From 0b9819f1ab4ad4f28f124e853ad793e601930ded Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 8 Feb 2023 10:32:33 +0100 Subject: [PATCH] Code formatted --- .../oaf/utils/GraphCleaningFunctions.java | 4 +-- .../ebi/SparkCreateBaselineDataFrame.scala | 3 +- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 32 ++++++++++++------- 3 files changed, 24 insertions(+), 15 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 b24daaa5d..fc515b5b1 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 87116f00a..8ac8b00bf 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 24caaa553..d1611300d 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))