SubreadSet Example

SubreadSetExternalResources.scala

import com.pacbio.secondary.analysis.datasets.io._ 
import java.nio.file.{Paths, Path}

import collection.JavaConversions._
import collection.JavaConverters._ 

import com.pacbio.secondary.analysis.datasets.io._ 
import com.pacificbiosciences.pacbiobasedatamodel.ExternalResources
import com.pacificbiosciences.pacbiobasedatamodel.ExternalResource

def getPaths(externalResources: ExternalResources): Seq[String] = {
      Option(externalResources).map { ex =>
        ex.getExternalResource
            .flatMap { e => Seq(e.getResourceId) ++ getPaths(e.getExternalResources)}
  
      }.getOrElse(Seq.empty[String])
    } 

val p = "/Users/mkocher/gh_mk_projects/smrtflow/smrt-analysis/src/test/resources/dataset-subreads/m54006_160224_002151.subreadset.xml" 

val s = DataSetLoader.loadSubreadSetIO(Paths.get(p)) 
val paths = getPaths(s.dataset.getExternalResources) 

// generalize to iterate over External Resources and 
// convert E -> T
// and filter specific E
def getFromExternalResources[T](externalResources: ExternalResources,
                                  g: (ExternalResource => T),
                                  f: (ExternalResource => Boolean)): Seq[T] = {
    Option(externalResources).map { ex =>
      ex.getExternalResource
          .filter(f)
          .flatMap { e => Seq(g(e)) ++ getFromExternalResources[T](e.getExternalResources, g, f) }

    }.getOrElse(Seq.empty[T])
}

// extract/translate External resource a Type, For example, get the abspath
// of the DataSet via partial application. Here's a simple E -> Path
def fx(e: ExternalResource): Path = Paths.get(e.getResourceId)
// enable filtering by MetaType
def efilter(e: ExternalResource): Boolean = true

val paths = getFromExternalResources[Path](s.dataset.getExternalResources, fx, efilter)