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Merge pull request 'tolerant parsing of OAF-store-graph mdstores' (#180) from graph_interpretation_mdstores into beta

Reviewed-on: D-Net/dnet-hadoop#180
This commit is contained in:
Claudio Atzori 2022-01-04 11:32:29 +01:00
commit cb30770a0b
12 changed files with 141 additions and 29 deletions

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@ -1,7 +1,9 @@
package eu.dnetlib.dhp.collection
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.schema.common.ModelSupport
import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation}
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode}
object CollectionUtils {
@ -46,4 +48,15 @@ object CollectionUtils {
List()
}
def saveDataset(d: Dataset[Oaf], targetPath: String):Unit = {
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
val mapper = new ObjectMapper
d
.flatMap(i => CollectionUtils.fixRelations(i))
.filter(i => i != null)
.map(r => mapper.writeValueAsString(r))(Encoders.STRING)
.write.mode(SaveMode.Overwrite).save(targetPath)
}
}

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@ -2,14 +2,14 @@ package eu.dnetlib.dhp.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
@ -73,12 +73,12 @@ class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log
implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
CollectionUtils.saveDataset(
spark.read.load(sourcePath).as[DataciteType]
.filter(d => d.isActive)
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
.filter(d => d != null)
.flatMap(i => fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
.filter(d => d != null),
targetPath)
}
}

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@ -6,7 +6,7 @@ import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
object SparkTransformBioDatabaseToOAF {
@ -36,13 +36,13 @@ object SparkTransformBioDatabaseToOAF {
import spark.implicits._
database.toUpperCase() match {
case "UNIPROT" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))), targetPath)
case "PDB" =>
spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))), targetPath)
case "SCHOLIX" =>
spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)), targetPath)
case "CROSSREF_LINKS" =>
spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))), targetPath)
}
}

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@ -1,8 +1,9 @@
package eu.dnetlib.dhp.sx.bio.ebi
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.oaf.Result
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import eu.dnetlib.dhp.sx.bio.pubmed._
import eu.dnetlib.dhp.utils.ISLookupClientFactory
import org.apache.commons.io.IOUtils
@ -177,7 +178,7 @@ object SparkCreateBaselineDataFrame {
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
if (!"true".equalsIgnoreCase(skipUpdate)) {
downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
@ -192,9 +193,10 @@ object SparkCreateBaselineDataFrame {
}
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
exported_dataset
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
.filter(p => p != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
CollectionUtils.saveDataset(exported_dataset
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Oaf]
.filter(p => p != null),
targetPath)
}
}

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@ -34,10 +34,9 @@ object SparkEBILinksToOaf {
val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{"))
ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
CollectionUtils.saveDataset(ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
.filter(p => BioDBToOAF.EBITargetLinksFilter(p))
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p))
.flatMap(i => CollectionUtils.fixRelations(i)).filter(i => i != null)
.write.mode(SaveMode.Overwrite).save(targetPath)
.flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
targetPath)
}
}

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@ -109,7 +109,7 @@ object PubMedToOaf {
* @param vocabularies the vocabularies
* @return The OAF instance if the mapping did not fail
*/
def convert(article: PMArticle, vocabularies: VocabularyGroup): Result = {
def convert(article: PMArticle, vocabularies: VocabularyGroup): Oaf = {
if (article.getPublicationTypes == null)
return null

