTED:
hProv = getHighestTrust(hProv, p);
break;
case Constants.INFERRED:
iProv = getHighestTrust(iProv, p);
// To be removed as soon as the new beta run has been done
// this fixex issue of not set trust during bulktagging
if (StringUtils.isEmpty(iProv.getTrust())) {
iProv.setTrust(Constants.DEFAULT_TRUST);
}
break;
case Constants.USER_CLAIM:
lProv = getHighestTrust(lProv, p);
break;
default:
throw new NoAvailableEntityTypeException();
}
}
return Arrays
.asList(iProv, hProv, lProv)
.stream()
.filter(p -> !StringUtils.isEmpty(p.getProvenance()))
.collect(Collectors.toList());
}
private static Provenance getHighestTrust(Provenance hProv, Provenance p) {
if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust()))
return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p;
return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p;
}
private static Subject getSubject(StructuredProperty s) {
Subject subject = new Subject();
subject.setSubject(SubjectSchemeValue.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
if (di.isPresent()) {
Provenance p = new Provenance();
p.setProvenance(di.get().getProvenanceaction().getClassname());
p.setTrust(di.get().getTrust());
subject.setProvenance(p);
}
return subject;
}
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
Author a = new Author();
a.setFullname(oa.getFullname());
a.setName(oa.getName());
a.setSurname(oa.getSurname());
a.setRank(oa.getRank());
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
AuthorPid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
}
return a;
}
private static AuthorPid getAuthorPid(StructuredProperty pid) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return AuthorPid
.newInstance(
AuthorPidSchemeValue
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue()),
Provenance
.newInstance(
di.get().getProvenanceaction().getClassname(),
di.get().getTrust()));
} else {
return AuthorPid
.newInstance(
AuthorPidSchemeValue
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue())
);
}
}
private static AuthorPid getOrcid(List<StructuredProperty> p) {
List<StructuredProperty> pidList = p.stream().map(pid -> {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) ||
(pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) {
return pid;
}
return null;
}).filter(Objects::nonNull).collect(Collectors.toList());
if (pidList.size() == 1) {
return getAuthorPid(pidList.get(0));
}
List<StructuredProperty> orcid = pidList
.stream()
.filter(
ap -> ap
.getQualifier()
.getClassid()
.equals(ModelConstants.ORCID))
.collect(Collectors.toList());
if (orcid.size() == 1) {
return getAuthorPid(orcid.get(0));
}
orcid = pidList
.stream()
.filter(
ap -> ap
.getQualifier()
.getClassid()
.equals(ModelConstants.ORCID_PENDING))
.collect(Collectors.toList());
if (orcid.size() == 1) {
return getAuthorPid(orcid.get(0));
}
return null;
}
}

99
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java
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@ -1,99 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.dom4j.DocumentException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
/**
* This class connects with the IS related to the isLookUpUrl got as parameter. It saves the information about the
* context that will guide the dump of the results. The information saved is a HashMap. The key is the id of a community
* - research infrastructure/initiative , the value is the label of the research community - research
* infrastructure/initiative.
*/
public class SaveCommunityMap implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class);
private final transient QueryInformationSystem queryInformationSystem;
private final transient BufferedWriter writer;
public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException {
final Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
Path hdfsWritePath = new Path(hdfsPath);
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, true);
}
queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
}
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SaveCommunityMap.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String nameNode = parser.get("nameNode");
log.info("nameNode: {}", nameNode);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl);
final Boolean singleCommunity = Optional
.ofNullable(parser.get("singleDeposition"))
.map(Boolean::valueOf)
.orElse(false);
final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null);
final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl);
scm.saveCommunityMap(singleCommunity, community_id);
}
private void saveCommunityMap(boolean singleCommunity, String communityId)
throws ISLookUpException, IOException, DocumentException, SAXException {
final String communityMapString = Utils.OBJECT_MAPPER
.writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId));
log.info("communityMap {} ", communityMapString);
writer
.write(
communityMapString);
writer.close();
}
}

100
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java
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@ -1,100 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.api.MissingConceptDoiException;
import eu.dnetlib.dhp.common.api.ZenodoAPIClient;
import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException;
public class SendToZenodoHDFS implements Serializable {
private static final String NEW = "new"; // to be used for a brand new deposition in zenodo
private static final String VERSION = "version"; // to be used to upload a new version of a published deposition
private static final String UPDATE = "update"; // to upload content to an open deposition not published
public static void main(final String[] args) throws Exception, MissingConceptDoiException {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
SendToZenodoHDFS.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json")));
parser.parseArgument(args);
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("nameNode");
final String access_token = parser.get("accessToken");
final String connection_url = parser.get("connectionUrl");
final String metadata = parser.get("metadata");
final String depositionType = parser.get("depositionType");
final String concept_rec_id = Optional
.ofNullable(parser.get("conceptRecordId"))
.orElse(null);
final Boolean publish = Optional
.ofNullable(parser.get("publish"))
.map(Boolean::valueOf)
.orElse(false);
final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
.listFiles(
new Path(hdfsPath), true);
ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token);
switch (depositionType) {
case NEW:
zenodoApiClient.newDeposition();
break;
case VERSION:
if (concept_rec_id == null) {
throw new MissingConceptDoiException("No concept record id has been provided");
}
zenodoApiClient.newVersion(concept_rec_id);
break;
case UPDATE:
if (depositionId == null) {
throw new MissingConceptDoiException("No deposition id has been provided");
}
zenodoApiClient.uploadOpenDeposition(depositionId);
break;
default:
throw new NoAvailableEntityTypeException();
}
while (fileStatusListIterator.hasNext()) {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
Path p = fileStatus.getPath();
String pString = p.toString();
if (!pString.endsWith("_SUCCESS")) {
String name = pString.substring(pString.lastIndexOf("/") + 1);
FSDataInputStream inputStream = fileSystem.open(p);
zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen());
}
}
if (!metadata.equals("")) {
zenodoApiClient.sendMretadata(metadata);
}
if (Boolean.TRUE.equals(publish)) {
zenodoApiClient.publish();
}
}
}

77
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java
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@ -1,77 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.oa.graph.dump.complete.Constants;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class Utils {
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private Utils() {
}
public static void removeOutputDir(SparkSession spark, String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
public static ISLookUpService getIsLookUpService(String isLookUpUrl) {
return ISLookupClientFactory.getLookUpService(isLookUpUrl);
}
public static String getContextId(String id) {
return String
.format(
"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
DHPUtils.md5(id));
}
public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) {
return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class);
}
public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath))));
StringBuilder sb = new StringBuilder();
try {
String line;
while ((line = br.readLine()) != null) {
sb.append(line);
}
} finally {
br.close();
}
return new Gson().fromJson(sb.toString(), CommunityMap.class);
}
}

8
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java
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@ -1,8 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.Serializable;
import java.util.HashMap;
public class CommunityMap extends HashMap<String, String> implements Serializable {
}

81
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java
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@ -1,81 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Context;
/**
* This class splits the dumped results according to the research community - research initiative/infrastructure they
* are related to. The information about the community is found in the element "context.id" in the result. Since the
* context that can be found in the result can be associated not only to communities, a community Map is provided. It
* will guide the splitting process. Note: the repartition(1) just before writing the results related to a community.
* This is a choice due to uploading constraints (just one file for each community) As soon as a better solution will be
* in place remove the repartition
*/
public class CommunitySplit implements Serializable {
public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath) {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
execSplit(spark, inputPath, outputPath, communityMap);
});
}
private static void execSplit(SparkSession spark, String inputPath, String outputPath,
CommunityMap communities) {
Dataset<CommunityResult> result = Utils
.readPath(spark, inputPath + "/publication", CommunityResult.class)
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
communities
.keySet()
.stream()
.forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_")));
}
private static void printResult(String c, Dataset<CommunityResult> result, String outputPath) {
Dataset<CommunityResult> communityProducts = result
.filter((FilterFunction<CommunityResult>) r -> containsCommunity(r, c));
communityProducts
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
private static boolean containsCommunity(CommunityResult r, String c) {
if (Optional.ofNullable(r.getContext()).isPresent()) {
return r
.getContext()
.stream()
.map(Context::getCode)
.collect(Collectors.toList())
.contains(c);
}
return false;
}
}

28
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java
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@ -1,28 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.Serializable;
import java.util.List;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
public class ResultProject implements Serializable {
private String resultId;
private List<Project> projectsList;
public String getResultId() {
return resultId;
}
public void setResultId(String resultId) {
this.resultId = resultId;
}
public List<Project> getProjectsList() {
return projectsList;
}
public void setProjectsList(List<Project> projectsList) {
this.projectsList = projectsList;
}
}

67
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java
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@ -1,67 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Spark action to trigger the dump of results associated to research community - reseach initiative/infrasctructure The
* actual dump if performed via the class DumpProducts that is used also for the entire graph dump
*/
public class SparkDumpCommunityProducts implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkDumpCommunityProducts.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
String communityMapPath = parser.get("communityMapPath");
final String dumpType = Optional
.ofNullable(parser.get("dumpType"))
.map(String::valueOf)
.orElse("community");
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
DumpProducts dump = new DumpProducts();
dump
.run(
isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class,
dumpType);
}
}

193
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java
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@ -1,193 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
import eu.dnetlib.dhp.schema.dump.oaf.community.Validated;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
/**
* Preparation of the Project information to be added to the dumped results. For each result associated to at least one
* Project, a serialization of an instance af ResultProject class is done. ResultProject contains the resultId, and the
* list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to
*/
public class SparkPrepareResultProject implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkPrepareResultProject.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
prepareResultProjectList(spark, inputPath, outputPath);
});
}
private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = Utils
.readPath(spark, inputPath + "/relation", Relation.class)
.filter(
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equalsIgnoreCase(ModelConstants.IS_PRODUCED_BY));
Dataset<eu.dnetlib.dhp.schema.oaf.Project> projects = Utils
.readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class);
projects
.joinWith(relation, projects.col("id").equalTo(relation.col("target")), "inner")
.groupByKey(
(MapFunction<Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation>, String>) value -> value
._2()
.getSource(),
Encoders.STRING())
.mapGroups(
(MapGroupsFunction<String, Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation>, ResultProject>) (s,
it) -> {
Set<String> projectSet = new HashSet<>();
Tuple2<eu.dnetlib.dhp.schema.oaf.Project, Relation> first = it.next();
ResultProject rp = new ResultProject();
rp.setResultId(s);
eu.dnetlib.dhp.schema.oaf.Project p = first._1();
projectSet.add(p.getId());
Project ps = getProject(p, first._2);
List<Project> projList = new ArrayList<>();
projList.add(ps);
rp.setProjectsList(projList);
it.forEachRemaining(c -> {
eu.dnetlib.dhp.schema.oaf.Project op = c._1();
if (!projectSet.contains(op.getId())) {
projList
.add(getProject(op, c._2));
projectSet.add(op.getId());
}
});
return rp;
}, Encoders.bean(ResultProject.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) {
Project p = Project
.newInstance(
op.getId(),
op.getCode().getValue(),
Optional
.ofNullable(op.getAcronym())
.map(Field::getValue)
.orElse(null),
Optional
.ofNullable(op.getTitle())
.map(Field::getValue)
.orElse(null),
Optional
.ofNullable(op.getFundingtree())
.map(value -> {
List<Funder> tmp = value
.stream()
.map(ft -> getFunder(ft.getValue()))
.collect(Collectors.toList());
if (!tmp.isEmpty()) {
return tmp.get(0);
} else {
return null;
}
})
.orElse(null));
Optional<DataInfo> di = Optional.ofNullable(op.getDataInfo());
Provenance provenance = new Provenance();
if (di.isPresent()) {
provenance.setProvenance(di.get().getProvenanceaction().getClassname());
provenance.setTrust(di.get().getTrust());
p.setProvenance(provenance);
}
if (Boolean.TRUE.equals(relation.getValidated())) {
p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate()));
}
return p;
}
private static Funder getFunder(String fundingtree) {
final Funder f = new Funder();
final Document doc;
try {
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
doc = reader.read(new StringReader(fundingtree));
f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText());
f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
for (Object o : doc.selectNodes("//funding_level_0")) {
List<Node> node = ((Node) o).selectNodes("./name");
f.setFundingStream((node.get(0)).getText());
}
return f;
} catch (DocumentException | SAXException e) {
throw new IllegalArgumentException(e);
}
}
}

50
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java
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@ -1,50 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
/**
* Spark job to trigger the split of results associated to research community - reseach initiative/infrasctructure. The
* actual split is performed by the class CommunitySplit
*/
public class SparkSplitForCommunity implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkSplitForCommunity.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String communityMapPath = parser.get("communityMapPath");
CommunitySplit split = new CommunitySplit();
split.run(isSparkSessionManaged, inputPath, outputPath, communityMapPath);
}
}

90
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java
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@ -1,90 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.community;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import scala.Tuple2;
public class SparkUpdateProjectInfo implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class);
public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkUpdateProjectInfo.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String preparedInfoPath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", preparedInfoPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
extend(spark, inputPath, outputPath, preparedInfoPath);
});
}
private static void extend(
SparkSession spark,
String inputPath,
String outputPath,
String preparedInfoPath) {
Dataset<CommunityResult> result = Utils.readPath(spark, inputPath, CommunityResult.class);
Dataset<ResultProject> resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class);
result
.joinWith(
resultProject, result.col("id").equalTo(resultProject.col("resultId")),
"left")
.map((MapFunction<Tuple2<CommunityResult, ResultProject>, CommunityResult>) value -> {
CommunityResult r = value._1();
Optional.ofNullable(value._2()).ifPresent(rp -> r.setProjects(rp.getProjectsList()));
return r;
}, Encoders.bean(CommunityResult.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Append)
.json(outputPath);
}
}

