From 554df257abfdf5a979bb733f8e25c3231c5ddf01 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 13 Feb 2023 16:05:58 +0100 Subject: [PATCH 1/3] null values in date range conditions --- .../dhp/broker/oa/util/SubscriptionUtils.java | 18 +++++++++++++++--- .../broker/oa/util/SubscriptionUtilsTest.java | 12 ++++++++++++ 2 files changed, 27 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java index cf35621934..4792a7719e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java @@ -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) { diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java index d93390e4af..63b49d3620 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -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 From 9a03f71db1ab600743ed34f05d5fe4d4f750ca26 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 13 Feb 2023 16:25:47 +0100 Subject: [PATCH 2/3] code formatting --- .../oaf/utils/GraphCleaningFunctions.java | 4 +- .../ebi/SparkCreateBaselineDataFrame.scala | 3 +- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 32 +++++++++------ .../crossref/CrossrefMappingTest.scala | 4 +- .../orcid/MappingORCIDToOAFTest.scala | 8 ++-- .../doiboost/uw/UnpayWallMappingTest.scala | 4 +- .../dhp/oa/graph/clean/CleanCountryTest.java | 41 +++++++++---------- .../resolution/ResolveEntitiesTest.scala | 8 ++-- .../sx/graph/scholix/ScholixGraphTest.scala | 5 ++- 9 files changed, 61 insertions(+), 48 deletions(-) diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index b24daaa5d4..fc515b5b13 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -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 { diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index 87116f00a8..8ac8b00bfa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -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("") diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 24caaa5533..d1611300d2 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -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) @@ -173,9 +175,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + 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)) @@ -194,9 +197,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + 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)) @@ -239,9 +243,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + 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) @@ -276,14 +281,17 @@ class BioScholixTest extends AbstractVocabularyTest { getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved") ) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input => - lazy val json = parse(input) - json.extract[ScholixResolved] - }.toList + val l: List[ScholixResolved] = records.linesWithSeparators + .map(l => l.stripLineEnd) + .map { input => + lazy val json = parse(input) + json.extract[ScholixResolved] + } + .toList val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s)) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index aba8cee123..12a61454dd 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -31,13 +31,13 @@ class CrossrefMappingTest { .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")) .mkString - for (line <- funder_doi.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- funder_doi.linesWithSeparators.map(l => l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) checkRelation(resultList) } - for (line <- funder_name.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- funder_name.linesWithSeparators.map(l => l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala index d7a6a94a53..8033f02fb3 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -25,9 +25,11 @@ class MappingORCIDToOAFTest { .mkString assertNotNull(json) assertFalse(json.isEmpty) - json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => { - assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) - }) + json.linesWithSeparators + .map(l => l.stripLineEnd) + .foreach(s => { + assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) + }) } @Test diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala index 7fe0e9935a..30001acb55 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala @@ -22,7 +22,7 @@ class UnpayWallMappingTest { .mkString var i: Int = 0 - for (line <- Ilist.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- Ilist.linesWithSeparators.map(l => l.stripLineEnd)) { val p = UnpayWallToOAF.convertToOAF(line) if (p != null) { @@ -43,7 +43,7 @@ class UnpayWallMappingTest { i = i + 1 } - val l = Ilist.linesWithSeparators.map(l =>l.stripLineEnd).next() + val l = Ilist.linesWithSeparators.map(l => l.stripLineEnd).next() val item = UnpayWallToOAF.convertToOAF(l) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index de9e4fc903..3bc69cfd1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -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 { @@ -151,41 +151,40 @@ public class CleanCountryTest { @Test public void testDatasetClean() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") + .getPath(); spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .json(workingDir.toString() + "/dataset"); + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .json(workingDir.toString() + "/dataset"); CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/dataset", - "-graphTableClassName", Dataset.class.getCanonicalName(), - "-workingDir", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS", - "-hostedBy", getClass() + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/dataset", + "-graphTableClassName", Dataset.class.getCanonicalName(), + "-workingDir", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS", + "-hostedBy", getClass() .