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This commit is contained in:
Sandro La Bruzzo 2023-02-08 10:32:33 +01:00
parent 6c81a161d2
commit 0b9819f1ab
3 changed files with 24 additions and 15 deletions
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4
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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@ -13,6 +13,8 @@ import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils; 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.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists; 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.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import me.xuender.unidecode.Unidecode; import me.xuender.unidecode.Unidecode;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
public class GraphCleaningFunctions extends CleaningFunctions { public class GraphCleaningFunctions extends CleaningFunctions {

3
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala
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@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = { def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") 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=")) .filter(l => l.startsWith("<a href="))
.map { l => .map { l =>
val end = l.lastIndexOf("\">") val end = l.lastIndexOf("\">")

32
dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
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@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")) .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
.mkString .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(s => mapper.readValue(s, classOf[PMArticle]))
.map(a => PubMedToOaf.convert(a, vocabularies)) .map(a => PubMedToOaf.convert(a, vocabularies))
assertEquals(10, r.size) assertEquals(10, r.size)
@ -173,9 +175,10 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")) .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump"))
.mkString .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) assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r)) result.foreach(r => assertNotNull(r))
@ -194,9 +197,10 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")) .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump"))
.mkString .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) assertTrue(result.nonEmpty)
result.foreach(r => assertNotNull(r)) result.foreach(r => assertNotNull(r))
@ -239,9 +243,10 @@ class BioScholixTest extends AbstractVocabularyTest {
val records: String = Source val records: String = Source
.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")) .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links"))
.mkString .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) assertNotNull(result)
assertTrue(result.nonEmpty) assertTrue(result.nonEmpty)
@ -276,14 +281,17 @@ class BioScholixTest extends AbstractVocabularyTest {
getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved") getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")
) )
.mkString .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 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
lazy val json = parse(input) .map(l => l.stripLineEnd)
json.extract[ScholixResolved] .map { input =>
}.toList lazy val json = parse(input)
json.extract[ScholixResolved]
}
.toList
val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s)) val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))