26
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Constants.java
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@ -1,26 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
public class Constants implements Serializable {
public static final String IS_HOSTED_BY = "isHostedBy";
public static final String HOSTS = "hosts";
public static final String IS_FUNDED_BY = "isFundedBy";
public static final String FUNDS = "funds";
public static final String FUNDINGS = "fundings";
public static final String RESULT_ENTITY = "result";
public static final String DATASOURCE_ENTITY = "datasource";
public static final String CONTEXT_ENTITY = "context";
public static final String ORGANIZATION_ENTITY = "organization";
public static final String PROJECT_ENTITY = "project";
public static final String CONTEXT_ID = "00";
public static final String CONTEXT_NS_PREFIX = "context_____";
public static final String UNKNOWN = "UNKNOWN";
}

84
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/ContextInfo.java
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@ -1,84 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
import java.util.List;
/**
* Deserialization of the information in the context needed to create Context Entities, and relations between context
* entities and datasources and projects
*/
public class ContextInfo implements Serializable {
private String id;
private String description;
private String type;
private String zenodocommunity;
private String name;
private List<String> projectList;
private List<String> datasourceList;
private List<String> subject;
public List<String> getSubject() {
return subject;
}
public void setSubject(List<String> subject) {
this.subject = subject;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public String getZenodocommunity() {
return zenodocommunity;
}
public void setZenodocommunity(String zenodocommunity) {
this.zenodocommunity = zenodocommunity;
}
public List<String> getProjectList() {
return projectList;
}
public void setProjectList(List<String> projectList) {
this.projectList = projectList;
}
public List<String> getDatasourceList() {
return datasourceList;
}
public void setDatasourceList(List<String> datasourceList) {
this.datasourceList = datasourceList;
}
}

110
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextEntities.java
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@ -1,110 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.compress.CompressionCodec;
import org.apache.hadoop.io.compress.CompressionCodecFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
/**
* Writes on HDFS Context entities. It queries the Information System at the lookup url provided as parameter and
* collects the general information for contexes of type community or ri. The general information is the id of the
* context, its label, the subjects associated to the context, its zenodo community, description and type. This
* information is used to create a new Context Entity
*/
public class CreateContextEntities implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class);
private final transient Configuration conf;
private final transient BufferedWriter writer;
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
CreateContextEntities.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String hdfsPath = parser.get("hdfsPath");
log.info("hdfsPath: {}", hdfsPath);
final String hdfsNameNode = parser.get("nameNode");
log.info("nameNode: {}", hdfsNameNode);
final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl);
final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode);
log.info("Processing contexts...");
cce.execute(Process::getEntity, isLookUpUrl);
cce.close();
}
private void close() throws IOException {
writer.close();
}
public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fsDataOutputStream = fileSystem.append(hdfsWritePath);
} else {
fsDataOutputStream = fileSystem.create(hdfsWritePath);
}
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodecByClassName("org.apache.hadoop.io.compress.GzipCodec");
this.writer = new BufferedWriter(new OutputStreamWriter(codec.createOutputStream(fsDataOutputStream),
StandardCharsets.UTF_8));
}
public <R extends ResearchInitiative> void execute(final Function<ContextInfo, R> producer, String isLookUpUrl)
throws ISLookUpException {
QueryInformationSystem queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
final Consumer<ContextInfo> consumer = ci -> writeEntity(producer.apply(ci));
queryInformationSystem.getContextInformation(consumer);
}
protected <R extends ResearchInitiative> void writeEntity(final R r) {
try {
writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
writer.newLine();
} catch (final IOException e) {
throw new IllegalArgumentException(e);
}
}
}

128
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java
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@ -1,128 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.function.Consumer;
import java.util.function.Function;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
/**
* Writes the set of new Relation between the context and datasources. At the moment the relation between the context
* and the project is not created because of a low coverage in the profiles of openaire ids related to projects
*/
public class CreateContextRelation implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CreateContextRelation.class);
private final transient Configuration conf;
private final transient BufferedWriter writer;
private final transient QueryInformationSystem queryInformationSystem;
private static final String CONTEX_RELATION_DATASOURCE = "contentproviders";
private static final String CONTEX_RELATION_PROJECT = "projects";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
Objects
.requireNonNull(
CreateContextRelation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String hdfsPath = parser.get("hdfsPath");
log.info("hdfsPath: {}", hdfsPath);
final String hdfsNameNode = parser.get("nameNode");
log.info("nameNode: {}", hdfsNameNode);
final String isLookUpUrl = parser.get("isLookUpUrl");
log.info("isLookUpUrl: {}", isLookUpUrl);
final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode, isLookUpUrl);
log.info("Creating relation for datasource...");
cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class));
log.info("Creating relations for projects... ");
cce
.execute(
Process::getRelation, CONTEX_RELATION_PROJECT,
ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class));
cce.close();
}
private void close() throws IOException {
writer.close();
}
public CreateContextRelation(String hdfsPath, String hdfsNameNode, String isLookUpUrl)
throws IOException, ISLookUpException {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl));
queryInformationSystem.execContextRelationQuery();
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fsDataOutputStream = fileSystem.append(hdfsWritePath);
} else {
fsDataOutputStream = fileSystem.create(hdfsWritePath);
}
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
}
public void execute(final Function<ContextInfo, List<Relation>> producer, String category, String prefix) {
final Consumer<ContextInfo> consumer = ci -> producer.apply(ci).forEach(this::writeEntity);
queryInformationSystem.getContextRelation(consumer, category, prefix);
}
protected void writeEntity(final Relation r) {
try {
writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
writer.newLine();
} catch (final Exception e) {
throw new MyRuntimeException(e);
}
}
}

518
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java
View File

@ -1,518 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
/**
* Dumps of entities in the model defined in eu.dnetlib.dhp.schema.dump.oaf.graph. Results are dumped using the same
* Mapper as for eu.dnetlib.dhp.schema.dump.oaf.community, while for the other entities the mapping is defined below
*/
public class DumpGraphEntities implements Serializable {
public void run(Boolean isSparkSessionManaged,
String inputPath,
String outputPath,
Class<? extends OafEntity> inputClazz,
String communityMapPath) {
SparkConf conf = new SparkConf();
switch (ModelSupport.idPrefixMap.get(inputClazz)) {
case "50":
DumpProducts d = new DumpProducts();
d
.run(
isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, GraphResult.class,
eu.dnetlib.dhp.oa.graph.dump.Constants.DUMPTYPE.COMPLETE.getType());
break;
case "40":
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
projectMap(spark, inputPath, outputPath, inputClazz);
});
break;
case "20":
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
organizationMap(spark, inputPath, outputPath, inputClazz);
});
break;
case "10":
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
datasourceMap(spark, inputPath, outputPath, inputClazz);
});
break;
}
}
private static <E extends OafEntity> void datasourceMap(SparkSession spark, String inputPath, String outputPath,
Class<E> inputClazz) {
Utils
.readPath(spark, inputPath, inputClazz)
.map(
(MapFunction<E, Datasource>) d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d),
Encoders.bean(Datasource.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static <E extends OafEntity> void projectMap(SparkSession spark, String inputPath, String outputPath,
Class<E> inputClazz) {
Utils
.readPath(spark, inputPath, inputClazz)
.map(
(MapFunction<E, Project>) p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p),
Encoders.bean(Project.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) {
Datasource datasource = new Datasource();
datasource.setId(d.getId());
Optional
.ofNullable(d.getOriginalId())
.ifPresent(
oId -> datasource.setOriginalId(oId.stream().filter(Objects::nonNull).collect(Collectors.toList())));
Optional
.ofNullable(d.getPid())
.ifPresent(
pids -> pids
.stream()
.map(p -> DatasourcePid.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList()));
Optional
.ofNullable(d.getDatasourcetype())
.ifPresent(
dsType -> datasource
.setDatasourcetype(DatasourceSchemeValue.newInstance(dsType.getClassid(), dsType.getClassname())));
Optional
.ofNullable(d.getOpenairecompatibility())
.ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname()));
Optional
.ofNullable(d.getOfficialname())
.ifPresent(oname -> datasource.setOfficialname(oname.getValue()));
Optional
.ofNullable(d.getEnglishname())
.ifPresent(ename -> datasource.setEnglishname(ename.getValue()));
Optional
.ofNullable(d.getWebsiteurl())
.ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue()));
Optional
.ofNullable(d.getLogourl())
.ifPresent(lurl -> datasource.setLogourl(lurl.getValue()));
Optional
.ofNullable(d.getDateofvalidation())
.ifPresent(dval -> datasource.setDateofvalidation(dval.getValue()));
Optional
.ofNullable(d.getDescription())
.ifPresent(dex -> datasource.setDescription(dex.getValue()));
Optional
.ofNullable(d.getSubjects())
.ifPresent(
sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList())));
Optional
.ofNullable(d.getOdpolicies())
.ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue())));
Optional
.ofNullable(d.getOdlanguages())
.ifPresent(
langs -> datasource
.setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList())));
Optional
.ofNullable(d.getOdcontenttypes())
.ifPresent(
ctypes -> datasource
.setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList())));
Optional
.ofNullable(d.getReleasestartdate())
.ifPresent(rd -> datasource.setReleasestartdate(rd.getValue()));
Optional
.ofNullable(d.getReleaseenddate())
.ifPresent(ed -> datasource.setReleaseenddate(ed.getValue()));
Optional
.ofNullable(d.getMissionstatementurl())
.ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue()));
Optional
.ofNullable(d.getDatabaseaccesstype())
.ifPresent(ar -> datasource.setAccessrights(ar.getValue()));
Optional
.ofNullable(d.getDatauploadtype())
.ifPresent(dut -> datasource.setUploadrights(dut.getValue()));
Optional
.ofNullable(d.getDatabaseaccessrestriction())
.ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue()));
Optional
.ofNullable(d.getDatauploadrestriction())
.ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue()));
Optional
.ofNullable(d.getVersioning())
.ifPresent(v -> datasource.setVersioning(v.getValue()));
Optional
.ofNullable(d.getCitationguidelineurl())
.ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue()));
Optional
.ofNullable(d.getPidsystems())
.ifPresent(ps -> datasource.setPidsystems(ps.getValue()));
Optional
.ofNullable(d.getCertificates())
.ifPresent(c -> datasource.setCertificates(c.getValue()));
Optional
.ofNullable(d.getPolicies())
.ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList())));
Optional
.ofNullable(d.getJournal())
.ifPresent(j -> datasource.setJournal(getContainer(j)));
return datasource;
}
private static Container getContainer(Journal j) {
Container c = new Container();
Optional
.ofNullable(j.getName())
.ifPresent(n -> c.setName(n));
Optional
.ofNullable(j.getIssnPrinted())
.ifPresent(issnp -> c.setIssnPrinted(issnp));
Optional
.ofNullable(j.getIssnOnline())
.ifPresent(issno -> c.setIssnOnline(issno));
Optional
.ofNullable(j.getIssnLinking())
.ifPresent(isnl -> c.setIssnLinking(isnl));
Optional
.ofNullable(j.getEp())
.ifPresent(ep -> c.setEp(ep));
Optional
.ofNullable(j.getIss())
.ifPresent(iss -> c.setIss(iss));
Optional
.ofNullable(j.getSp())
.ifPresent(sp -> c.setSp(sp));
Optional
.ofNullable(j.getVol())
.ifPresent(vol -> c.setVol(vol));
Optional
.ofNullable(j.getEdition())
.ifPresent(edition -> c.setEdition(edition));
Optional
.ofNullable(j.getConferencedate())
.ifPresent(cdate -> c.setConferencedate(cdate));
Optional
.ofNullable(j.getConferenceplace())
.ifPresent(cplace -> c.setConferenceplace(cplace));
return c;
}
private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException {
Project project = new Project();
Optional
.ofNullable(p.getId())
.ifPresent(id -> project.setId(id));
Optional
.ofNullable(p.getWebsiteurl())
.ifPresent(w -> project.setWebsiteurl(w.getValue()));
Optional
.ofNullable(p.getCode())
.ifPresent(code -> project.setCode(code.getValue()));
Optional
.ofNullable(p.getAcronym())
.ifPresent(acronynim -> project.setAcronym(acronynim.getValue()));
Optional
.ofNullable(p.getTitle())
.ifPresent(title -> project.setTitle(title.getValue()));
Optional
.ofNullable(p.getStartdate())
.ifPresent(sdate -> project.setStartdate(sdate.getValue()));
Optional
.ofNullable(p.getEnddate())
.ifPresent(edate -> project.setEnddate(edate.getValue()));
Optional
.ofNullable(p.getCallidentifier())
.ifPresent(cide -> project.setCallidentifier(cide.getValue()));
Optional
.ofNullable(p.getKeywords())
.ifPresent(key -> project.setKeywords(key.getValue()));
Optional<Field<String>> omandate = Optional.ofNullable(p.getOamandatepublications());
Optional<Field<String>> oecsc39 = Optional.ofNullable(p.getEcsc39());
boolean mandate = false;
if (omandate.isPresent()) {
if (omandate.get().getValue().equals("true")) {
mandate = true;
}
}
if (oecsc39.isPresent()) {
if (oecsc39.get().getValue().equals("true")) {
mandate = true;
}
}
project.setOpenaccessmandateforpublications(mandate);
project.setOpenaccessmandatefordataset(false);
Optional
.ofNullable(p.getEcarticle29_3())
.ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true")));
project
.setSubject(
Optional
.ofNullable(p.getSubjects())
.map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList()))
.orElse(new ArrayList<>()));
Optional
.ofNullable(p.getSummary())
.ifPresent(summary -> project.setSummary(summary.getValue()));
Optional<Float> ofundedamount = Optional.ofNullable(p.getFundedamount());
Optional<Field<String>> ocurrency = Optional.ofNullable(p.getCurrency());
Optional<Float> ototalcost = Optional.ofNullable(p.getTotalcost());
if (ocurrency.isPresent()) {
if (ofundedamount.isPresent()) {
if (ototalcost.isPresent()) {
project
.setGranted(
Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get()));
} else {
project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get()));
}
}
}
project
.setH2020programme(
Optional
.ofNullable(p.getH2020classification())
.map(
classification -> classification
.stream()
.map(
c -> Programme
.newInstance(
c.getH2020Programme().getCode(), c.getH2020Programme().getDescription()))
.collect(Collectors.toList()))
.orElse(new ArrayList<>()));
Optional<List<Field<String>>> ofundTree = Optional
.ofNullable(p.getFundingtree());
List<Funder> funList = new ArrayList<>();
if (ofundTree.isPresent()) {
for (Field<String> fundingtree : ofundTree.get()) {
funList.add(getFunder(fundingtree.getValue()));
}
}
project.setFunding(funList);
return project;
}
public static Funder getFunder(String fundingtree) throws DocumentException {
Funder f = new Funder();
final Document doc;
doc = new SAXReader().read(new StringReader(fundingtree));
f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText());
f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText());
f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText());
// f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText());
String id = "";
String description = "";
// List<Levels> fundings = new ArrayList<>();
int level = 0;
List<org.dom4j.Node> nodes = doc.selectNodes("//funding_level_" + level);
while (nodes.size() > 0) {
for (org.dom4j.Node n : nodes) {
List node = n.selectNodes("./id");
id = ((org.dom4j.Node) node.get(0)).getText();
id = id.substring(id.indexOf("::") + 2);
node = n.selectNodes("./description");
description += ((Node) node.get(0)).getText() + " - ";
}
level += 1;
nodes = doc.selectNodes("//funding_level_" + level);
}
if (!id.equals("")) {
Fundings fundings = new Fundings();
fundings.setId(id);
fundings.setDescription(description.substring(0, description.length() - 3).trim());
f.setFunding_stream(fundings);
}
return f;
}
private static <E extends OafEntity> void organizationMap(SparkSession spark, String inputPath, String outputPath,
Class<E> inputClazz) {
Utils
.readPath(spark, inputPath, inputClazz)
.map(
(MapFunction<E, Organization>) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o),
Encoders.bean(Organization.class))
.filter((FilterFunction<Organization>) o -> o != null)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization(
eu.dnetlib.dhp.schema.oaf.Organization org) {
if (org.getDataInfo().getDeletedbyinference())
return null;
Organization organization = new Organization();
Optional
.ofNullable(org.getLegalshortname())
.ifPresent(value -> organization.setLegalshortname(value.getValue()));
Optional
.ofNullable(org.getLegalname())
.ifPresent(value -> organization.setLegalname(value.getValue()));
Optional
.ofNullable(org.getWebsiteurl())
.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
Optional
.ofNullable(org.getAlternativeNames())
.ifPresent(
value -> organization
.setAlternativenames(
value
.stream()
.map(v -> v.getValue())
.collect(Collectors.toList())));
Optional
.ofNullable(org.getCountry())
.ifPresent(
value -> {
if (!value.getClassid().equals(Constants.UNKNOWN)) {
organization.setCountry(Country.newInstance(value.getClassid(), value.getClassname()));
}
});
Optional
.ofNullable(org.getId())
.ifPresent(value -> organization.setId(value));
Optional
.ofNullable(org.getPid())
.ifPresent(
value -> organization
.setPid(
value
.stream()
.map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
.collect(Collectors.toList())));
return organization;
}
}

