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

This commit is contained in:
Miriam Baglioni 2023-02-16 15:54:59 +01:00
parent bb5bba51b3 118c1fc3b3
commit 016337a0f9
13 changed files with 1652 additions and 1585 deletions
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4
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -13,6 +13,8 @@ import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import me.xuender.unidecode.Unidecode;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
public class GraphCleaningFunctions extends CleaningFunctions {

3
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
View File

@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
val result = data.linesWithSeparators.map(l =>l.stripLineEnd)
val result = data.linesWithSeparators
.map(l => l.stripLineEnd)
.filter(l => l.startsWith("<a href="))
.map { l =>
val end = l.lastIndexOf("\">")

20
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
View File

@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
.mkString
val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList
val r: List[Oaf] = records.linesWithSeparators
.map(l => l.stripLineEnd)
.toList
.map(s => mapper.readValue(s, classOf[PMArticle]))
.map(a => PubMedToOaf.convert(a, vocabularies))
assertEquals(10, r.size)
@ -175,7 +177,8 @@ class BioScholixTest extends AbstractVocabularyTest {
.mkString
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
val result: List[Oaf] =
records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r))
@ -196,7 +199,8 @@ class BioScholixTest extends AbstractVocabularyTest {
.mkString
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
val result: List[Oaf] =
records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r))
@ -241,7 +245,8 @@ class BioScholixTest extends AbstractVocabularyTest {
.mkString
records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
val result: List[Oaf] =
records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
assertNotNull(result)
assertTrue(result.nonEmpty)
@ -280,10 +285,13 @@ class BioScholixTest extends AbstractVocabularyTest {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input =>
val l: List[ScholixResolved] = records.linesWithSeparators
.map(l => l.stripLineEnd)
.map { input =>
lazy val json = parse(input)
json.extract[ScholixResolved]
}.toList
}
.toList
val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))

18
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java
View File

@ -37,12 +37,24 @@ public class SubscriptionUtils {
}
public static boolean verifyDateRange(final long date, final String min, final String max) {
long from = 0;
long to = Long.MAX_VALUE;
try {
return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime()
&& date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY;
from = min != null ? DateUtils.parseDate(min, "yyyy-MM-dd").getTime() : 0;
} catch (final ParseException e) {
return false;
from = 0;
}
try {
to = max != null ? DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY : Long.MAX_VALUE;
} catch (final ParseException e) {
to = Long.MAX_VALUE;
}
return date >= from && date < to;
}
public static boolean verifyExact(final String s1, final String s2) {

12
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java
View File

@ -41,6 +41,18 @@ public class SubscriptionUtilsTest {
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01"));
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01"));
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "NULL"));
assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", null));
assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "2011-01-01"));
assertTrue(SubscriptionUtils.verifyDateRange(date, null, "2011-01-01"));
assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "NULL"));
assertTrue(SubscriptionUtils.verifyDateRange(date, null, null));
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", null));
assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "NULL"));
assertFalse(SubscriptionUtils.verifyDateRange(date, null, "2005-01-01"));
assertFalse(SubscriptionUtils.verifyDateRange(date, "NULL", "2005-01-01"));
}
@Test

