Package gorsat.process

Class SparkPipeInstance

  • All Implemented Interfaces:
    java.lang.AutoCloseable, java.util.Iterator<java.lang.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, java.lang.String cachePath)  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()  
      static SparkPipeInstance createGorIterator​(org.gorpipe.gor.session.GorContext context)  
      java.lang.String getHeader()  
      org.gorpipe.gor.model.GenomicIterator getIterator()  
      java.nio.file.Path getRelativeCachePath()  
      boolean hasNext()  
      boolean hasResourceHints()  
      org.gorpipe.gor.model.GenomicIterator init​(java.lang.String inputQuery, boolean useStdin, java.lang.String forcedInputHeader)  
      void init​(java.lang.String params, org.gorpipe.gor.monitor.GorMonitor gm)  
      java.lang.String next()  
      org.gorpipe.gor.model.GenomicIterator runSparkOperator​(org.gorpipe.gor.monitor.GorMonitor gm, java.lang.String[] commands, java.lang.String[] resourceSplit)  
      void seek​(java.lang.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 Detail

      • SparkPipeInstance

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

      • SparkPipeInstance

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

    • Method Detail

      • createGorIterator

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

      • getRelativeCachePath

        public java.nio.file.Path getRelativeCachePath()

      • hasResourceHints

        public boolean hasResourceHints()

      • runSparkOperator

        public org.gorpipe.gor.model.GenomicIterator runSparkOperator​(org.gorpipe.gor.monitor.GorMonitor gm,
                                                              java.lang.String[] commands,
                                                              java.lang.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​(java.lang.String inputQuery,
                                                  boolean useStdin,
                                                  java.lang.String forcedInputHeader)
        Overrides:
        init in class gorsat.process.PipeInstance

      • init

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

      • getHeader

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

      • seek

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

      • hasNext

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

      • next

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

      • close

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