201
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java
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@ -1,201 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Creates new Relations (as in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation) from the information in the Entity. The
* new Relations are created for the datasource in the collectedfrom and hostedby elements and for the context related
* to communities and research initiative/infrastructures. For collectedfrom elements it creates: datasource -> provides
* -> result and result -> isProvidedBy -> datasource For hostedby elements it creates: datasource -> hosts -> result
* and result -> isHostedBy -> datasource For context elements it creates: context <-> isRelatedTo <-> result. Note for
* context: it gets the first provenance in the dataInfo. If more than one is present the others are not dumped
*/
public class Extractor implements Serializable {
public void run(Boolean isSparkSessionManaged,
String inputPath,
String outputPath,
Class<? extends Result> inputClazz,
String communityMapPath) {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
extractRelationResult(
spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath));
});
}
private <R extends Result> void extractRelationResult(SparkSession spark,
String inputPath,
String outputPath,
Class<R> inputClazz,
CommunityMap communityMap) {
Set<Integer> hashCodes = new HashSet<>();
Utils
.readPath(spark, inputPath, inputClazz)
.flatMap((FlatMapFunction<R, Relation>) value -> {
List<Relation> relationList = new ArrayList<>();
extractRelationsFromInstance(hashCodes, value, relationList);
Set<String> communities = communityMap.keySet();
Optional
.ofNullable(value.getContext())
.ifPresent(contexts -> contexts.forEach(context -> {
String id = context.getId();
if (id.contains(":")) {
id = id.substring(0, id.indexOf(":"));
}
if (communities.contains(id)) {
String contextId = Utils.getContextId(id);
Provenance provenance = Optional
.ofNullable(context.getDataInfo())
.map(
dinfo -> Optional
.ofNullable(dinfo.get(0).getProvenanceaction())
.map(
paction -> Provenance
.newInstance(
paction.getClassid(),
dinfo.get(0).getTrust()))
.orElse(null))
.orElse(null);
Relation r = getRelation(
value.getId(), contextId,
Constants.RESULT_ENTITY,
Constants.CONTEXT_ENTITY,
ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP, provenance);
if (!hashCodes.contains(r.hashCode())) {
relationList
.add(r);
hashCodes.add(r.hashCode());
}
r = getRelation(
contextId, value.getId(),
Constants.CONTEXT_ENTITY,
Constants.RESULT_ENTITY,
ModelConstants.IS_RELATED_TO,
ModelConstants.RELATIONSHIP, provenance);
if (!hashCodes.contains(r.hashCode())) {
relationList
.add(
r);
hashCodes.add(r.hashCode());
}
}
}));
return relationList.iterator();
}, Encoders.bean(Relation.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
private <R extends Result> void extractRelationsFromInstance(Set<Integer> hashCodes, R value,
List<Relation> relationList) {
Optional
.ofNullable(value.getInstance())
.ifPresent(inst -> inst.forEach(instance -> {
Optional
.ofNullable(instance.getCollectedfrom())
.ifPresent(
cf -> getRelatioPair(
value, relationList, cf,
ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes));
Optional
.ofNullable(instance.getHostedby())
.ifPresent(
hb -> getRelatioPair(
value, relationList, hb,
Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes));
}));
}
private static <R extends Result> void getRelatioPair(R value, List<Relation> relationList, KeyValue cf,
String resultDatasource, String datasourceResult,
Set<Integer> hashCodes) {
Provenance provenance = Optional
.ofNullable(cf.getDataInfo())
.map(
dinfo -> Optional
.ofNullable(dinfo.getProvenanceaction())
.map(
paction -> Provenance
.newInstance(
paction.getClassname(),
dinfo.getTrust()))
.orElse(
Provenance
.newInstance(
eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED,
eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)))
.orElse(
Provenance
.newInstance(
eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED,
eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST));
Relation r = getRelation(
value.getId(),
cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY,
resultDatasource, ModelConstants.PROVISION,
provenance);
if (!hashCodes.contains(r.hashCode())) {
relationList
.add(r);
hashCodes.add(r.hashCode());
}
r = getRelation(
cf.getKey(), value.getId(),
Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY,
datasourceResult, ModelConstants.PROVISION,
provenance);
if (!hashCodes.contains(r.hashCode())) {
relationList
.add(r);
hashCodes.add(r.hashCode());
}
}
private static Relation getRelation(String source, String target, String sourceType, String targetType,
String relName, String relType, Provenance provenance) {
Relation r = new Relation();
r.setSource(Node.newInstance(source, sourceType));
r.setTarget(Node.newInstance(target, targetType));
r.setReltype(RelType.newInstance(relName, relType));
r.setProvenance(provenance);
return r;
}
}

25
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/MergedRels.java
View File

@ -1,25 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
public class MergedRels implements Serializable {
private String organizationId;
private String representativeId;
public String getOrganizationId() {
return organizationId;
}
public void setOrganizationId(String organizationId) {
this.organizationId = organizationId;
}
public String getRepresentativeId() {
return representativeId;
}
public void setRepresentativeId(String representativeId) {
this.representativeId = representativeId;
}
}

21
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/OrganizationMap.java
View File

@ -1,21 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
public class OrganizationMap extends HashMap<String, List<String>> {
public OrganizationMap() {
super();
}
public List<String> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

99
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java
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@ -1,99 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
/**
* It process the ContextInfo information to produce a new Context Entity or a set of Relations between the generic
* context entity and datasource/projects related to the context.
*/
public class Process implements Serializable {
@SuppressWarnings("unchecked")
public static <R extends ResearchInitiative> R getEntity(ContextInfo ci) {
try {
ResearchInitiative ri;
if (ci.getType().equals("community")) {
ri = new ResearchCommunity();
((ResearchCommunity) ri).setSubject(ci.getSubject());
ri.setType(Constants.RESEARCH_COMMUNITY);
} else {
ri = new ResearchInitiative();
ri.setType(Constants.RESEARCH_INFRASTRUCTURE);
}
ri.setId(Utils.getContextId(ci.getId()));
ri.setAcronym(ci.getId());
ri.setDescription(ci.getDescription());
ri.setName(ci.getName());
if (StringUtils.isNotEmpty(ci.getZenodocommunity())) {
ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity());
}
return (R) ri;
} catch (final Exception e) {
throw new MyRuntimeException(e);
}
}
public static List<Relation> getRelation(ContextInfo ci) {
try {
List<Relation> relationList = new ArrayList<>();
ci
.getDatasourceList()
.forEach(ds -> {
String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2));
String contextId = Utils.getContextId(ci.getId());
relationList
.add(
Relation
.newInstance(
Node
.newInstance(
contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
Node.newInstance(ds, nodeType),
RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
Provenance
.newInstance(
Constants.USER_CLAIM,
Constants.DEFAULT_TRUST)));
relationList
.add(
Relation
.newInstance(
Node.newInstance(ds, nodeType),
Node
.newInstance(
contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
Provenance
.newInstance(
Constants.USER_CLAIM,
Constants.DEFAULT_TRUST)));
});
return relationList;
} catch (final Exception e) {
throw new MyRuntimeException(e);
}
}
}

195
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java
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@ -1,195 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.StringReader;
import java.util.*;
import java.util.function.Consumer;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.jetbrains.annotations.NotNull;
import org.xml.sax.SAXException;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class QueryInformationSystem {
private ISLookUpService isLookUp;
private List<String> contextRelationResult;
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and $x//context/param[./@name = 'status']/text() = 'all' " +
" return " +
"$x//context";
private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
"where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return "
+
"concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " +
"$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', "
+
"$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)";
public void getContextInformation(final Consumer<ContextInfo> consumer) throws ISLookUpException {
isLookUp
.quickSearchProfile(XQUERY_ENTITY)
.forEach(c -> {
ContextInfo cinfo = new ContextInfo();
String[] cSplit = c.split("@@");
cinfo.setId(cSplit[0]);
cinfo.setName(cSplit[1]);
cinfo.setDescription(cSplit[2]);
if (!cSplit[3].trim().equals("")) {
cinfo.setSubject(Arrays.asList(cSplit[3].split(",")));
}
cinfo.setZenodocommunity(cSplit[4]);
cinfo.setType(cSplit[5]);
consumer.accept(cinfo);
});
}
public List<String> getContextRelationResult() {
return contextRelationResult;
}
public void setContextRelationResult(List<String> contextRelationResult) {
this.contextRelationResult = contextRelationResult;
}
public ISLookUpService getIsLookUp() {
return isLookUp;
}
public void setIsLookUp(ISLookUpService isLookUpService) {
this.isLookUp = isLookUpService;
}
public void execContextRelationQuery() throws ISLookUpException {
contextRelationResult = isLookUp.quickSearchProfile(XQUERY);
}
public void getContextRelation(final Consumer<ContextInfo> consumer, String category, String prefix) {
contextRelationResult.forEach(xml -> {
ContextInfo cinfo = new ContextInfo();
final Document doc;
try {
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
doc = reader.read(new StringReader(xml));
Element root = doc.getRootElement();
cinfo.setId(root.attributeValue("id"));
Iterator<Element> it = root.elementIterator();
while (it.hasNext()) {
Element el = it.next();
if (el.getName().equals("category")) {
String categoryId = el.attributeValue("id");
categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2);
if (categoryId.equals(category)) {
cinfo.setDatasourceList(getCategoryList(el, prefix));
}
}
}
consumer.accept(cinfo);
} catch (DocumentException | SAXException e) {
e.printStackTrace();
}
});
}
@NotNull
private List<String> getCategoryList(Element el, String prefix) {
List<String> datasourceList = new ArrayList<>();
for (Object node : el.selectNodes(".//concept")) {
String oid = getOpenaireId((Node) node, prefix);
if (oid != null)
datasourceList.add(oid);
}
return datasourceList;
}
private String getOpenaireId(Node el, String prefix) {
for (Object node : el.selectNodes(".//param")) {
Node n = (Node) node;
if (n.valueOf("./@name").equals("openaireId")) {
return prefix + "|" + n.getText();
}
}
return makeOpenaireId(el, prefix);
}
private String makeOpenaireId(Node el, String prefix) {
if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) {
return null;
}
String funder = "";
String grantId = null;
String funding = null;
for (Object node : el.selectNodes(".//param")) {
Node n = (Node) node;
switch (n.valueOf("./@name")) {
case "funding":
funding = n.getText();
break;
case "funder":
funder = n.getText();
break;
case "CD_PROJECT_NUMBER":
grantId = n.getText();
break;
default:
break;
}
}
String nsp = null;
switch (funder.toLowerCase()) {
case "ec":
if (funding == null) {
return null;
}
if (funding.toLowerCase().contains("h2020")) {
nsp = "corda__h2020::";
} else {
nsp = "corda_______::";
}
break;
case "tubitak":
nsp = "tubitakf____::";
break;
case "dfg":
nsp = "dfgf________::";
break;
default:
StringBuilder bld = new StringBuilder();
bld.append(funder.toLowerCase());
for (int i = funder.length(); i < 12; i++)
bld.append("_");
bld.append("::");
nsp = bld.toString();
}
return prefix + "|" + nsp + DHPUtils.md5(grantId);
}
}