49
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -309,6 +309,8 @@ case object Crossref2Oaf {
result
}
def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
val a = new Author
a.setName(given)
@ -370,10 +372,57 @@ case object Crossref2Oaf {
case dataset: Dataset => convertDataset(dataset)
}
val doisReference:List[String] = for {
JObject(reference_json) <- json \ "reference"
JField("DOI", JString(doi_json)) <- reference_json
} yield doi_json
if (doisReference!= null && doisReference.nonEmpty) {
val citation_relations:List[Relation] = generateCitationRelations(doisReference, result)
resultList = resultList ::: citation_relations
}
resultList = resultList ::: List(result)
resultList
}
private def createCiteRelation(source:Result, targetPid:String, targetPidType:String) :List[Relation] = {
val targetId = IdentifierFactory.idFromPid("50",targetPidType, targetPid, true)
val from = new Relation
from.setSource(source.getId)
from.setTarget(targetId)
from.setRelType(ModelConstants.RESULT_RESULT)
from.setRelClass(ModelConstants.CITES)
from.setSubRelType(ModelConstants.CITATION)
from.setCollectedfrom(source.getCollectedfrom)
from.setDataInfo(source.getDataInfo)
from.setLastupdatetimestamp(source.getLastupdatetimestamp)
val to = new Relation
to.setTarget(source.getId)
to.setSource(targetId)
to.setRelType(ModelConstants.RESULT_RESULT)
to.setRelClass(ModelConstants.IS_CITED_BY)
to.setSubRelType(ModelConstants.CITATION)
to.setCollectedfrom(source.getCollectedfrom)
to.setDataInfo(source.getDataInfo)
to.setLastupdatetimestamp(source.getLastupdatetimestamp)
List(from,to)
}
def generateCitationRelations(dois:List[String], result:Result):List[Relation] = {
dois.flatMap(d => createCiteRelation(result, d, "doi"))
}
def mappingFunderToRelations(
funders: List[mappingFunder],
sourceId: String,

