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@ -1,9 +1,9 @@
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package eu.dnetlib.dhp.sx.bio.pubmed
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package eu.dnetlib.dhp.sx.graph.bio.pubmed
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import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF
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import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
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import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
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import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString}
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import org.json4s.jackson.JsonMethods.parse
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@ -72,7 +72,7 @@ class BioScholixTest extends AbstractVocabularyTest{
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assertNotNull(vocabularies)
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assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/pdb_dump")).mkString
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")).mkString
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records.lines.foreach(s => assertTrue(s.nonEmpty))
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val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.pdbTOOaf(o))
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@ -94,7 +94,7 @@ class BioScholixTest extends AbstractVocabularyTest{
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assertNotNull(vocabularies)
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assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/uniprot_dump")).mkString
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")).mkString
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records.lines.foreach(s => assertTrue(s.nonEmpty))
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val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.uniprotToOAF(o))
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@ -133,7 +133,7 @@ class BioScholixTest extends AbstractVocabularyTest{
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@Test
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def testCrossrefLinksToOAF():Unit = {
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/crossref_links")).mkString
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")).mkString
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records.lines.foreach(s => assertTrue(s.nonEmpty))
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@ -148,7 +148,7 @@ class BioScholixTest extends AbstractVocabularyTest{
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@Test
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def testEBILinksToOAF():Unit = {
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val iterator = GzFileIterator(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi_links.gz"), "UTF-8")
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val iterator = GzFileIterator(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz"), "UTF-8")
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val data = iterator.next()
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val res = BioDBToOAF.parse_ebi_links(BioDBToOAF.extractEBILinksFromDump(data).links).filter(BioDBToOAF.EBITargetLinksFilter).flatMap(BioDBToOAF.convertEBILinksToOaf)
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@ -165,7 +165,7 @@ class BioScholixTest extends AbstractVocabularyTest{
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@Test
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def scholixResolvedToOAF():Unit ={
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/scholix_resolved")).mkString
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved")).mkString
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records.lines.foreach(s => assertTrue(s.nonEmpty))
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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