122
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkCollectAndSave.java
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package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation;
/**
* Reads all the entities of the same type (Relation / Results) and saves them in the same folder
*/
public class SparkCollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkCollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final Boolean aggregateResult = Optional
.ofNullable(parser.get("resultAggregation"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath + "/result");
run(spark, inputPath, outputPath, aggregateResult);
});
}
private static void run(SparkSession spark, String inputPath, String outputPath, boolean aggregate) {
if (aggregate) {
Utils
.readPath(spark, inputPath + "/result/publication", GraphResult.class)
.union(Utils.readPath(spark, inputPath + "/result/dataset", GraphResult.class))
.union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class))
.union(Utils.readPath(spark, inputPath + "/result/software", GraphResult.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath + "/result");
} else {
write(
Utils
.readPath(spark, inputPath + "/result/publication", GraphResult.class),
outputPath + "/publication");
write(
Utils
.readPath(spark, inputPath + "/result/dataset", GraphResult.class),
outputPath + "/dataset");
write(
Utils
.readPath(spark, inputPath + "/result/otherresearchproduct", GraphResult.class),
outputPath + "/otheresearchproduct");
write(
Utils
.readPath(spark, inputPath + "/result/software", GraphResult.class),
outputPath + "/software");
}
Utils
.readPath(spark, inputPath + "/relation/publication", Relation.class)
.union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class))
.union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class))
.union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class))
.union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class))
.union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class))
.union(Utils.readPath(spark, inputPath + "/relation/relation", Relation.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/relation");
}
private static void write(Dataset<GraphResult> dataSet, String outputPath) {
dataSet
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

54
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpEntitiesJob.java
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package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
/**
* Spark Job that fires the dump for the entites
*/
public class SparkDumpEntitiesJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkDumpEntitiesJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String communityMapPath = parser.get("communityMapPath");
Class<? extends OafEntity> inputClazz = (Class<? extends OafEntity>) Class.forName(resultClassName);
DumpGraphEntities dg = new DumpGraphEntities();
dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath);
}
}

132
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java
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package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Relation;
/**
* Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation
*/
public class SparkDumpRelationJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkDumpRelationJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
Optional<String> rs = Optional.ofNullable(parser.get("removeSet"));
final Set<String> removeSet = new HashSet<>();
if (rs.isPresent()) {
Collections.addAll(removeSet, rs.get().split(";"));
}
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
dumpRelation(spark, inputPath, outputPath, removeSet);
});
}
private static void dumpRelation(SparkSession spark, String inputPath, String outputPath, Set<String> removeSet) {
Dataset<Relation> relations = Utils.readPath(spark, inputPath, Relation.class);
relations
.filter((FilterFunction<Relation>) r -> !removeSet.contains(r.getRelClass()))
.map((MapFunction<Relation, eu.dnetlib.dhp.schema.dump.oaf.graph.Relation>) relation -> {
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation();
relNew
.setSource(
Node
.newInstance(
relation.getSource(),
ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2))));
relNew
.setTarget(
Node
.newInstance(
relation.getTarget(),
ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2))));
relNew
.setReltype(
RelType
.newInstance(
relation.getRelClass(),
relation.getSubRelType()));
Optional<DataInfo> odInfo = Optional.ofNullable(relation.getDataInfo());
if (odInfo.isPresent()) {
DataInfo dInfo = odInfo.get();
if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() &&
Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) {
relNew
.setProvenance(
Provenance
.newInstance(
dInfo.getProvenanceaction().getClassname(),
dInfo.getTrust()));
}
}
if (Boolean.TRUE.equals(relation.getValidated())) {
relNew.setValidated(relation.getValidated());
relNew.setValidationDate(relation.getValidationDate());
}
return relNew;
}, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

54
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkExtractRelationFromEntities.java
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@ -1,54 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.oaf.Result;
/**
* Spark job that fires the extraction of relations from entities
*/
public class SparkExtractRelationFromEntities implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkExtractRelationFromEntities.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String communityMapPath = parser.get("communityMapPath");
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
Extractor extractor = new Extractor();
extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath);
}
}

176
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java
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@ -1,176 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.*;
import java.util.function.Consumer;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Node;
import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType;
import eu.dnetlib.dhp.schema.oaf.Relation;
/**
* Create new Relations between Context Entities and Organizations whose products are associated to the context. It
* produces relation such as: organization <-> isRelatedTo <-> context
*/
public class SparkOrganizationRelation implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkOrganizationRelation.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final OrganizationMap organizationMap = new Gson()
.fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class);
final String serializedOrganizationMap = new Gson().toJson(organizationMap);
log.info("organization map : {}", serializedOrganizationMap);
final String communityMapPath = parser.get("communityMapPath");
log.info("communityMapPath: {}", communityMapPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
extractRelation(spark, inputPath, organizationMap, outputPath, communityMapPath);
});
}
private static void extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap,
String outputPath, String communityMapPath) {
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
Dataset<Relation> relationDataset = Utils.readPath(spark, inputPath, Relation.class);
relationDataset.createOrReplaceTempView("relation");
List<eu.dnetlib.dhp.schema.dump.oaf.graph.Relation> relList = new ArrayList<>();
Dataset<MergedRels> mergedRelsDataset = spark
.sql(
"SELECT target organizationId, source representativeId " +
"FROM relation " +
"WHERE datainfo.deletedbyinference = false " +
"AND relclass = 'merges' " +
"AND substr(source, 1, 2) = '20'")
.as(Encoders.bean(MergedRels.class));
mergedRelsDataset.map((MapFunction<MergedRels, MergedRels>) mergedRels -> {
if (organizationMap.containsKey(mergedRels.getOrganizationId())) {
return mergedRels;
}
return null;
}, Encoders.bean(MergedRels.class))
.filter(Objects::nonNull)
.collectAsList()
.forEach(getMergedRelsConsumer(organizationMap, relList, communityMap));
organizationMap
.keySet()
.forEach(
oId -> organizationMap
.get(oId)
.forEach(community -> {
if (communityMap.containsKey(community)) {
addRelations(relList, community, oId);
}
}));
spark
.createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
@NotNull
private static Consumer<MergedRels> getMergedRelsConsumer(OrganizationMap organizationMap,
List<eu.dnetlib.dhp.schema.dump.oaf.graph.Relation> relList, CommunityMap communityMap) {
return mergedRels -> {
String oId = mergedRels.getOrganizationId();
organizationMap
.get(oId)
.forEach(community -> {
if (communityMap.containsKey(community)) {
addRelations(relList, community, mergedRels.getRepresentativeId());
}
});
organizationMap.remove(oId);
};
}
private static void addRelations(List<eu.dnetlib.dhp.schema.dump.oaf.graph.Relation> relList, String community,
String organization) {
String id = Utils.getContextId(community);
log.info("create relation for organization: {}", organization);
relList
.add(
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation
.newInstance(
Node.newInstance(id, Constants.CONTEXT_ENTITY),
Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))),
RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
Provenance
.newInstance(
eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM,
eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)));
relList
.add(
eu.dnetlib.dhp.schema.dump.oaf.graph.Relation
.newInstance(
Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))),
Node.newInstance(id, Constants.CONTEXT_ENTITY),
RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
Provenance
.newInstance(
eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM,
eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)));
}
}

136
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java
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@ -1,136 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.complete;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference
* and if both the source and the target node are present in the graph and are not deleted by inference nor invisible.
* To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists
* with this view for both the source and the target
*/
public class SparkSelectValidRelationsJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkSelectValidRelationsJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
selectValidRelation(spark, inputPath, outputPath);
});
}
private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) {
Dataset<Relation> relation = Utils.readPath(spark, inputPath + "/relation", Relation.class);
Dataset<Publication> publication = Utils.readPath(spark, inputPath + "/publication", Publication.class);
Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = Utils
.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
Dataset<Software> software = Utils.readPath(spark, inputPath + "/software", Software.class);
Dataset<OtherResearchProduct> other = Utils
.readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class);
Dataset<Organization> organization = Utils.readPath(spark, inputPath + "/organization", Organization.class);
Dataset<Project> project = Utils.readPath(spark, inputPath + "/project", Project.class);
Dataset<Datasource> datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class);
relation.createOrReplaceTempView("relation");
publication.createOrReplaceTempView("publication");
dataset.createOrReplaceTempView("dataset");
other.createOrReplaceTempView("other");
software.createOrReplaceTempView("software");
organization.createOrReplaceTempView("organization");
project.createOrReplaceTempView("project");
datasource.createOrReplaceTempView("datasource");
spark
.sql(
"SELECT id " +
"FROM publication " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM dataset " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM other " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM software " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM organization " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM project " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " +
"UNION ALL " +
"SELECT id " +
"FROM datasource " +
"WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ")
.createOrReplaceTempView("identifiers");
spark
.sql(
"SELECT relation.* " +
"FROM relation " +
"JOIN identifiers i1 " +
"ON source = i1.id " +
"JOIN identifiers i2 " +
"ON target = i2.id " +
"WHERE datainfo.deletedbyinference = false")
.as(Encoders.bean(Relation.class))
.write()
.option("compression", "gzip")
.mode(SaveMode.Overwrite)
.json(outputPath);
}
}

30
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java
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@ -1,30 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.exceptions;
public class MyRuntimeException extends RuntimeException {
public MyRuntimeException() {
super();
}
public MyRuntimeException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public MyRuntimeException(final String message, final Throwable cause) {
super(message, cause);
}
public MyRuntimeException(final String message) {
super(message);
}
public MyRuntimeException(final Throwable cause) {
super(cause);
}
}

29
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java
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@ -1,29 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.exceptions;
public class NoAvailableEntityTypeException extends Exception {
public NoAvailableEntityTypeException() {
super();
}
public NoAvailableEntityTypeException(
final String message,
final Throwable cause,
final boolean enableSuppression,
final boolean writableStackTrace) {
super(message, cause, enableSuppression, writableStackTrace);
}
public NoAvailableEntityTypeException(final String message, final Throwable cause) {
super(message, cause);
}
public NoAvailableEntityTypeException(final String message) {
super(message);
}
public NoAvailableEntityTypeException(final Throwable cause) {
super(cause);
}
}

129
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java
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@ -1,129 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.funderresults;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
/**
* Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC
* for the EC it specifies also the fundingStream (FP7 or H2020)
*/
public class SparkDumpFunderResults implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkDumpFunderResults.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkDumpFunderResults.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
writeResultProjectList(spark, inputPath, outputPath);
});
}
private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath) {
Dataset<CommunityResult> result = Utils
.readPath(spark, inputPath + "/publication", CommunityResult.class)
.union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/otherresearchproduct", CommunityResult.class))
.union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class));
log.info("Number of result {}", result.count());
Dataset<String> tmp = result
.flatMap((FlatMapFunction<CommunityResult, String>) cr -> cr.getProjects().stream().map(p -> {
return getFunderName(p);
}).collect(Collectors.toList()).iterator(), Encoders.STRING())
.distinct();
List<String> funderList = tmp.collectAsList();
funderList.forEach(funder -> {
dumpResults(funder, result, outputPath);
});
}
@NotNull
private static String getFunderName(Project p) {
Optional<Funder> ofunder = Optional.ofNullable(p.getFunder());
if (ofunder.isPresent()) {
String fName = ofunder.get().getShortName();
if (fName.equalsIgnoreCase("ec")) {
fName += "_" + ofunder.get().getFundingStream();
}
return fName;
} else {
String fName = p.getId().substring(3, p.getId().indexOf("_")).toUpperCase();
if (fName.equalsIgnoreCase("ec")) {
if (p.getId().contains("h2020")) {
fName += "_H2020";
} else {
fName += "_FP7";
}
} else if (fName.equalsIgnoreCase("conicytf")) {
fName = "CONICYT";
} else if (fName.equalsIgnoreCase("dfgf")) {
fName = "DFG";
} else if (fName.equalsIgnoreCase("tubitakf")) {
fName = "TUBITAK";
} else if (fName.equalsIgnoreCase("euenvagency")) {
fName = "EEA";
}
return fName;
}
}
private static void dumpResults(String funder, Dataset<CommunityResult> results, String outputPath) {
results.map((MapFunction<CommunityResult, CommunityResult>) r -> {
if (!Optional.ofNullable(r.getProjects()).isPresent()) {
return null;
}
for (Project p : r.getProjects()) {
String fName = getFunderName(p);
if (fName.equalsIgnoreCase(funder)) {
return r;
}
}
return null;
}, Encoders.bean(CommunityResult.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/" + funder);
}
}

118
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java
View File

@ -1,118 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.funderresults;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import scala.Tuple2;
/**
* Selects the results linked to projects. Only for these results the dump will be performed.
* The code to perform the dump and to expend the dumped results with the information related to projects
* is the one used for the dump of the community products
*/
public class SparkResultLinkedToProject implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkResultLinkedToProject.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkResultLinkedToProject.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String resultProjectsPath = parser.get("graphPath");
log.info("graphPath: {}", resultProjectsPath);
String communityMapPath = parser.get("communityMapPath");
@SuppressWarnings("unchecked")
Class<? extends Result> inputClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
writeResultsLinkedToProjects(
communityMapPath, spark, inputClazz, inputPath, outputPath, resultProjectsPath);
});
}
private static <R extends Result> void writeResultsLinkedToProjects(String communityMapPath, SparkSession spark,
Class<R> inputClazz,
String inputPath, String outputPath, String resultProjectsPath) {
Dataset<R> results = Utils
.readPath(spark, inputPath, inputClazz)
.filter(
(FilterFunction<R>) r -> !r.getDataInfo().getDeletedbyinference() &&
!r.getDataInfo().getInvisible());
Dataset<ResultProject> resultProjectDataset = Utils
.readPath(spark, resultProjectsPath, ResultProject.class);
CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
results
.joinWith(resultProjectDataset, results.col("id").equalTo(resultProjectDataset.col("resultId")))
.map((MapFunction<Tuple2<R, ResultProject>, CommunityResult>) t2 -> {
CommunityResult cr = (CommunityResult) ResultMapper
.map(
t2._1(),
communityMap, Constants.DUMPTYPE.FUNDER.getType());
cr.setProjects(t2._2().getProjectsList());
return cr;
}, Encoders.bean(CommunityResult.class))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
}
}

