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@ -13,6 +13,8 @@ import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import me.xuender.unidecode.Unidecode;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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public class GraphCleaningFunctions extends CleaningFunctions {
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@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame {
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def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
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val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
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val result = data.linesWithSeparators.map(l =>l.stripLineEnd)
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val result = data.linesWithSeparators
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.map(l => l.stripLineEnd)
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.filter(l => l.startsWith("<a href="))
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.map { l =>
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val end = l.lastIndexOf("\">")
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@ -63,7 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest {
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val records: String = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump"))
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.mkString
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val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList
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val r: List[Oaf] = records.linesWithSeparators
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.map(l => l.stripLineEnd)
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.toList
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.map(s => mapper.readValue(s, classOf[PMArticle]))
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.map(a => PubMedToOaf.convert(a, vocabularies))
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assertEquals(10, r.size)
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@ -173,9 +175,10 @@ class BioScholixTest extends AbstractVocabularyTest {
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val records: String = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump"))
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.mkString
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records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
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assertTrue(result.nonEmpty)
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result.foreach(r => assertNotNull(r))
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@ -194,9 +197,10 @@ class BioScholixTest extends AbstractVocabularyTest {
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val records: String = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump"))
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.mkString
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records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
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assertTrue(result.nonEmpty)
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result.foreach(r => assertNotNull(r))
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@ -239,9 +243,10 @@ class BioScholixTest extends AbstractVocabularyTest {
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val records: String = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links"))
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.mkString
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records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
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val result: List[Oaf] =
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records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList
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assertNotNull(result)
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assertTrue(result.nonEmpty)
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@ -276,14 +281,17 @@ class BioScholixTest extends AbstractVocabularyTest {
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getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")
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)
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.mkString
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records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty))
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input =>
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lazy val json = parse(input)
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json.extract[ScholixResolved]
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}.toList
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val l: List[ScholixResolved] = records.linesWithSeparators
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.map(l => l.stripLineEnd)
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.map { input =>
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lazy val json = parse(input)
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json.extract[ScholixResolved]
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}
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.toList
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val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s))
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