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@ -1,6 +1,6 @@
package eu.dnetlib.dhp.oa.graph.raw
import com.fasterxml.jackson.databind.ObjectMapper
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper}
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.common.HdfsSupport
import eu.dnetlib.dhp.schema.common.ModelSupport
@ -8,7 +8,10 @@ import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
import org.apache.spark.{SparkConf, SparkContext}
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import org.slf4j.LoggerFactory
import scala.collection.JavaConverters._
import scala.io.Source
@ -45,18 +48,21 @@ object CopyHdfsOafSparkApplication {
log.info("hdfsPath: {}", hdfsPath)
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
import spark.implicits._
val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala
val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList
if (validPaths.nonEmpty) {
val oaf = spark.read.load(validPaths: _*).as[Oaf]
val mapper = new ObjectMapper()
val l = ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList
val oaf = spark.read.load(validPaths: _*).as[String]
val mapper = new ObjectMapper().configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
val l = ModelSupport.oafTypes.entrySet.asScala.toList
l.foreach(
e =>
oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e))
oaf
.filter(o => isOafType(o, e.getKey))
.map(j => mapper.readValue(j, e.getValue).asInstanceOf[Oaf])
.map(s => mapper.writeValueAsString(s))(Encoders.STRING)
.write
.option("compression", "gzip")
@ -65,4 +71,20 @@ object CopyHdfsOafSparkApplication {
)
}
}
def isOafType(input: String, oafType: String): Boolean = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: org.json4s.JValue = parse(input)
if (oafType == "relation") {
val hasSource = (json \ "source").extractOrElse[String](null)
val hasTarget = (json \ "target").extractOrElse[String](null)
hasSource != null && hasTarget != null
} else {
val hasId = (json \ "id").extractOrElse[String](null)
val resultType = (json \ "resulttype" \ "classid").extractOrElse[String](null)
hasId != null && oafType.equalsIgnoreCase(resultType)
}
}
}

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@ -0,0 +1,65 @@
package eu.dnetlib.dhp.oa.graph.raw;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
public class CopyHdfsOafSparkApplicationTest {
@Test
void testIsOafType() throws IOException {
assertTrue(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/publication_1.json")),
"publication"));
assertTrue(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json")),
"dataset"));
assertTrue(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/relation_1.json")),
"relation"));
assertFalse(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/publication_1.json")),
"dataset"));
assertFalse(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/raw/dataset_1.json")),
"publication"));
assertTrue(
CopyHdfsOafSparkApplication
.isOafType(
IOUtils
.toString(
getClass()
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/raw/publication_2_unknownProperty.json")),
"publication"));
}
}

File diff suppressed because one or more lines are too long

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@ -0,0 +1 @@
{"author":[{"fullname":"Makkonen, Lasse","name":"Lasse","pid":[],"rank":1,"surname":"Makkonen"}],"bestaccessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Watson, Rick"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"1997-01-01"},"dateofcollection":"2021-10-04T12:42:57.502Z","dateoftransformation":"2021-10-04T15:32:51.877Z","description":[],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::0b579a3501cf87921448e0a1c7fc8353","instance":[{"accessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"1997-01-01"},"distributionlocation":"","hostedby":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"instancetype":{"classid":"0005","classname":"Contribution for newspaper or weekly magazine","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://cris.vtt.fi/en/publications/5a6fbe30-2096-4106-96f4-ed36620d3f73"]}],"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1635433424020,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fcris.vtt.fi%2Fws%2Foai","datestamp":"2020-10-26T12:07:44Z","harvestDate":"2021-10-04T12:42:57.502Z","identifier":"oai:cris.vtt.fi:publications/5a6fbe30-2096-4106-96f4-ed36620d3f73","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"originalId":["50|355e65625b88::0b579a3501cf87921448e0a1c7fc8353","oai:cris.vtt.fi:publications/5a6fbe30-2096-4106-96f4-ed36620d3f73"],"pid":[],"publisher":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Irish Wind Energy Association"},"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Makkonen , L 1997 , Calculation of ice accretion on wind turbine blades . in R Watson (ed.) , EWEC '97: European Wind Energy Conference : Proceedings of the international conference . Irish Wind Energy Association , Slane , European Wind Energy Conference EWEC '97 , Dublin , Ireland , 6/10/97 ."}],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Calculation of ice accretion on wind turbine blades"}]}

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@ -0,0 +1 @@
{"id":"50|355e65625b88::0b579a3501cf87921448e0a1c7fc8353", "resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"}, "unknownProperty": "asdasd"}

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@ -0,0 +1,6 @@
{"source":"1a","target":"10a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
{"source":"10a","target":"1a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
{"source":"2a","target":"20a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
{"source":"20a","target":"2a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
{"source":"15a","target":"25a","collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1626336932282,"relType":"datasourceOrganization","subRelType":"provision","relClass":"provides","validated":false,"validationDate":null,"properties":[]}
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