82
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/projectssubset/ProjectsSubsetSparkJob.java
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@ -1,82 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump.projectssubset;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.dump.oaf.graph.Project;
import scala.Tuple2;
public class ProjectsSubsetSparkJob implements Serializable {
private static final Logger log = LoggerFactory.getLogger(ProjectsSubsetSparkJob.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
ProjectsSubsetSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/project_subset_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String projectListPath = parser.get("projectListPath");
log.info("projectListPath: {}", projectListPath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
Utils.removeOutputDir(spark, outputPath);
getNewProjectList(spark, inputPath, outputPath, projectListPath);
});
}
private static void getNewProjectList(SparkSession spark, String inputPath, String outputPath,
String projectListPath) {
Dataset<String> projectList = spark.read().textFile(projectListPath);
Dataset<Project> projects;
projects = Utils.readPath(spark, inputPath, Project.class);
projects
.joinWith(projectList, projects.col("id").equalTo(projectList.col("value")), "left")
.map((MapFunction<Tuple2<Project, String>, Project>) t2 -> {
if (Optional.ofNullable(t2._2()).isPresent())
return null;
return t2._1();
}, Encoders.bean(Project.class))
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath);
Utils
.readPath(spark, outputPath, Project.class)
.map((MapFunction<Project, String>) p -> p.getId(), Encoders.STRING())
.write()
.mode(SaveMode.Append)
.option("compression", "gzip")
.text(projectListPath);
}
}

52
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -267,10 +267,13 @@ public abstract class AbstractMdRecordToOafMapper {
res
.add(
getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate));
OafMapperUtils
.getRelation(
docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, entity, validationdDate));
res
.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate));
.add(
OafMapperUtils
.getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, entity, validationdDate));
}
}
@ -303,13 +306,16 @@ public abstract class AbstractMdRecordToOafMapper {
final String targetId = createOpenaireId(targetType, target, true);
rels
.add(
getRelation(
entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate));
OafMapperUtils
.getRelation(
entity.getId(), targetId, relType, subRelType, relClass, entity,
validationdDate));
rels
.add(
getRelation(
targetId, entity.getId(), relType, subRelType, relClassInverse, entity,
validationdDate));
OafMapperUtils
.getRelation(
targetId, entity.getId(), relType, subRelType, relClassInverse, entity,
validationdDate));
}
}
}
@ -317,36 +323,6 @@ public abstract class AbstractMdRecordToOafMapper {
return rels;
}
protected Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
protected Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setCollectedfrom(entity.getCollectedfrom());
rel.setDataInfo(entity.getDataInfo());
rel.setLastupdatetimestamp(entity.getLastupdatetimestamp());
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
return rel;
}
protected abstract List<Oaf> addOtherResultRels(
final Document doc,
final OafEntity entity);

155
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -1,32 +1,7 @@
package eu.dnetlib.dhp.oa.graph.raw;
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.DNET_PROVENANCE_ACTIONS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTICIPANT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_MERGED_IN;
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_PROVIDED_BY;
import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
import static eu.dnetlib.dhp.schema.common.ModelConstants.MERGES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE;
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.PARTICIPATION;
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.PROVIDES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVISION;
import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET;
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.RESULT_PROJECT;
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.*;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
import java.io.Closeable;
@ -45,6 +20,8 @@ import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
@ -68,6 +45,7 @@ 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.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
public class MigrateDbEntitiesApplication extends AbstractMigrationApplication implements Closeable {
@ -437,25 +415,14 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(DATASOURCE_ORGANIZATION);
r1.setSubRelType(PROVISION);
r1.setRelClass(IS_PROVIDED_BY);
r1.setSource(dsId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(
dsId, orgId, DATASOURCE_ORGANIZATION, PRODUCES, IS_PROVIDED_BY, collectedFrom, info,
lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType(DATASOURCE_ORGANIZATION);
r2.setSubRelType(PROVISION);
r2.setRelClass(PROVIDES);
r2.setSource(orgId);
r2.setTarget(dsId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = OafMapperUtils
.getRelation(
orgId, dsId, DATASOURCE_ORGANIZATION, PRODUCES, PROVIDES, collectedFrom, info, lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
@ -471,25 +438,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(PROJECT_ORGANIZATION);
r1.setSubRelType(PARTICIPATION);
r1.setRelClass(HAS_PARTICIPANT);
r1.setSource(projectId);
r1.setTarget(orgId);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final List<KeyValue> properties = Lists
.newArrayList(
keyValue("contribution", String.valueOf(rs.getDouble("contribution"))),
keyValue("currency", rs.getString("currency")));
final Relation r2 = new Relation();
r2.setRelType(PROJECT_ORGANIZATION);
r2.setSubRelType(PARTICIPATION);
r2.setRelClass(IS_PARTICIPANT);
r2.setSource(orgId);
r2.setTarget(projectId);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(
projectId, orgId, PROJECT_ORGANIZATION, PARTICIPATION, HAS_PARTICIPANT, collectedFrom, info,
lastUpdateTimestamp, null, properties);
final Relation r2 = OafMapperUtils
.getRelation(
orgId, projectId, PROJECT_ORGANIZATION, PARTICIPATION, IS_PARTICIPANT, collectedFrom, info,
lastUpdateTimestamp, null, properties);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
@ -703,25 +665,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(ORG_ORG_RELTYPE);
r1.setSubRelType(ModelConstants.DEDUP);
r1.setRelClass(MERGES);
r1.setSource(orgId1);
r1.setTarget(orgId2);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r1 = OafMapperUtils
.getRelation(orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, MERGES, collectedFrom, info, lastUpdateTimestamp);
final Relation r2 = new Relation();
r2.setRelType(ORG_ORG_RELTYPE);
r2.setSubRelType(ModelConstants.DEDUP);
r2.setRelClass(IS_MERGED_IN);
r2.setSource(orgId2);
r2.setTarget(orgId1);
r2.setCollectedfrom(collectedFrom);
r2.setDataInfo(info);
r2.setLastupdatetimestamp(lastUpdateTimestamp);
final Relation r2 = OafMapperUtils
.getRelation(
orgId2, orgId1, ORG_ORG_RELTYPE, DEDUP, IS_MERGED_IN, collectedFrom, info, lastUpdateTimestamp);
return Arrays.asList(r1, r2);
} catch (final Exception e) {
throw new RuntimeException(e);
@ -738,17 +687,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r = new Relation();
r.setRelType(ORG_ORG_RELTYPE);
r.setSubRelType(ModelConstants.RELATIONSHIP);
r.setRelClass(rs.getString("type"));
r.setSource(orgId1);
r.setTarget(orgId2);
r.setCollectedfrom(collectedFrom);
r.setDataInfo(info);
r.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(r);
return Arrays
.asList(
OafMapperUtils
.getRelation(
orgId1, orgId2, ORG_ORG_RELTYPE, RELATIONSHIP, rs.getString("type"), collectedFrom, info,
lastUpdateTimestamp));
} catch (final Exception e) {
throw new RuntimeException(e);
}
@ -765,29 +709,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
final Relation r1 = new Relation();
r1.setRelType(ORG_ORG_RELTYPE);
r1.setSubRelType(ModelConstants.DEDUP);
r1.setRelClass(relClass);
r1.setSource(orgId1);
r1.setTarget(orgId2);
r1.setCollectedfrom(collectedFrom);
r1.setDataInfo(info);
r1.setLastupdatetimestamp(lastUpdateTimestamp);
// removed because there's no difference between two sides //TODO
// final Relation r2 = new Relation();
// r2.setRelType(ORG_ORG_RELTYPE);
// r2.setSubRelType(ORG_ORG_SUBRELTYPE);
// r2.setRelClass(relClass);
// r2.setSource(orgId2);
// r2.setTarget(orgId1);
// r2.setCollectedfrom(collectedFrom);
// r2.setDataInfo(info);
// r2.setLastupdatetimestamp(lastUpdateTimestamp);
// return Arrays.asList(r1, r2);
return Arrays.asList(r1);
return Arrays
.asList(
OafMapperUtils
.getRelation(
orgId1, orgId2, ORG_ORG_RELTYPE, DEDUP, relClass, collectedFrom, info,
lastUpdateTimestamp));
} catch (final Exception e) {
throw new RuntimeException(e);
}

13
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
View File

@ -19,7 +19,6 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.oa.graph.raw.common.RelationIdMapping;
import eu.dnetlib.dhp.schema.oaf.Relation;
import scala.Tuple2;
@ -78,8 +77,8 @@ public class PatchRelationsApplication {
final String relationPath = graphBasePath + "/relation";
final Dataset<Relation> rels = Utils.readPath(spark, relationPath, Relation.class);
final Dataset<RelationIdMapping> idMapping = Utils.readPath(spark, idMappingPath, RelationIdMapping.class);
final Dataset<Relation> rels = readPath(spark, relationPath, Relation.class);
final Dataset<RelationIdMapping> idMapping = readPath(spark, idMappingPath, RelationIdMapping.class);
log.info("relations: {}", rels.count());
log.info("idMapping: {}", idMapping.count());
@ -122,4 +121,12 @@ public class PatchRelationsApplication {
.text(relationPath);
}
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark
.read()
.textFile(inputPath)
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
}

26
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json
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@ -1,26 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "gp",
"paramLongName": "graphPath",
"paramDescription": "the relationPath",
"paramRequired": false
}
]

37
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json
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@ -1,37 +0,0 @@
[
{
"paramName":"is",
"paramLongName":"isLookUpUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{
"paramName":"nn",
"paramLongName":"nameNode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "sd",
"paramLongName": "singleDeposition",
"paramDescription": "true if the dump should be created for a single community",
"paramRequired": true
},
{
"paramName": "ci",
"paramLongName": "communityId",
"paramDescription": "the id of the community for which to create the dump",
"paramRequired": true
}
]

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_collect_and_save.json
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@ -1,30 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "ra",
"paramLongName": "resultAggregation",
"paramDescription": "true if all the result type should be saved under the generic result name. false to get a different dump for each result type",
"paramRequired": true
}
]

35
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_complete_parameters.json
View File

@ -1,35 +0,0 @@
[
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the serialization of the community map",
"paramRequired": true
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
}
]

24
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_entity_parameter.json
View File

@ -1,24 +0,0 @@
[
{
"paramName":"is",
"paramLongName":"isLookUpUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": false
},
{
"paramName": "hdfs",
"paramLongName": "hdfsPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "nameNode",
"paramDescription": "the name node",
"paramRequired": true
}
]

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json
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@ -1,30 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "hdp",
"paramLongName": "hdfsPath",
"paramDescription": "the path used to store the output archive",
"paramRequired": true
},
{
"paramName":"nn",
"paramLongName":"nameNode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName":"ss",
"paramLongName":"splitSize",
"paramDescription": "the maximum size of the archive",
"paramRequired": false
}
]

36
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_organization_parameters.json
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@ -1,36 +0,0 @@
[
{
"paramName":"ocm",
"paramLongName":"organizationCommunityMap",
"paramDescription": "the organization community map association",
"paramRequired": false
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the serialization of the community map",
"paramRequired": true
}
]

20
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameter_select_relation.json
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@ -1,20 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}
]

47
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json
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@ -1,47 +0,0 @@
[
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the serialization of the community map",
"paramRequired": true
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName":"dt",
"paramLongName":"dumpType",
"paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project",
"paramRequired": false
}, {
"paramName":"cid",
"paramLongName":"communityId",
"paramDescription": "the id of the community to be dumped",
"paramRequired": false
}
]

41
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json
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@ -1,41 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{
"paramName":"gp",
"paramLongName":"graphPath",
"paramDescription": "the path to the relations",
"paramRequired": true
},
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the relations",
"paramRequired": true
}
]

32
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_relationdump_parameters.json
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@ -1,32 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "rs",
"paramLongName": "removeSet",
"paramDescription": "the list of classname relations, split by ';', not to be dumped",
"paramRequired": false
}
]

29
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json
View File

@ -1,29 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
},
{
"paramName": "pip",
"paramLongName": "preparedInfoPath",
"paramDescription": "the path of the association result projectlist",
"paramRequired": true
}
]

20
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json
View File

@ -1,20 +0,0 @@
[
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}
]

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/config-default.xml
View File

@ -1,30 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

171
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/projectsubset/oozie_app/workflow.xml
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@ -1,171 +0,0 @@
<workflow-app name="dump_graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>projectListPath</name>
<description>the path to the project list</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>accessToken</name>
<description>the access token used for the deposition in Zenodo</description>
</property>
<property>
<name>connectionUrl</name>
<description>the connection url for Zenodo</description>
</property>
<property>
<name>metadata</name>
<description> the metadata associated to the deposition</description>
</property>
<property>
<name>depositionType</name>
<description>the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided)</description>
</property>
<property>
<name>conceptRecordId</name>
<description>for new version, the id of the record for the old deposition</description>
</property>
<property>
<name>depositionId</name>
<description>the depositionId of a deposition open that has to be added content</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="dump_project"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="dump_project">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table project </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/project</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--outputPath</arg><arg>${workingDir}/project</arg>
<arg>--communityMapPath</arg><arg>noneed</arg>
</spark>
<ok to="get_new_projects"/>
<error to="Kill"/>
</action>
<action name="get_new_projects">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table project </name>
<class>eu.dnetlib.dhp.oa.graph.dump.projectssubset.ProjectsSubsetSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/project</arg>
<arg>--outputPath</arg><arg>${workingDir}/tar/project</arg>
<arg>--projectListPath</arg><arg>${projectListPath}</arg>
</spark>
<ok to="make_archive"/>
<error to="Kill"/>
</action>
<action name="make_archive">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--sourcePath</arg><arg>${workingDir}/tar</arg>
</java>
<ok to="send_zenodo"/>
<error to="Kill"/>
</action>
<action name="send_zenodo">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--accessToken</arg><arg>${accessToken}</arg>
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
<arg>--metadata</arg><arg>${metadata}</arg>
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
<arg>--depositionType</arg><arg>${depositionType}</arg>
<arg>--depositionId</arg><arg>${depositionId}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