62
dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json
View File

@ -94,7 +94,6 @@
"family": "Stein",
"sequence": "first",
"affiliation": [
]
},
{
@ -104,7 +103,6 @@
"family": "Velzen",
"sequence": "additional",
"affiliation": [
]
},
{
@ -114,7 +112,6 @@
"family": "Kowalski",
"sequence": "additional",
"affiliation": [
]
},
{
@ -122,7 +119,6 @@
"family": "Franckowiak",
"sequence": "additional",
"affiliation": [
]
},
{
@ -132,7 +128,6 @@
"family": "Gezari",
"sequence": "additional",
"affiliation": [
]
},
{
@ -142,7 +137,6 @@
"family": "Miller-Jones",
"sequence": "additional",
"affiliation": [
]
},
{
@ -150,7 +144,6 @@
"family": "Frederick",
"sequence": "additional",
"affiliation": [
]
},
{
@ -160,7 +153,6 @@
"family": "Sfaradi",
"sequence": "additional",
"affiliation": [
]
},
{
@ -168,7 +160,6 @@
"family": "Bietenholz",
"sequence": "additional",
"affiliation": [
]
},
{
@ -178,7 +169,6 @@
"family": "Horesh",
"sequence": "additional",
"affiliation": [
]
},
{
@ -186,7 +176,6 @@
"family": "Fender",
"sequence": "additional",
"affiliation": [
]
},
{
@ -196,7 +185,6 @@
"family": "Garrappa",
"sequence": "additional",
"affiliation": [
]
},
{
@ -206,7 +194,6 @@
"family": "Ahumada",
"sequence": "additional",
"affiliation": [
]
},
{
@ -214,7 +201,6 @@
"family": "Andreoni",
"sequence": "additional",
"affiliation": [
]
},
{
@ -222,7 +208,6 @@
"family": "Belicki",
"sequence": "additional",
"affiliation": [
]
},
{
@ -232,7 +217,6 @@
"family": "Bellm",
"sequence": "additional",
"affiliation": [
]
},
{
@ -240,7 +224,6 @@
"family": "Böttcher",
"sequence": "additional",
"affiliation": [
]
},
{
@ -248,7 +231,6 @@
"family": "Brinnel",
"sequence": "additional",
"affiliation": [
]
},
{
@ -256,7 +238,6 @@
"family": "Burruss",
"sequence": "additional",
"affiliation": [
]
},
{
@ -266,7 +247,6 @@
"family": "Cenko",
"sequence": "additional",
"affiliation": [
]
},
{
@ -276,7 +256,6 @@
"family": "Coughlin",
"sequence": "additional",
"affiliation": [
]
},
{
@ -286,7 +265,6 @@
"family": "Cunningham",
"sequence": "additional",
"affiliation": [
]
},
{
@ -294,7 +272,6 @@
"family": "Drake",
"sequence": "additional",
"affiliation": [
]
},
{
@ -302,7 +279,6 @@
"family": "Farrar",
"sequence": "additional",
"affiliation": [
]
},
{
@ -310,7 +286,6 @@
"family": "Feeney",
"sequence": "additional",
"affiliation": [
]
},
{
@ -318,7 +293,6 @@
"family": "Foley",
"sequence": "additional",
"affiliation": [
]
},
{
@ -328,7 +302,6 @@
"family": "Gal-Yam",
"sequence": "additional",
"affiliation": [
]
},
{
@ -336,7 +309,6 @@
"family": "Golkhou",
"sequence": "additional",
"affiliation": [
]
},
{
@ -346,7 +318,6 @@
"family": "Goobar",
"sequence": "additional",
"affiliation": [
]
},
{
@ -356,7 +327,6 @@
"family": "Graham",
"sequence": "additional",
"affiliation": [
]
},
{
@ -364,7 +334,6 @@
"family": "Hammerstein",
"sequence": "additional",
"affiliation": [
]
},
{
@ -374,7 +343,6 @@
"family": "Helou",
"sequence": "additional",
"affiliation": [
]
},
{
@ -384,7 +352,6 @@
"family": "Hung",
"sequence": "additional",
"affiliation": [
]
},
{
@ -392,7 +359,6 @@
"family": "Kasliwal",
"sequence": "additional",
"affiliation": [
]
},
{
@ -402,7 +368,6 @@
"family": "Kilpatrick",
"sequence": "additional",
"affiliation": [
]
},
{
@ -412,7 +377,6 @@
"family": "Kong",
"sequence": "additional",
"affiliation": [
]
},
{
@ -422,7 +386,6 @@
"family": "Kupfer",
"sequence": "additional",
"affiliation": [
]
},
{
@ -432,7 +395,6 @@
"family": "Laher",
"sequence": "additional",
"affiliation": [
]
},
{
@ -442,7 +404,6 @@
"family": "Mahabal",
"sequence": "additional",
"affiliation": [
]
},
{
@ -452,7 +413,6 @@
"family": "Masci",
"sequence": "additional",
"affiliation": [
]
},
{
@ -462,7 +422,6 @@
"family": "Necker",
"sequence": "additional",
"affiliation": [
]
},
{
@ -472,7 +431,6 @@
"family": "Nordin",
"sequence": "additional",
"affiliation": [
]
},
{
@ -480,7 +438,6 @@
"family": "Perley",
"sequence": "additional",
"affiliation": [
]
},
{
@ -490,7 +447,6 @@
"family": "Rigault",
"sequence": "additional",
"affiliation": [
]
},
{
@ -500,7 +456,6 @@
"family": "Reusch",
"sequence": "additional",
"affiliation": [
]
},
{
@ -508,7 +463,6 @@
"family": "Rodriguez",
"sequence": "additional",
"affiliation": [
]
},
{
@ -518,7 +472,6 @@
"family": "Rojas-Bravo",
"sequence": "additional",
"affiliation": [
]
},
{
@ -528,7 +481,6 @@
"family": "Rusholme",
"sequence": "additional",
"affiliation": [
]
},
{
@ -538,7 +490,6 @@
"family": "Shupe",
"sequence": "additional",
"affiliation": [
]
},
{
@ -548,7 +499,6 @@
"family": "Singer",
"sequence": "additional",
"affiliation": [
]
},
{
@ -558,7 +508,6 @@
"family": "Sollerman",
"sequence": "additional",
"affiliation": [
]
},
{
@ -566,7 +515,6 @@
"family": "Soumagnac",
"sequence": "additional",
"affiliation": [
]
},
{
@ -574,7 +522,6 @@
"family": "Stern",
"sequence": "additional",
"affiliation": [
]
},
{
@ -582,7 +529,6 @@
"family": "Taggart",
"sequence": "additional",
"affiliation": [
]
},
{
@ -590,7 +536,6 @@
"family": "van Santen",
"sequence": "additional",
"affiliation": [
]
},
{
@ -598,7 +543,6 @@
"family": "Ward",
"sequence": "additional",
"affiliation": [
]
},
{
@ -606,7 +550,6 @@
"family": "Woudt",
"sequence": "additional",
"affiliation": [
]
},
{
@ -616,7 +559,6 @@
"family": "Yao",
"sequence": "additional",
"affiliation": [
]
}
],
@ -1412,7 +1354,6 @@
"Nature Astronomy"
],
"original-title": [
],
"language": "en",
"link": [
@ -1448,10 +1389,8 @@
},
"score": 1.0,
"subtitle": [
],
"short-title": [
],
"issued": {
"date-parts": [
@ -1480,7 +1419,6 @@
"URL": "http://dx.doi.org/10.1038/s41550-020-01295-8",
"relation": {
"cites": [
]
},
"ISSN": [

