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| Original file line number | Diff line number | Diff line change |
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| @@ -1 +1 @@ | ||
| sbt.version = 1.10.4 | ||
| sbt.version = 1.10.5 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| sbt.version=1.10.4 | ||
| sbt.version=1.10.5 |
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@@ -94,3 +94,7 @@ googlecloud { | |
| "153601": 0.045 | ||
| } | ||
| } | ||
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| firecloud { | ||
| max-filematching-bucket-files = 25000 | ||
| } | ||
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124 changes: 124 additions & 0 deletions
124
src/main/scala/org/broadinstitute/dsde/firecloud/filematch/FileMatcher.scala
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| package org.broadinstitute.dsde.firecloud.filematch | ||
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| import com.typesafe.scalalogging.LazyLogging | ||
| import org.broadinstitute.dsde.firecloud.filematch.result.{FailedMatchResult, FileMatchResult, SuccessfulMatchResult} | ||
| import org.broadinstitute.dsde.firecloud.filematch.strategy.{FileRecognitionStrategy, IlluminaPairedEndStrategy} | ||
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| import java.nio.file.Path | ||
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| /** | ||
| * Given a list of files, pair those files based on their naming conventions. | ||
| * At the time of writing, this involves recognizing Illumina single end and paired end read patterns | ||
| * such as those defined at https://support.illumina.com/help/BaseSpace_Sequence_Hub_OLH_009008_2/Source/Informatics/BS/NamingConvention_FASTQ-files-swBS.htm | ||
| * | ||
| * In the future, we may support additional naming conventions | ||
| */ | ||
| class FileMatcher extends LazyLogging { | ||
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| // the list of recognition strategies to use | ||
| private val matchingStrategies: List[FileRecognitionStrategy] = List(new IlluminaPairedEndStrategy()) | ||
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| /** | ||
| * Given a list of files, pair up those files according to our known recognition strategies. | ||
| * @param pathList the list of files to inspect | ||
| * @return pairing results | ||
| */ | ||
| def pairPaths(pathList: List[Path]): List[FileMatchResult] = | ||
| performPairing(pathList) | ||
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| /** | ||
| * Given a list of files, pair up those files according to our known recognition strategies. | ||
| * @param fileList the list of files to inspect, as Strings | ||
| * @return pairing results | ||
| */ | ||
| def pairFiles(fileList: List[String]): List[FileMatchResult] = { | ||
| // convert fileList to pathList | ||
| val pathList = fileList.map(file => new java.io.File(file).toPath) | ||
| pairPaths(pathList) | ||
| } | ||
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| /** | ||
| * Implementation for file pairing. This executes in three steps: | ||
| * 1. Use our known file recognition strategies to identify all "read 1" files in the file list | ||
| * 2. Search for all "read 2" files in the file list which match the previously-identified "read 1"s | ||
| * 3. Handle the remaining files which are not recognized as either "read 1" or "read 2" | ||
| * | ||
| * @param pathList the list of files to inspect | ||
| * @return pairing results | ||
| */ | ||
| private def performPairing(pathList: List[Path]): List[FileMatchResult] = { | ||
| // find every path in the incoming pathList that is recognized by one of our known patterns | ||
| val desiredPairings: List[SuccessfulMatchResult] = findFirstFiles(pathList) | ||
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| // remove the recognized firstFiles from the outstanding pathList | ||
| val remainingPaths: List[Path] = pathList diff desiredPairings.map(_.firstFile) | ||
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| // process the recognized "read 1" files, and look for their desired pairings in the outstanding pathList. | ||
| // this will result in either SuccessfulMatchResult when the desired pairing is found, or PartialMatchResult | ||
| // when the desired pairing is not found | ||
| val pairingResults: List[FileMatchResult] = findSecondFiles(remainingPaths, desiredPairings) | ||