37
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json
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@ -1,37 +0,0 @@
[
{
"paramName":"cmp",
"paramLongName":"communityMapPath",
"paramDescription": "the path to the serialization of the community map",
"paramRequired": false
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false
}, {
"paramName":"cid",
"paramLongName":"communityId",
"paramDescription": "the id of the community to be dumped",
"paramRequired": false
}
]

58
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json
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@ -1,58 +0,0 @@
[
{
"paramName":"dt",
"paramLongName":"depositionType",
"paramDescription": "the type of the deposition (new, version, update)",
"paramRequired": true
},
{
"paramName":"cri",
"paramLongName":"conceptRecordId",
"paramDescription": "The id of the concept record for a new version",
"paramRequired": false
},
{
"paramName":"di",
"paramLongName":"depositionId",
"paramDescription": "the id of an open deposition which has not been published",
"paramRequired": false
},
{
"paramName":"hdfsp",
"paramLongName":"hdfsPath",
"paramDescription": "the path of the folder tofind files to send to Zenodo",
"paramRequired": true
},
{
"paramName": "nn",
"paramLongName": "nameNode",
"paramDescription": "the name node",
"paramRequired": true
},
{
"paramName": "at",
"paramLongName": "accessToken",
"paramDescription": "the access token for the deposition",
"paramRequired": false
},
{
"paramName":"cu",
"paramLongName":"connectionUrl",
"paramDescription": "the url to connect to deposit",
"paramRequired": false
},
{
"paramName":"m",
"paramLongName":"metadata",
"paramDescription": "metadata associated to the deposition",
"paramRequired": false
},
{
"paramName":"p",
"paramLongName":"publish",
"paramDescription": "if to publish the upload",
"paramRequired": false
}
]

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml
View File

@ -1,30 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt
View File

@ -1,4 +0,0 @@
## This is a classpath-based import file (this header is required)
dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app
dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app
dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app

306
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml
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@ -1,306 +0,0 @@
<workflow-app name="dump_graph" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>singleDeposition</name>
<description>Indicates if it is a single community deposition</description>
</property>
<property>
<name>communityId</name>
<description>the id of the community to be dumped if a dump for a single community should be done</description>
</property>
<property>
<name>dumpType</name>
<description>the type of the dump one of {complete, community, funder}</description>
</property>
<property>
<name>onlyUpload</name>
<description>true if the dump is already done and should only be upload in zenodo</description>
</property>
<property>
<name>upload</name>
<description>true if the dump should be upload in zenodo</description>
</property>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>resultAggregation</name>
<description>true if all the result type have to be dumped under result. false otherwise</description>
</property>
<property>
<name>accessToken</name>
<description>the access token used for the deposition in Zenodo</description>
</property>
<property>
<name>connectionUrl</name>
<description>the connection url for Zenodo</description>
</property>
<property>
<name>metadata</name>
<description> the metadata associated to the deposition</description>
</property>
<property>
<name>depositionType</name>
<description>the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided)</description>
</property>
<property>
<name>conceptRecordId</name>
<description>for new version, the id of the record for the old deposition</description>
</property>
<property>
<name>depositionId</name>
<description>the depositionId of a deposition open that has to be added content</description>
</property>
<property>
<name>organizationCommunityMap</name>
<description>the organization community map</description>
</property>
<property>
<name>hiveDbName</name>
<description>the target hive database name</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="only_upload"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<decision name="only_upload">
<switch>
<case to="send_zenodo">${wf:conf('onlyUpload') eq true}</case>
<default to="reset_outputpath"/>
</switch>
</decision>
<action name="reset_outputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="save_community_map"/>
<error to="Kill"/>
</action>
<action name="save_community_map">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
<arg>--singleDeposition</arg><arg>${singleDeposition}</arg>
<arg>--communityId</arg><arg>${communityId}</arg>
</java>
<ok to="choose_dump"/>
<error to="Kill"/>
</action>
<decision name="choose_dump">
<switch>
<case to="dump_funder">${wf:conf('dumpType') eq "funder"}</case>
<case to="dump_community">${wf:conf('dumpType') eq "community"}</case>
<default to="dump_complete"/>
</switch>
</decision>
<!-- Sub-workflow which runs the dump for the complete graph -->
<action name="dump_complete">
<sub-workflow>
<app-path>${wf:appPath()}/dump_complete
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>communityMapPath</name>
<value>${workingDir}/communityMap</value>
</property>
<property>
<name>outputPath</name>
<value>${workingDir}/tar</value>
</property>
<property>
<name>sourcePath</name>
<value>${sourcePath}</value>
</property>
<property>
<name>organizationCommunityMap</name>
<value>${organizationCommunityMap}</value>
</property>
<property>
<name>isLookUpUrl</name>
<value>${isLookUpUrl}</value>
</property>
<property>
<name>resultAggregation</name>
<value>${resultAggregation}</value>
</property>
</configuration>
</sub-workflow>
<ok to="make_archive" />
<error to="Kill" />
</action>
<!-- Sub-workflow which runs the dump for the complete graph -->
<action name="dump_community">
<sub-workflow>
<app-path>${wf:appPath()}/dump_community
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>sourcePath</name>
<value>${sourcePath}</value>
</property>
<property>
<name>communityMapPath</name>
<value>${workingDir}/communityMap</value>
</property>
<property>
<name>outputPath</name>
<value>${workingDir}/tar</value>
</property>
</configuration>
</sub-workflow>
<ok to="make_archive" />
<error to="Kill" />
</action>
<action name="dump_funder">
<sub-workflow>
<app-path>${wf:appPath()}/dump_funder
</app-path>
<propagate-configuration/>
<configuration>
<property>
<name>communityMapPath</name>
<value>${workingDir}/communityMap</value>
</property>
<property>
<name>outputPath</name>
<value>${workingDir}/tar</value>
</property>
<property>
<name>sourcePath</name>
<value>${sourcePath}</value>
</property>
<property>
<name>dumpType</name>
<value>${dumpType}</value>
</property>
</configuration>
</sub-workflow>
<ok to="make_archive" />
<error to="Kill" />
</action>
<action name="make_archive">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--sourcePath</arg><arg>${workingDir}/tar</arg>
</java>
<ok to="should_upload"/>
<error to="Kill"/>
</action>
<decision name="should_upload">
<switch>
<case to="send_zenodo">${wf:conf('upload') eq true}</case>
<default to="End"/>
</switch>
</decision>
<action name="send_zenodo">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
<arg>--hdfsPath</arg><arg>${outputPath}</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--accessToken</arg><arg>${accessToken}</arg>
<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
<arg>--metadata</arg><arg>${metadata}</arg>
<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
<arg>--depositionType</arg><arg>${depositionType}</arg>
<arg>--depositionId</arg><arg>${depositionId}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml
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@ -1,30 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

362
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml
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@ -1,362 +0,0 @@
<workflow-app name="sub_dump_community_products" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>hiveDbName</name>
<description>the target hive database name</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="fork_dump"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<fork name="fork_dump">
<path start="dump_publication"/>
<path start="dump_dataset"/>
<path start="dump_orp"/>
<path start="dump_software"/>
</fork>
<action name="dump_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table publication for community/funder related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/publication</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
<arg>--dumpType</arg><arg>${dumpType}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table dataset for community/funder related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/dataset</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table ORP for community related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table software for community related products</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/dump/software</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<join name="join_dump" to="prepareResultProject"/>
<action name="prepareResultProject">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Prepare association result subset of project info</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="fork_extendWithProject"/>
<error to="Kill"/>
</action>
<fork name="fork_extendWithProject">
<path start="extend_publication"/>
<path start="extend_dataset"/>
<path start="extend_orp"/>
<path start="extend_software"/>
</fork>
<action name="extend_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped publications with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/ext/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped dataset with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/ext/dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped ORP with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/ext/orp</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<action name="extend_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extend dumped software with information about project</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/dump/software</arg>
<arg>--outputPath</arg><arg>${workingDir}/ext/software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="join_extend"/>
<error to="Kill"/>
</action>
<join name="join_extend" to="splitForCommunities"/>
<action name="splitForCommunities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Split dumped result for community</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/ext</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml
View File

@ -1,30 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

539
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml
View File

@ -1,539 +0,0 @@
<workflow-app name="sub-dump_complete" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>resultAggregation</name>
<description>true if all the result type have to be dumped under result. false otherwise</description>
</property>
<property>
<name>organizationCommunityMap</name>
<description>the organization community map</description>
</property>
<property>
<name>hiveDbName</name>
<description>the target hive database name</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="fork_dump" />
<fork name="fork_dump">
<path start="dump_publication"/>
<path start="dump_dataset"/>
<path start="dump_orp"/>
<path start="dump_software"/>
<path start="dump_organization"/>
<path start="dump_project"/>
<path start="dump_datasource"/>
<path start="select_relation"/>
</fork>
<action name="dump_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table dataset </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table ORP </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table software </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_organization">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table organization </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/organization</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
<arg>--outputPath</arg><arg>${outputPath}/organization</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_project">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table project </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/project</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
<arg>--outputPath</arg><arg>${outputPath}/project</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="dump_datasource">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table datasource </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/datasource</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
<arg>--outputPath</arg><arg>${outputPath}/datasource</arg>
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<action name="select_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Select valid table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
--conf spark.sql.shuffle.partitions=3840
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/validrelation</arg>
</spark>
<ok to="dump_relation"/>
<error to="Kill"/>
</action>
<action name="dump_relation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/validrelation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/relation</arg>
<arg>--removeSet</arg><arg>${removeSet}</arg>
</spark>
<ok to="join_dump"/>
<error to="Kill"/>
</action>
<join name="join_dump" to="fork_context"/>
<fork name="fork_context">
<path start="create_entities_fromcontext"/>
<path start="create_relation_fromcontext"/>
<path start="create_relation_fromorgs"/>
</fork>
<action name="create_entities_fromcontext">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities</main-class>
<arg>--hdfsPath</arg><arg>${outputPath}/communities_infrastructures/communities_infrastructure.json.gz</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</java>
<ok to="join_context"/>
<error to="Kill"/>
</action>
<action name="create_relation_fromcontext">
<java>
<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation</main-class>
<arg>--hdfsPath</arg><arg>${workingDir}/relation/context</arg>
<arg>--nameNode</arg><arg>${nameNode}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</java>
<ok to="join_context"/>
<error to="Kill"/>
</action>
<action name="create_relation_fromorgs">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table relation </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/contextOrg</arg>
<arg>--organizationCommunityMap</arg><arg>${organizationCommunityMap}</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_context"/>
<error to="Kill"/>
</action>
<join name="join_context" to="fork_extract_relations"/>
<fork name="fork_extract_relations">
<path start="rels_from_pubs"/>
<path start="rels_from_dats"/>
<path start="rels_from_orp"/>
<path start="rels_from_sw"/>
</fork>
<action name="rels_from_pubs">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Extract Relations from publication </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/publication</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_extract_relations"/>
<error to="Kill"/>
</action>
<action name="rels_from_dats">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table dataset </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/dataset</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_extract_relations"/>
<error to="Kill"/>
</action>
<action name="rels_from_orp">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table ORP </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/orp</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_extract_relations"/>
<error to="Kill"/>
</action>
<action name="rels_from_sw">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump table software </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/relation/software</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_extract_relations"/>
<error to="Kill"/>
</action>
<join name="join_extract_relations" to="collect_and_save"/>
<action name="collect_and_save">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Collect Results and Relations and put them in the right path </name>
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
<arg>--resultAggregation</arg><arg>${resultAggregation}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<kill name="Kill">
<message>Sub-workflow dump complete failed with error message ${wf:errorMessage()}
</message>
</kill>
<end name="End" />
</workflow-app>

30
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml
View File

@ -1,30 +0,0 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>hiveMetastoreUris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hiveJdbcUrl</name>
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
</property>
<property>
<name>hiveDbName</name>
<value>openaire</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

255
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml
View File

@ -1,255 +0,0 @@
<workflow-app name="sub_dump_funder_results" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
<property>
<name>hiveDbName</name>
<description>the target hive database name</description>
</property>
<property>
<name>hiveJdbcUrl</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hiveMetastoreUris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>sparkDriverMemory</name>
<description>memory for driver process</description>
</property>
<property>
<name>sparkExecutorMemory</name>
<description>memory for individual executor</description>
</property>
<property>
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>oozieActionShareLibForSpark2</name>
<description>oozie action sharelib for spark 2.*</description>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
<description>spark 2.* extra listeners classname</description>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
<description>spark 2.* sql query execution listeners classname</description>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<description>spark 2.* yarn history server address</description>
</property>
<property>
<name>spark2EventLogDir</name>
<description>spark 2.* event log dir location</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>mapreduce.job.queuename</name>
<value>${queueName}</value>
</property>
<property>
<name>oozie.launcher.mapred.job.queue.name</name>
<value>${oozieLauncherQueueName}</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="prepareResultProject"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="prepareResultProject">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Prepare association result subset of project info</name>
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
</spark>
<ok to="fork_result_linked_to_projects"/>
<error to="Kill"/>
</action>
<fork name="fork_result_linked_to_projects">
<path start="select_publication_linked_to_projects"/>
<path start="select_dataset_linked_to_projects"/>
<path start="select_orp_linked_to_project"/>
<path start="select_software_linked_to_projects"/>
</fork>
<action name="select_publication_linked_to_projects">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump funder results </name>
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
<arg>--graphPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_link"/>
<error to="Kill"/>
</action>
<action name="select_dataset_linked_to_projects">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump funder results </name>
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
<arg>--graphPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_link"/>
<error to="Kill"/>
</action>
<action name="select_orp_linked_to_project">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump funder results </name>
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
<arg>--graphPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_link"/>
<error to="Kill"/>
</action>
<action name="select_software_linked_to_projects">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump funder results </name>
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
<arg>--graphPath</arg><arg>${workingDir}/preparedInfo</arg>
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
</spark>
<ok to="join_link"/>
<error to="Kill"/>
</action>
<join name="join_link" to="dump_funder_results"/>
<action name="dump_funder_results">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Dump funder results </name>
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/result</arg>
<arg>--outputPath</arg><arg>${outputPath}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