43
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala
View File

@ -1,9 +1,14 @@
package eu.dnetlib.dhp.doiboost.crossref
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf._
import eu.dnetlib.dhp.utils.DHPUtils
import eu.dnetlib.doiboost.crossref.Crossref2Oaf
import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
import org.json4s
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.{DefaultFormats, JValue}
import org.json4s.jackson.JsonMethods
import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.Test
import org.slf4j.{Logger, LoggerFactory}
@ -109,6 +114,44 @@ class CrossrefMappingTest {
}
private def parseJson(input:String):JValue = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = JsonMethods.parse(input)
json
}
@Test
def testCitationRelations():Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString
assertNotNull(json)
assertFalse(json.isEmpty)
val result:List[Oaf] = Crossref2Oaf.convert(json)
assertTrue(result.nonEmpty)
val j = parseJson(json)
val doisReference: List[String] = for {
JObject(reference_json) <- j \ "reference"
JField("DOI", JString(doi_json)) <- reference_json
} yield doi_json
val relationList:List[Relation] = result.filter(s => s.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation]).filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION))
assertNotNull(relationList)
assertFalse(relationList.isEmpty)
assertEquals(doisReference.size*2, relationList.size)
}
@Test
def testEmptyTitle(): Unit = {
val json = Source

4
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala
View File

@ -25,7 +25,9 @@ class MappingORCIDToOAFTest {
.mkString
assertNotNull(json)
assertFalse(json.isEmpty)
json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => {
json.linesWithSeparators
.map(l => l.stripLineEnd)
.foreach(s => {
assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
})
}

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java
View File

@ -5,7 +5,6 @@ import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import org.apache.commons.io.FileUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
@ -27,6 +26,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.graph.clean.country.CleanCountrySparkJob;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Publication;
public class CleanCountryTest {
@ -185,7 +185,6 @@ public class CleanCountryTest {
Assertions.assertEquals(0, tmp.first().getCountry().size());
}
}

6
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala
View File

@ -53,7 +53,8 @@ class ResolveEntitiesTest extends Serializable {
def generateUpdates(spark: SparkSession): Unit = {
val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString
val pids: List[String] = template.linesWithSeparators.map(l =>l.stripLineEnd)
val pids: List[String] = template.linesWithSeparators
.map(l => l.stripLineEnd)
.map { id =>
val r = new Result
r.setId(id.toLowerCase.trim)
@ -264,7 +265,8 @@ class ResolveEntitiesTest extends Serializable {
Source
.fromInputStream(this.getClass.getResourceAsStream(s"publication"))
.mkString
.linesWithSeparators.map(l =>l.stripLineEnd)
.linesWithSeparators
.map(l => l.stripLineEnd)
.next(),
classOf[Publication]
)

3
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala
View File

@ -69,7 +69,8 @@ class ScholixGraphTest extends AbstractVocabularyTest {
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix")
)
.mkString
val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd)
val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators
.map(l => l.stripLineEnd)
.sliding(2)
.map(s => (s.head, s(1)))
.map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary])))