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .getPath() }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); Assertions.assertEquals(1, tmp.count()); Assertions.assertEquals(0, tmp.first().getCountry().size()); - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala index d415b7fc95..022168de57 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -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) @@ -127,7 +128,7 @@ class ResolveEntitiesTest extends Serializable { entities.foreach { e => val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString spark - .createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l =>l.stripLineEnd).toList)) + .createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l => l.stripLineEnd).toList)) .as[String] .write .option("compression", "gzip") @@ -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] ) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala index 0ea9082900..b838ae0659 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -47,7 +47,7 @@ class ScholixGraphTest extends AbstractVocabularyTest { val inputRelations = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/oaf_to_summary")) .mkString - val items = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd).toList + val items = inputRelations.linesWithSeparators.map(l => l.stripLineEnd).toList assertNotNull(items) items.foreach(i => assertTrue(i.nonEmpty)) val result = @@ -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]))) From a8ac79fa25636a5a7995c148f5536d342feafbc6 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 15 Feb 2023 10:29:13 +0100 Subject: [PATCH 3/3] Added citation relation on crossref Mapping --- .../doiboost/crossref/Crossref2Oaf.scala | 49 + .../crossref/publication_license_embargo.json | 3006 ++++++++--------- .../crossref/CrossrefMappingTest.scala | 43 + 3 files changed, 1564 insertions(+), 1534 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 7fb10863f6..a271f4c338 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -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, diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json index 788946fead..b66147b2d6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -1,1537 +1,1475 @@ { -"indexed": { -"date-parts": [ -[ -2021, -7, -2 -] -], -"date-time": "2021-07-02T07:30:10Z", -"timestamp": 1625211010708 -}, 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J. 878, 82 (2019).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR18", -"doi-asserted-by": "crossref", -"first-page": "5655", -"DOI": "10.1093/mnras/staa192", -"volume": "492", -"author": "A Mummery", -"year": "2020", -"unstructured": "Mummery, A. & Balbus, S. A. The spectral evolution of disc dominated tidal disruption events. Mon. Not. R. Astron. Soc. 492, 5655–5674 (2020).", -"journal-title": "Mon. Not. R. Astron. Soc." -}, -{ -"key": "1295_CR19", -"doi-asserted-by": "crossref", -"first-page": "184", -"DOI": "10.1088/0004-637X/764/2/184", -"volume": "764", -"author": "NJ McConnell", -"year": "2013", -"unstructured": "McConnell, N. J. & Ma, C. P. Revisiting the scaling relations of black hole masses and host galaxy properties. Astrophys. J. 764, 184 (2013).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR20", -"doi-asserted-by": "crossref", -"first-page": "149", -"DOI": "10.3847/1538-4357/aa633b", -"volume": "838", -"author": "K Auchettl", -"year": "2017", -"unstructured": "Auchettl, K., Guillochon, J. & Ramirez-Ruiz, E. New physical insights about tidal disruption events from a comprehensive observational inventory at X-ray wavelengths. Astrophys. J. 838, 149 (2017).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR21", -"doi-asserted-by": "crossref", -"first-page": "4136", -"DOI": "10.1093/mnras/stz1602", -"volume": "487", -"author": "T Wevers", -"year": "2019", -"unstructured": "Wevers, T. et al. Black hole masses of tidal disruption event host galaxies II. Mon. Not. R. Astron. Soc. 487, 4136–4152 (2019).", -"journal-title": "Mon. Not. R. Astron. Soc." -}, -{ -"key": "1295_CR22", -"doi-asserted-by": "crossref", -"first-page": "198", -"DOI": "10.3847/1538-4357/aafe0c", -"volume": "872", -"author": "S van Velzen", -"year": "2019", -"unstructured": "van Velzen, S. et al. The first tidal disruption flare in ZTF: from photometric selection to multi-wavelength characterization. Astrophys. J. 872, 198 (2019).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR23", -"doi-asserted-by": "crossref", -"first-page": "A81", -"DOI": "10.1051/0004-6361/201117855", -"volume": "538", -"author": "G Morlino", -"year": "2012", -"unstructured": "Morlino, G. & Caprioli, D. Strong evidence for hadron acceleration in Tycho’s supernova remnant. Astron. Astrophys. 538, A81 (2012).", -"journal-title": "Astron. 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