1
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql
View File

@ -3,6 +3,7 @@ SELECT
po.resporganization AS resporganization,
po.participantnumber AS participantnumber,
po.contribution AS contribution,
po.currency AS currency,
NULL AS startdate,
NULL AS enddate,
false AS inferred,

17
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java
View File

@ -5,7 +5,6 @@ import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.Locale;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
@ -21,19 +20,9 @@ import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.Constants;
import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleanContextTest {
@ -48,11 +37,11 @@ public class CleanContextTest {
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
workingDir = Files.createTempDirectory(CleanContextTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(DumpJobTest.class.getSimpleName());
conf.setAppName(CleanContextTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
@ -63,7 +52,7 @@ public class CleanContextTest {
spark = SparkSession
.builder()
.appName(DumpJobTest.class.getSimpleName())
.appName(CleanContextTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}

967
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java
View File

@ -1,967 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.List;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.Instance;
import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Software;
//@Disabled
public class DumpJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class);
private static final CommunityMap map = new CommunityMap();
static {
map.put("egi", "EGI Federation");
map.put("fet-fp7", "FET FP7");
map.put("fet-h2020", "FET H2020");
map.put("clarin", "CLARIN");
map.put("fam", "Fisheries and Aquaculture Management");
map.put("ni", "Neuroinformatics");
map.put("mes", "European Marine Scinece");
map.put("instruct", "Instruct-Eric");
map.put("rda", "Research Data Alliance");
map.put("elixir-gr", "ELIXIR GR");
map.put("aginfra", "Agricultural and Food Sciences");
map.put("dariah", "DARIAH EU");
map.put("risis", "RISI");
map.put("ee", "SDSN - Greece");
map.put("oa-pg", "EC Post-Grant Open Access Pilot");
map.put("beopen", "Transport Research");
map.put("euromarine", "Euromarine");
map.put("ifremer", "Ifremer");
map.put("dh-ch", "Digital Humanities and Cultural Heritage");
map.put("science-innovation-policy", "Science and Innovation Policy Studies");
map.put("covid-19", "COVID-19");
map.put("enrmaps", "Energy Research");
map.put("epos", "EPOS");
}
List<String> communityMap = Arrays
.asList(
"<community id=\"egi\" label=\"EGI Federation\"/>",
"<community id=\"fet-fp7\" label=\"FET FP7\"/>",
"<community id=\"fet-h2020\" label=\"FET H2020\"/>",
"<community id=\"clarin\" label=\"CLARIN\"/>",
"<community id=\"rda\" label=\"Research Data Alliance\"/>",
"<community id=\"ee\" label=\"SDSN - Greece\"/>",
"<community id=\"dh-ch\" label=\"Digital Humanities and Cultural Heritage\"/>",
"<community id=\"fam\" label=\"Fisheries and Aquaculture Management\"/>",
"<community id=\"ni\" label=\"Neuroinformatics\"/>",
"<community id=\"mes\" label=\"European Marine Science\"/>",
"<community id=\"instruct\" label=\"Instruct-ERIC\"/>",
"<community id=\"elixir-gr\" label=\"ELIXIR GR\"/>",
"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
"<community id=\"dariah\" label=\"DARIAH EU\"/>",
"<community id=\"risis\" label=\"RISIS\"/>",
"<community id=\"epos\" label=\"EPOS\"/>",
"<community id=\"beopen\" label=\"Transport Research\"/>",
"<community id=\"euromarine\" label=\"EuroMarine\"/>",
"<community id=\"ifremer\" label=\"Ifremer\"/>",
"<community id=\"oa-pg\" label=\"EC Post-Grant Open Access Pilot\"/>",
"<community id=\"science-innovation-policy\" label=\"Science and Innovation Policy Studies\"/>",
"<community id=\"covid-19\" label=\"COVID-19\"/>",
"<community id=\"enermaps\" label=\"Energy Research\"/>");
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" return " +
"<community> " +
"{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" +
"</community>";
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(DumpJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(DumpJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
public void testMap() {
System.out.println(new Gson().toJson(map));
}
@Test
public void testPublicationDump() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(1, verificationDataset.count());
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(6, gr.getAuthor().size());
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Nikolaidou,Charitini") &&
a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou")
&& a.getRank() == 1 && a.getPid() == null));
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Votsi,Nefta") &&
a.getName().equals("Nefta") && a.getSurname().equals("Votsi")
&& a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
&& a.getPid().getProvenance() != null));
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Sgardelis,Steanos") &&
a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis")
&& a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
&& a.getPid().getProvenance() != null));
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Halley,John") &&
a.getName().equals("John") && a.getSurname().equals("Halley")
&& a.getRank() == 4 && a.getPid() == null));
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Pantis,John") &&
a.getName().equals("John") && a.getSurname().equals("Pantis")
&& a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
&& a.getPid().getProvenance() != null));
Assertions
.assertTrue(
gr
.getAuthor()
.stream()
.anyMatch(
a -> a.getFullname().equals("Tsiafouli,Maria") &&
a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli")
&& a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
&& a.getPid().getProvenance() != null));
Assertions.assertEquals("publication", gr.getType());
Assertions.assertEquals("eng", gr.getLanguage().getCode());
Assertions.assertEquals("English", gr.getLanguage().getLabel());
Assertions.assertEquals(1, gr.getCountry().size());
Assertions.assertEquals("IT", gr.getCountry().get(0).getCode());
Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel());
Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null);
Assertions.assertEquals(12, gr.getSubjects().size());
Assertions
.assertTrue(
gr
.getSubjects()
.stream()
.anyMatch(
s -> s.getSubject().getValue().equals("Ecosystem Services hotspots")
&& s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null &&
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
Assertions
.assertTrue(
gr
.getSubjects()
.stream()
.anyMatch(
s -> s.getSubject().getValue().equals("Natura 2000")
&& s.getSubject().getScheme().equals("") && s.getProvenance() != null &&
s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
Assertions
.assertEquals(
"Ecosystem Service capacity is higher in areas of multiple designation types",
gr.getMaintitle());
Assertions.assertEquals(null, gr.getSubtitle());
Assertions.assertEquals(1, gr.getDescription().size());
Assertions
.assertTrue(
gr
.getDescription()
.get(0)
.startsWith("The implementation of the Ecosystem Service (ES) concept into practice"));
Assertions
.assertTrue(
gr
.getDescription()
.get(0)
.endsWith(
"start complying with new standards and demands for nature conservation and environmental management."));
Assertions.assertEquals("2017-01-01", gr.getPublicationdate());
Assertions.assertEquals("Pensoft Publishers", gr.getPublisher());
Assertions.assertEquals(null, gr.getEmbargoenddate());
Assertions.assertEquals(1, gr.getSource().size());
Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0));
Assertions.assertEquals(1, gr.getFormat().size());
Assertions.assertEquals("text/html", gr.getFormat().get(0));
Assertions.assertEquals(0, gr.getContributor().size());
Assertions.assertEquals(0, gr.getCoverage().size());
Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel());
Assertions
.assertEquals(
Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode());
Assertions.assertEquals("One Ecosystem", gr.getContainer().getName());
Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline());
Assertions.assertEquals("", gr.getContainer().getIssnPrinted());
Assertions.assertEquals("", gr.getContainer().getIssnLinking());
Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0);
Assertions.assertTrue(null == gr.getCodeRepositoryUrl());
Assertions.assertEquals(null, gr.getProgrammingLanguage());
Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0);
Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0);
Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0);
Assertions.assertEquals(null, gr.getSize());
Assertions.assertEquals(null, gr.getVersion());
Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0);
Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
Assertions.assertEquals(1, gr.getOriginalId().size());
Assertions
.assertTrue(
gr.getOriginalId().contains("10.3897/oneeco.2.e13718"));
Assertions.assertEquals(1, gr.getPid().size());
Assertions
.assertTrue(
gr.getPid().get(0).getScheme().equals("doi")
&& gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004"));
Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection());
Assertions.assertEquals(1, gr.getInstance().size());
Instance instance = gr.getInstance().get(0);
Assertions.assertEquals(0, instance.getPid().size());
Assertions.assertEquals(1, instance.getAlternateIdentifier().size());
Assertions
.assertTrue(
instance.getAlternateIdentifier().get(0).getScheme().equals("doi")
&& instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718"));
Assertions.assertEquals(null, instance.getLicense());
Assertions
.assertTrue(
instance
.getAccessright()
.getCode()
.equals(
Constants.accessRightsCoarMap
.get(ModelConstants.ACCESS_RIGHT_OPEN)));
Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN));
Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green));
Assertions.assertTrue(instance.getType().equals("Article"));
Assertions.assertEquals(2, instance.getUrl().size());
Assertions
.assertTrue(
instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718")
&& instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/"));
Assertions.assertEquals("2017-01-01", instance.getPublicationdate());
Assertions.assertEquals(null, instance.getArticleprocessingcharge());
Assertions.assertEquals("peerReviewed", instance.getRefereed());
}
@Test
public void testDatasetDump() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result",
communityMapPath, Dataset.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count());
// the common fields in the result have been already checked. Now checking only
// community specific fields
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(2, gr.getGeolocation().size());
Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count());
Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count());
Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count());
Assertions
.assertEquals(
1,
gr
.getGeolocation()
.stream()
.filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada"))
.count());
Assertions
.assertEquals(
1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count());
Assertions
.assertEquals(
1,
gr
.getGeolocation()
.stream()
.filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals(""))
.count());
Assertions
.assertEquals(
1,
gr
.getGeolocation()
.stream()
.filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals(""))
.count());
Assertions.assertEquals("1024Gb", gr.getSize());
Assertions.assertEquals("1.01", gr.getVersion());
Assertions.assertEquals(null, gr.getContainer());
Assertions.assertEquals(null, gr.getCodeRepositoryUrl());
Assertions.assertEquals(null, gr.getProgrammingLanguage());
Assertions.assertEquals(null, gr.getDocumentationUrl());
Assertions.assertEquals(null, gr.getContactperson());
Assertions.assertEquals(null, gr.getContactgroup());
Assertions.assertEquals(null, gr.getTool());
}
@Test
public void testSoftwareDump() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result",
communityMapPath, Software.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count());
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(2, gr.getDocumentationUrl().size());
Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1"));
Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2"));
Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl());
Assertions.assertEquals("perl", gr.getProgrammingLanguage());
Assertions.assertEquals(null, gr.getContainer());
Assertions.assertEquals(null, gr.getContactperson());
Assertions.assertEquals(null, gr.getContactgroup());
Assertions.assertEquals(null, gr.getTool());
Assertions.assertEquals(null, gr.getGeolocation());
Assertions.assertEquals(null, gr.getSize());
Assertions.assertEquals(null, gr.getVersion());
}
@Test
public void testOrpDump() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result",
communityMapPath, OtherResearchProduct.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count());
GraphResult gr = verificationDataset.first();
Assertions.assertEquals(2, gr.getContactperson().size());
Assertions.assertTrue(gr.getContactperson().contains(("contact_person1")));
Assertions.assertTrue(gr.getContactperson().contains(("contact_person2")));
Assertions.assertEquals(1, gr.getContactgroup().size());
Assertions.assertTrue(gr.getContactgroup().contains(("contact_group")));
Assertions.assertEquals(2, gr.getTool().size());
Assertions.assertTrue(gr.getTool().contains("tool1"));
Assertions.assertTrue(gr.getTool().contains("tool2"));
Assertions.assertEquals(null, gr.getContainer());
Assertions.assertEquals(null, gr.getDocumentationUrl());
Assertions.assertEquals(null, gr.getCodeRepositoryUrl());
Assertions.assertEquals(null, gr.getProgrammingLanguage());
Assertions.assertEquals(null, gr.getGeolocation());
Assertions.assertEquals(null, gr.getSize());
Assertions.assertEquals(null, gr.getVersion());
}
@Test
public void testPublicationDumpCommunity() throws JsonProcessingException {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count());
// the common fields in the result have been already checked. Now checking only
// community specific fields
CommunityResult cr = verificationDataset.first();
Assertions.assertEquals(1, cr.getContext().size());
Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode());
Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel());
Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size());
Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance());
Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust());
Assertions.assertEquals(1, cr.getCollectedfrom().size());
Assertions
.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey());
Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue());
Assertions.assertEquals(1, cr.getInstance().size());
Assertions
.assertEquals(
"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db",
cr.getInstance().get(0).getCollectedfrom().getKey());
Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue());
Assertions
.assertEquals(
"10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey());
Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue());
}
@Test
public void testDataset() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(90, verificationDataset.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
.filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset
.filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset
.filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'")
.count());
Assertions
.assertTrue(
verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset
.filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'")
.count());
Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90);
Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
}
@Test
public void testDataset2All() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class));
org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class));
Assertions.assertEquals(5, verificationDataset.count());
}
@Test
public void testDataset2Communities() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(0, verificationDataset.count());
}
@Test
public void testPublication() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(74, verificationDataset.count());
verificationDataset.show(false);
Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count());
}
@Test
public void testSoftware() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(6, verificationDataset.count());
Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count());
}
@Test
public void testORP() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(3, verificationDataset.count());
Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count());
}
@Test
public void testRecord() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(2, verificationDataset.count());
verificationDataset.show(false);
Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count());
}
@Test
public void testArticlePCA() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
DumpProducts dump = new DumpProducts();
dump
.run(
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<GraphResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
Assertions.assertEquals(23, verificationDataset.count());
Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count());
verificationDataset.createOrReplaceTempView("check");
org.apache.spark.sql.Dataset<Row> temp = spark
.sql(
"select id " +
"from check " +
"lateral view explode (instance) i as inst " +
"where inst.articleprocessingcharge is not null");
Assertions.assertTrue(temp.count() == 2);
Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1);
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
temp = spark
.sql(
"select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " +
"from check " +
"lateral view explode (instance) i as inst " +
"where inst.articleprocessingcharge is not null");
Assertions
.assertEquals(
"3131.64",
temp
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
.collectAsList()
.get(0)
.getString(1));
Assertions
.assertEquals(
"EUR",
temp
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
.collectAsList()
.get(0)
.getString(2));
Assertions
.assertEquals(
"2578.35",
temp
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
.collectAsList()
.get(0)
.getString(1));
Assertions
.assertEquals(
"EUR",
temp
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
.collectAsList()
.get(0)
.getString(2));
}
}

