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dnet-hadoop
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updated lines function to it's implementation linesWithSeparators.map(l => l.stripLineEnd) in this way we force scala plugin compiler to consider this pipeline scala code and not java.string.lines() pipeline

This commit is contained in:
Sandro La Bruzzo 2022-12-21 11:21:17 +01:00
parent 6aa91204a5
commit 3c9826f186
7 changed files with 20 additions and 20 deletions
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2
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
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@ -27,7 +27,7 @@ object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
val result = data.lines
val result = data.linesWithSeparators.map(l =>l.stripLineEnd)
.filter(l => l.startsWith("<a href="))
.map { l =>
val end = l.lastIndexOf("\">")

18
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
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@ -63,7 +63,7 @@ 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.lines.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 +173,9 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump"))
.mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.lines.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 +194,9 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump"))
.mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.lines.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 +239,9 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links"))
.mkString
records.lines.foreach(s => assertTrue(s.nonEmpty))
records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
val result: List[Oaf] = records.lines.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)
@ -276,11 +276,11 @@ class BioScholixTest extends AbstractVocabularyTest {
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")
)
.mkString
records.lines.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.lines.map { input =>
val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input =>
lazy val json = parse(input)
json.extract[ScholixResolved]
}.toList

4
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala
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@ -31,13 +31,13 @@ class CrossrefMappingTest {
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi"))
.mkString
for (line <- funder_doi.lines) {
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.lines) {
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)

2
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala
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@ -25,7 +25,7 @@ class MappingORCIDToOAFTest {
.mkString
assertNotNull(json)
assertFalse(json.isEmpty)
json.lines.foreach(s => {
json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => {
assertNotNull(ORCIDToOAF.extractValueFromInputString(s))
})
}

4
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala
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@ -22,7 +22,7 @@ class UnpayWallMappingTest {
.mkString
var i: Int = 0
for (line <- Ilist.lines) {
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.lines.next()
val l = Ilist.linesWithSeparators.map(l =>l.stripLineEnd).next()
val item = UnpayWallToOAF.convertToOAF(l)

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

@ -53,7 +53,7 @@ class ResolveEntitiesTest extends Serializable {
def generateUpdates(spark: SparkSession): Unit = {
val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString
val pids: List[String] = template.lines
val pids: List[String] = template.linesWithSeparators.map(l =>l.stripLineEnd)
.map { id =>
val r = new Result
r.setId(id.toLowerCase.trim)
@ -127,7 +127,7 @@ class ResolveEntitiesTest extends Serializable {
entities.foreach { e =>
val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString
spark
.createDataset(spark.sparkContext.parallelize(template.lines.toList))
.createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l =>l.stripLineEnd).toList))
.as[String]
.write
.option("compression", "gzip")
@ -264,7 +264,7 @@ class ResolveEntitiesTest extends Serializable {
Source
.fromInputStream(this.getClass.getResourceAsStream(s"publication"))
.mkString
.lines
.linesWithSeparators.map(l =>l.stripLineEnd)
.next(),
classOf[Publication]
)

4
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala
View File

@ -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.lines.toList
val items = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd).toList
assertNotNull(items)
items.foreach(i => assertTrue(i.nonEmpty))
val result =
@ -69,7 +69,7 @@ class ScholixGraphTest extends AbstractVocabularyTest {
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix")
)
.mkString
val result: List[(Relation, ScholixSummary)] = inputRelations.lines
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])))