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| // remove the recognized "read 2" files from the outstanding pathList | ||
| val unrecognizedPaths: List[Path] = remainingPaths diff pairingResults.collect { case s: SuccessfulMatchResult => | ||
| s.secondFile | ||
| } | ||
| // translate the unrecognized paths into a FileMatchResult | ||
| val unrecognizedResults: List[FailedMatchResult] = unrecognizedPaths.map(path => FailedMatchResult(path)) | ||
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| // return results, sorted by firstFile | ||
| (pairingResults ++ unrecognizedResults).sortBy(r => r.firstFile) | ||
| } | ||
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| /** | ||
| * find every path in the incoming pathList that is recognized as a "read 1" by our known patterns | ||
| * @param pathList the list of files to inspect | ||
| * @return pairing results | ||
| */ | ||
| private def findFirstFiles(pathList: List[Path]): List[SuccessfulMatchResult] = | ||
| pathList.collect { path => | ||
| tryPairingStrategies(path) match { | ||
| case success: SuccessfulMatchResult => success | ||
| } | ||
| } | ||
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| /** | ||
| * find every path in the incoming pathList that is recognized as a "read 2" by our known patterns | ||
| * | ||
| * @param pathList the list of files to inspect | ||
| * @param desiredPairings the "read 2" files to look for in the pathList | ||
| * @return pairing results | ||
| */ | ||
| private def findSecondFiles(pathList: List[Path], | ||
| desiredPairings: List[SuccessfulMatchResult] | ||
| ): List[FileMatchResult] = | ||
| desiredPairings.map { desiredPairing => | ||
| // search for the desired pairing's secondFile in the list of actual files | ||
| pathList.find(p => p.equals(desiredPairing.secondFile)) match { | ||
| case Some(_) => desiredPairing | ||
| case None => desiredPairing.toPartial | ||
| } | ||
| } | ||
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| /** | ||
| * Attempt all the configured file recognition strategies against the supplied file. | ||
| * | ||
| * @param file the file to try to recognize | ||
| * @return SuccessfulMatchResult if the file is recognized; FailedMatchResult if not | ||
| */ | ||
| private def tryPairingStrategies(file: Path): FileMatchResult = { | ||
| // does the current file hit on any of our file-matching patterns? | ||
| // Iterate over the matching strategies and return the first successful match result. | ||
| val strategyHit = matchingStrategies.collectFirst(strategy => | ||
| strategy.matchFirstFile(file) match { | ||
| case success: SuccessfulMatchResult => success | ||
| } | ||
| ) | ||
| strategyHit match { | ||
| // The current file is recognized by one of our recognition strategies | ||
| case Some(desiredResult: SuccessfulMatchResult) => desiredResult | ||
| // the current file is not recognized | ||
| case _ => FailedMatchResult(file) | ||
| } | ||
| } | ||
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| } |
22 changes: 22 additions & 0 deletions
22
src/main/scala/org/broadinstitute/dsde/firecloud/filematch/FileMatchingOptions.scala
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| @@ -0,0 +1,22 @@ | ||
| package org.broadinstitute.dsde.firecloud.filematch | ||
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| import spray.json.DefaultJsonProtocol.jsonFormat4 | ||
| import spray.json.RootJsonFormat | ||
| import spray.json.DefaultJsonProtocol._ | ||
|
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| /** | ||
| * Request payload, specified by end users, to control file-matching functionality | ||
| * @param prefix bucket prefix in which to list files | ||
| * @param read1Name name for the "read1" column | ||
| * @param read2Name name for the "read2" column | ||
| * @param recursive should bucket-listing be recursive? | ||
| */ | ||
| case class FileMatchingOptions(prefix: String, | ||
| read1Name: Option[String] = None, | ||
| read2Name: Option[String] = None, | ||
| recursive: Option[Boolean] = None | ||
| ) | ||
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| object FileMatchingOptionsFormat { | ||
| implicit val fileMatchingOptionsFormat: RootJsonFormat[FileMatchingOptions] = jsonFormat4(FileMatchingOptions) | ||
| } |
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