76 lines
2.6 KiB
Scala
76 lines
2.6 KiB
Scala
package eu.dnetlib.dhp.sx.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.PDBToOAF
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import org.junit.jupiter.api.Assertions._
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import org.junit.jupiter.api.extension.ExtendWith
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import org.junit.jupiter.api.{BeforeEach, Test}
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import org.mockito.junit.jupiter.MockitoExtension
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import scala.collection.JavaConverters._
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import scala.io.Source
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import scala.xml.pull.XMLEventReader
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@ExtendWith(Array(classOf[MockitoExtension]))
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class BioScholixTest extends AbstractVocabularyTest{
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@BeforeEach
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def setUp() :Unit = {
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super.setUpVocabulary()
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}
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@Test
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def testEBIData() = {
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val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
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val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString
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val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
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new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
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}
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@Test
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def testPubmedToOaf(): Unit = {
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assertNotNull(vocabularies)
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assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
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val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
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mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false)
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("pubmed_dump")).mkString
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val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies))
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assertEquals(10, r.size)
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assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p)))
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println(mapper.writeValueAsString(r.head))
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}
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@Test
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def testPDBToOAF():Unit = {
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assertNotNull(vocabularies)
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assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
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val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
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mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false)
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val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/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 => PDBToOAF.convert(o))
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assertTrue(result.nonEmpty)
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result.foreach(r => assertNotNull(r))
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println(result.count(o => o.isInstanceOf[Relation]))
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println(mapper.writeValueAsString(result.head))
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}
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}
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