Package gorsat.process

Class SparkPipeInstance

java.lang.Object
org.gorpipe.gor.model.GorIterator
gorsat.gorsatGorIterator.gorsatGorIterator
gorsat.process.PipeInstance
gorsat.process.SparkPipeInstance
All Implemented Interfaces:
AutoCloseable, Iterator<String>
public class SparkPipeInstance extends gorsat.process.PipeInstance

  • Field Summary

    Fields inherited from class org.gorpipe.gor.model.GorIterator

    chrFrom, chromosomes, chrTo, DEFAULT_COMMAND, fileName, filter, groupSize, isCancelled, maxRows, paintRange, posFrom, posTo

  • Constructor Summary

    Constructors
    Constructor
    Description
    SparkPipeInstance(org.gorpipe.gor.session.GorContext context)
     
    SparkPipeInstance(org.gorpipe.gor.session.GorContext context, String cachePath)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
     
    static SparkPipeInstance
    createGorIterator(org.gorpipe.gor.session.GorContext context)
     
    String
    getHeader()
     
    org.gorpipe.gor.model.GenomicIterator
    getIterator()
     
    Path
    getRelativeCachePath()
     
    boolean
    hasNext()
     
    boolean
    hasResourceHints()
     
    org.gorpipe.gor.model.GenomicIterator
    init(String inputQuery, boolean useStdin, String forcedInputHeader)
     
    void
    init(String params, org.gorpipe.gor.monitor.GorMonitor gm)
     
    String
    next()
     
    org.gorpipe.gor.model.GenomicIterator
    runSparkOperator(org.gorpipe.gor.monitor.GorMonitor gm, String[] commands, String[] resourceSplit)
     
    void
    seek(String chr, int pos)
     
    org.gorpipe.gor.model.GenomicIterator
    wrapGenomicIterator(org.gorpipe.gor.model.GenomicIterator gi)
     

    Methods inherited from class gorsat.process.PipeInstance

    $lessinit$greater$default$2, actualGetPipeHeader, checkHeader, commandFromPipeStep, createFileReader, createPipestep, createPipestep$default$2, createScriptEngine, DEFAULT_REQUEST_ID, fixGorString, getIgnoreCase, getPipeStep, getRowSource, getSession, getUsedFiles, handlePlaceholderCommands, init, init, initialize, injectTypeInferral, injectTypeInferral$default$2, insertProjectContext, parseCommand, prepareInputSource, preparePipeStep, processArguments, processArguments$default$3, processWhitelistedCommands, processWhitelistedInputSource, pushdownCalc, pushdownCmd, pushdownFilter, pushdownTop, pushdownWrite, scalaInit, scalaInit$default$2, subProcessArguments, subProcessArguments, theInputSource, theInputSource_$eq, thePipeStep, thePipeStep_$eq

    Methods inherited from class gorsat.gorsatGorIterator.gorsatGorIterator

    fixHeader, fixHeader_$eq, isNorContext, isNorContext_$eq

    Methods inherited from class org.gorpipe.gor.model.GorIterator

    forceReload, getAverageSeekCount, getCommand, getGSecurityKey, getHeaderCols, getParamsWithValues, init, init, init, populateCommand, populateCommand, seekable, setCommand, setCommandWithValues

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface java.util.Iterator

    forEachRemaining, remove

  • Constructor Details

    • SparkPipeInstance

      public SparkPipeInstance(org.gorpipe.gor.session.GorContext context)

    • SparkPipeInstance

      public SparkPipeInstance(org.gorpipe.gor.session.GorContext context, String cachePath)

  • Method Details

    • createGorIterator

      public static SparkPipeInstance createGorIterator(org.gorpipe.gor.session.GorContext context)

    • getRelativeCachePath

      public Path getRelativeCachePath()

    • hasResourceHints

      public boolean hasResourceHints()

    • runSparkOperator

      public org.gorpipe.gor.model.GenomicIterator runSparkOperator(org.gorpipe.gor.monitor.GorMonitor gm, String[] commands, String[] resourceSplit)

    • getIterator

      public org.gorpipe.gor.model.GenomicIterator getIterator()
      Overrides:
      getIterator in class gorsat.process.PipeInstance

    • wrapGenomicIterator

      public org.gorpipe.gor.model.GenomicIterator wrapGenomicIterator(org.gorpipe.gor.model.GenomicIterator gi)

    • init

      public org.gorpipe.gor.model.GenomicIterator init(String inputQuery, boolean useStdin, String forcedInputHeader)
      Overrides:
      init in class gorsat.process.PipeInstance

    • init

      public void init(String params, org.gorpipe.gor.monitor.GorMonitor gm)
      Overrides:
      init in class gorsat.process.PipeInstance

    • getHeader

      public String getHeader()
      Overrides:
      getHeader in class gorsat.process.PipeInstance

    • seek

      public void seek(String chr, int pos)
      Overrides:
      seek in class gorsat.process.PipeInstance

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface Iterator<String>
      Overrides:
      hasNext in class gorsat.process.PipeInstance

    • next

      public String next()
      Specified by:
      next in interface Iterator<String>
      Overrides:
      next in class gorsat.process.PipeInstance

    • close

      public void close()
      Specified by:
      close in interface AutoCloseable
      Overrides:
      close in class gorsat.process.PipeInstance