28
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java
View File

@ -1,28 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.JsonNode;
import com.github.victools.jsonschema.generator.*;
import eu.dnetlib.dhp.schema.dump.oaf.graph.*;
//@Disabled
class GenerateJsonSchema {
@Test
void generateSchema() {
SchemaGeneratorConfigBuilder configBuilder = new SchemaGeneratorConfigBuilder(SchemaVersion.DRAFT_7,
OptionPreset.PLAIN_JSON)
.with(Option.SCHEMA_VERSION_INDICATOR)
.without(Option.NONPUBLIC_NONSTATIC_FIELDS_WITHOUT_GETTERS);
configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName());
SchemaGeneratorConfig config = configBuilder.build();
SchemaGenerator generator = new SchemaGenerator(config);
JsonNode jsonSchema = generator.generateSchema(GraphResult.class);
System.out.println(jsonSchema.toString());
}
}

60
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java
View File

@ -1,60 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class MakeTarTest {
private static String workingDir;
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(MakeTarTest.class.getSimpleName())
.toString();
}
@Test
void testTar() throws IOException {
LocalFileSystem fs = FileSystem.getLocal(new Configuration());
fs
.copyFromLocalFile(
false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni")
.getPath()),
new Path(workingDir + "/zenodo/ni/part-00000"));
fs
.copyFromLocalFile(
false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi")
.getPath()),
new Path(workingDir + "/zenodo/ni/part-00001"));
fs
.copyFromLocalFile(
false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch")
.getPath()),
new Path(workingDir + "/zenodo/dh-ch/part-00000"));
fs
.copyFromLocalFile(
false, new Path(getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy")
.getPath()),
new Path(workingDir + "/zenodo/ni/part-00002"));
String inputPath = workingDir + "/zenodo/";
MakeTar.makeTArArchive(fs, inputPath, "/tmp/out", 0);
}
}

347
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@ -1,347 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject;
import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject;
public class PrepareResultProjectJobTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory
.getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testNoMatch() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
assertEquals(0, verificationDataset.count());
}
@Test
void testMatchOne() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
assertEquals(1, verificationDataset.count());
assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
verificationDataset.createOrReplaceTempView("table");
Dataset<Row> check = spark
.sql(
"Select projList.provenance.provenance " +
"from table " +
"lateral view explode (projectsList) pl as projList");
assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
verificationDataset.show(false);
}
@Test
void testMatch() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
assertEquals(2, verificationDataset.count());
assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance "
+ "from dataset "
+ "lateral view explode(projectsList) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
assertEquals(3, resultExplodedProvenance.count());
assertEquals(
2,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
assertEquals(
2,
resultExplodedProvenance
.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
assertEquals(
3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
}
@Test
public void testMatchValidated() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
org.apache.spark.sql.Dataset<ResultProject> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(ResultProject.class));
assertEquals(2, verificationDataset.count());
assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
assertEquals(
1,
verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, "
+
"MyT.validated.validatedByFunder, MyT.validated.validationDate "
+ "from dataset "
+ "lateral view explode(projectsList) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
assertEquals(3, resultExplodedProvenance.count());
assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count());
assertEquals(
2,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'")
.count());
assertEquals(
2,
resultExplodedProvenance
.filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
"and validatedByFunder = true " +
"and validationDate = '2021-08-06'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " +
"and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " +
"and validatedByFunder = true and validationDate = '2021-08-04'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'")
.count());
assertEquals(
1,
resultExplodedProvenance
.filter(
"project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " +
"and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " +
"and validatedByFunder = true and validationDate = '2021-08-05'")
.count());
assertEquals(
3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count());
}
@Test
void testMatchx() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match")
.getPath();
SparkPrepareResultProject.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-outputPath", workingDir.toString() + "/preparedInfo",
"-sourcePath", sourcePath
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<ResultProject> tmp = sc
.textFile(workingDir.toString() + "/preparedInfo")
.map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class));
tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
}
}

117
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java
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@ -1,117 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import static org.mockito.Mockito.lenient;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import org.dom4j.DocumentException;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.xml.sax.SAXException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@ExtendWith(MockitoExtension.class)
class QueryInformationSystemTest {
private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
+
" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
" and ($x//context/param[./@name = 'status']/text() = 'all') "
+
" return " +
"<community> " +
"{$x//CONFIGURATION/context/@id}" +
"{$x//CONFIGURATION/context/@label}" +
"</community>";
List<String> communityMap = Arrays
.asList(
"<community id=\"egi\" label=\"EGI Federation\"/>",
"<community id=\"fet-fp7\" label=\"FET FP7\"/>",
"<community id=\"fet-h2020\" label=\"FET H2020\"/>",
"<community id=\"clarin\" label=\"CLARIN\"/>",
"<community id=\"rda\" label=\"Research Data Alliance\"/>",
"<community id=\"ee\" label=\"SDSN - Greece\"/>",
"<community id=\"dh-ch\" label=\"Digital Humanities and Cultural Heritage\"/>",
"<community id=\"fam\" label=\"Fisheries and Aquaculture Management\"/>",
"<community id=\"ni\" label=\"Neuroinformatics\"/>",
"<community id=\"mes\" label=\"European Marine Science\"/>",
"<community id=\"instruct\" label=\"Instruct-ERIC\"/>",
"<community id=\"elixir-gr\" label=\"ELIXIR GR\"/>",
"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
"<community id=\"dariah\" label=\"DARIAH EU\"/>",
"<community id=\"risis\" label=\"RISIS\"/>",
"<community id=\"epos\" label=\"EPOS\"/>",
"<community id=\"beopen\" label=\"Transport Research\"/>",
"<community id=\"euromarine\" label=\"EuroMarine\"/>",
"<community id=\"ifremer\" label=\"Ifremer\"/>",
"<community id=\"oa-pg\" label=\"EC Post-Grant Open Access Pilot\"/>",
"<community id=\"science-innovation-policy\" label=\"Science and Innovation Policy Studies\"/>",
"<community id=\"covid-19\" label=\"COVID-19\"/>",
"<community id=\"enermaps\" label=\"Energy Research\"/>");
@Mock
private ISLookUpService isLookUpService;
private QueryInformationSystem queryInformationSystem;
private Map<String, String> map;
@BeforeEach
public void setUp() throws ISLookUpException, DocumentException, SAXException {
lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap);
queryInformationSystem = new QueryInformationSystem();
queryInformationSystem.setIsLookUp(isLookUpService);
map = queryInformationSystem.getCommunityMap(false, null);
}
@Test
void testSize() throws ISLookUpException {
Assertions.assertEquals(23, map.size());
}
@Test
void testContent() {
Assertions.assertTrue(map.containsKey("egi") && map.get("egi").equals("EGI Federation"));
Assertions.assertTrue(map.containsKey("fet-fp7") && map.get("fet-fp7").equals("FET FP7"));
Assertions.assertTrue(map.containsKey("fet-h2020") && map.get("fet-h2020").equals("FET H2020"));
Assertions.assertTrue(map.containsKey("clarin") && map.get("clarin").equals("CLARIN"));
Assertions.assertTrue(map.containsKey("rda") && map.get("rda").equals("Research Data Alliance"));
Assertions.assertTrue(map.containsKey("ee") && map.get("ee").equals("SDSN - Greece"));
Assertions
.assertTrue(
map.containsKey("dh-ch") && map.get("dh-ch").equals("Digital Humanities and Cultural Heritage"));
Assertions.assertTrue(map.containsKey("fam") && map.get("fam").equals("Fisheries and Aquaculture Management"));
Assertions.assertTrue(map.containsKey("ni") && map.get("ni").equals("Neuroinformatics"));
Assertions.assertTrue(map.containsKey("mes") && map.get("mes").equals("European Marine Science"));
Assertions.assertTrue(map.containsKey("instruct") && map.get("instruct").equals("Instruct-ERIC"));
Assertions.assertTrue(map.containsKey("elixir-gr") && map.get("elixir-gr").equals("ELIXIR GR"));
Assertions
.assertTrue(map.containsKey("aginfra") && map.get("aginfra").equals("Agricultural and Food Sciences"));
Assertions.assertTrue(map.containsKey("dariah") && map.get("dariah").equals("DARIAH EU"));
Assertions.assertTrue(map.containsKey("risis") && map.get("risis").equals("RISIS"));
Assertions.assertTrue(map.containsKey("epos") && map.get("epos").equals("EPOS"));
Assertions.assertTrue(map.containsKey("beopen") && map.get("beopen").equals("Transport Research"));
Assertions.assertTrue(map.containsKey("euromarine") && map.get("euromarine").equals("EuroMarine"));
Assertions.assertTrue(map.containsKey("ifremer") && map.get("ifremer").equals("Ifremer"));
Assertions.assertTrue(map.containsKey("oa-pg") && map.get("oa-pg").equals("EC Post-Grant Open Access Pilot"));
Assertions
.assertTrue(
map.containsKey("science-innovation-policy")
&& map.get("science-innovation-policy").equals("Science and Innovation Policy Studies"));
Assertions.assertTrue(map.containsKey("covid-19") && map.get("covid-19").equals("COVID-19"));
Assertions.assertTrue(map.containsKey("enermaps") && map.get("enermaps").equals("Energy Research"));
}
}

143
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java
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@ -1,143 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
public class SplitForCommunityTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class);
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(SplitForCommunityTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(SplitForCommunityTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void testCommunitySplit() {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity")
.getPath();
final String communityMapPath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
.getPath();
CommunitySplit split = new CommunitySplit();
split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath);
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(19, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/EGI_Federation")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(1, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/Neuroinformatics")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(5, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count());
tmp = sc
.textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
Assertions.assertEquals(4, verificationDataset.count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count());
Assertions
.assertEquals(
1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count());
}
}

236
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java
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@ -1,236 +0,0 @@
package eu.dnetlib.dhp.oa.graph.dump;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.HashMap;
import java.util.logging.Filter;
import java.util.stream.Collectors;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.Row;
import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo;
import eu.dnetlib.dhp.schema.dump.oaf.Result;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.dump.oaf.community.Funder;
import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
public class UpdateProjectInfoTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static SparkSession spark;
private static Path workingDir;
private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class);
private static final HashMap<String, String> map = new HashMap<>();
@BeforeAll
public static void beforeAll() throws IOException {
workingDir = Files
.createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName());
log.info("using work dir {}", workingDir);
SparkConf conf = new SparkConf();
conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName());
conf.setMaster("local[*]");
conf.set("spark.driver.host", "localhost");
conf.set("hive.metastore.local", "true");
conf.set("spark.ui.enabled", "false");
conf.set("spark.sql.warehouse.dir", workingDir.toString());
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
spark = SparkSession
.builder()
.appName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName())
.config(conf)
.getOrCreate();
}
@AfterAll
public static void afterAll() throws IOException {
FileUtils.deleteDirectory(workingDir.toFile());
spark.stop();
}
@Test
void test1() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo")
.getPath();
SparkUpdateProjectInfo.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-preparedInfoPath", sourcePath + "/preparedInfo",
"-outputPath", workingDir.toString() + "/result",
"-sourcePath", sourcePath + "/software.json"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
verificationDataset.show(false);
Assertions.assertEquals(6, verificationDataset.count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, "
+
"MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream "
+ "from dataset " +
"lateral view explode(projects) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(3, resultExplodedProvenance.count());
resultExplodedProvenance.show(false);
Assertions
.assertEquals(
2,
resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'")
.count());
resultExplodedProvenance.show(false);
}
@Test
public void testValidatedRelation() throws Exception {
final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo")
.getPath();
SparkUpdateProjectInfo.main(new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-preparedInfoPath", sourcePath + "/preparedInfoValidated",
"-outputPath", workingDir.toString() + "/result",
"-sourcePath", sourcePath + "/publication_extendedmodel"
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<CommunityResult> tmp = sc
.textFile(workingDir.toString() + "/result")
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
verificationDataset.show(false);
Assertions.assertEquals(2, verificationDataset.count());
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, "
+
"MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated "
+ "from dataset " +
"lateral view explode(projects) p as MyT ";
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
Assertions.assertEquals(2, resultExplodedProvenance.count());
resultExplodedProvenance.show(false);
Assertions
.assertEquals(
2,
resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'")
.count());
Assertions
.assertEquals(
1,
resultExplodedProvenance
.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'")
.count());
Project project = verificationDataset
.map(
(MapFunction<CommunityResult, Project>) cr -> cr
.getProjects()
.stream()
.filter(p -> p.getValidated() != null)
.collect(Collectors.toList())
.get(0),
Encoders.bean(Project.class))
.first();
Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland"));
Assertions.assertTrue(project.getFunder().getShortName().equals("AKA"));
Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI"));
Assertions.assertTrue(project.getFunder().getFundingStream() == null);
Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06"));
project = verificationDataset
.map(
(MapFunction<CommunityResult, Project>) cr -> cr
.getProjects()
.stream()
.filter(p -> p.getValidated() == null)
.collect(Collectors.toList())
.get(0),
Encoders.bean(Project.class))
.first();
Assertions.assertTrue(project.getFunder().getName().equals("European Commission"));
Assertions.assertTrue(project.getFunder().getShortName().equals("EC"));
Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU"));
Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020"));
}
}

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