Я получаю исключение ниже в потоке "main"
java.lang.UnsupportedOperationException: cannot have circular references in class, but got the circular reference of class org.det.pia.service.AnalysisCollection
at org.apache.spark.sql.catalyst.ScalaReflection$.$anonfun$serializerFor$1(ScalaReflection.scala:628)
at scala.reflect.internal.tpe.TypeConstraints$UndoLog.undo(TypeConstraints.scala:68)
at org.apache.spark.sql.catalyst.ScalaReflection.cleanUpReflectionObjects(ScalaReflection.scala:906)
at org.apache.spark.sql.catalyst.ScalaReflection.cleanUpReflectionObjects$(ScalaReflection.scala:905)
at org.apache.spark.sql.catalyst.ScalaReflection$.cleanUpReflectionObjects(ScalaReflection.scala:46)
at org.apache.spark.sql.catalyst.ScalaReflection$.serializerFor(ScalaReflection.scala:452)
at org.apache.spark.sql.catalyst.ScalaReflection$.$anonfun$serializerFor$6(ScalaReflection.scala:644)
at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
at scala.collection.immutable.List.foreach(List.scala:392)
Я хочу пропустить это исключение и заставить его работать
scala
case class FileList( val id: Long, val name: String, val fileName: String, val format: String,
val analysisCollection: AnalysisCollection, val analysisProtocolCollection: AnalysisProtocolCollection )
case class Inputs(val sourceFile:List[SourceFile],val searchDatabase:List[SearchDatabase],val spectraData:List[SpectraData])
case class AnalysisSoftwareList(val analysisSoftware: List[AnalysisSoftware])
case class PeptideSpectrumMatch(val id: Long, val charge: Int, val massToCharge: Double,
val deltaMass: Double, val retentionTime: Double, val sequence: String,
val missed: Int, val sourceID: String, val spectrumTitle: String, val pFile: PIAInputFile,
val spectrumID: SpectrumIdentification, val isUnique: Boolean = false,
val isDecoy: Boolean = false, val scores: List[ScoreModel],
val modifications: TreeMap[Integer, Modification], val paramList: List[AbstractParam],
val modificationString: String, val peptideStringID: String, val modificationChanged: Boolean = false,
val identificationKeys: Map[String, String], val peptide: Peptide)
case class Accession(val id: Long, val accessionStr: String, val files: Set[Long], val descriptions: Map[Long, String],
val dbSequence: String, val searchDatabaseRefs: Set[String], val pGroup: Group)
case class Peptide(val id: Long, val sequence: String, val spectra: List[PeptideSpectrumMatch],
val pGroup: Group, val occurrences: HashSet[AccessionOccurrence])
case class Group(val id: Long, val treeID: Long, val peptides: Map[String, Peptide], val children: TreeMap[Long, Group],
val parents: TreeMap[Long, Group],val accessions: Map[String, Accession],
val allAccessions: Map[String, Accession])
case class PiaMergedData(val _date :String,val _name:String, val _ns2:String, val _ns3:String, val filesList: FileList,
val inputs: Inputs, val analysisSoftwareList: AnalysisSoftwareList,
val spectraList: List[PeptideSpectrumMatch], val accessionsList: List[Accession],
val peptidesList: List[Peptide], val groupsList: List[Group]
)
case class AnalysisSoftware(var contactRole: ContactRole, val softwareName:Param, val customizations: String,
val version: String,val uri: String)
case class AnalysisCollection(val spectrumIdentification: List[SpectrumIdentification],
val proteinDetection: ProteinDetection)
case class SpectrumIdentification( val inputSpectra: List[InputSpectra], val searchDatabaseRef: List[SearchDatabaseRef],
val spectrumIdentificationProtocolRef: String , val spectrumIdentificationListRef: String,
val spectrumIdentificationList: SpectrumIdentificationList,
val spectrumIdentificationProtocol: SpectrumIdentificationProtocol
)
case class InputSpectra(val spectraDataRef: String, val spectraData: SpectraData)
case class SpectraData(val spectrumIDFormat:SpectrumIDFormat)
case class SpectrumIDFormat(val cvParam:CvParam)
case class CvParam(val cvRef: String, val accession: String,val cv: Cv)
case class Cv(val fullName: String, val version: String, val uri: String, val id: String)
case class SearchDatabaseRef(val searchDatabaseRef: String, val searchDatabase: SearchDatabase)
case class SearchDatabase()
case class SpectrumIdentificationList(val fragmentationTable: FragmentationTable, val spectrumIdentificationResult: List[SpectrumIdentificationResult],
val paramGroup: List[AbstractParam], val numSequencesSearched: Long)
case class FragmentationTable(val measure: List[Measure])
case class Measure(val cvParam: List[CvParam])
case class SpectrumIdentificationResult(val spectrumIdentificationItem: List[SpectrumIdentificationItem],
val paramGroup: List[AbstractParam], val spectrumID: String, val spectraDataRef: String, val spectraData: SpectraData)
case class SpectrumIdentificationItem(val peptideEvidenceRef: List[PeptideEvidenceRef], val fragmentation: Fragmentation,
val paramGroup: List[AbstractParam], val chargeState: Int, val experimentalMassToCharge: Double,
val calculatedMassToCharge: Double, val calculatedPI: Float, val peptideRef: String,
val rank: Int, val passThreshold: Boolean = false, val massTableRef: String,
val sampleRef: String, val peptide: Peptide, val massTable: MassTable, val sample: Sample )
case class PeptideEvidenceRef(val peptideEvidenceRef: String,
val peptideEvidence: PeptideEvidence)
case class PeptideEvidence( val paramGroup: List[AbstractParam] , val dbSequenceRef: String ,
val peptideRef: String , val start: Integer , val end: Integer ,
val pre: String , val post: String , val translationTableRef: String , val frame: Integer , val isDecoy: Boolean = false,
val dbSequence: DBSequence , val peptide: Peptide , val translationTable: TranslationTable )
case class AbstractParam(val name: String, val value: String, val unitAccession: String, val unitName: String, val unitCvRef: String, val unitCv: Cv)
case class DBSequence( val paramGroup: List[AbstractParam], val length: Integer,
val searchDatabaseRef: String, val accession:String , val searchDatabase: SearchDatabase )
case class PIAInputFile(val id: Long, val name: String, val fileName: String,
val format: String, val analysisCollection: AnalysisCollection, val analysisProtocolCollection: AnalysisProtocolCollection)
case class AnalysisProtocolCollection(val spectrumIdentificationProtocol: List[SpectrumIdentificationProtocol],
val proteinDetectionProtocol: ProteinDetectionProtocol
)
case class ProteinDetection(val inputSpectrumIdentifications: List[InputSpectrumIdentifications],
val proteinDetectionListRef: String, val proteinDetectionProtocolRef: String, val proteinDetectionList: ProteinDetectionList,
val proteinDetectionProtocol: ProteinDetectionProtocol)
Я также добавил тот же класс в Scala ииспользуя его, но получая исключение для этого пакета, поскольку в Java-библиотеке есть циклическая зависимость, которую я не могу изменить, есть ли способ пропустить это исключение?
Java-библиотека работает нормально, но возникает проблема при работе в spark итолько скала