Replace utils.Logger with grizzled.slf4j.Logger.

bigdatagenomics · Apr 26, 2019 · f132d8c · f132d8c
1 parent 122888b
commit f132d8c
Show file tree

Hide file tree

Showing 52 changed files with 191 additions and 187 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fasta.scala
@@ -17,11 +17,11 @@
  */
 package org.bdgenomics.adam.cli
 
+import grizzled.slf4j.Logging
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.cli.FileSystemUtils._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 class ADAM2FastaArgs extends Args4jBase {
@@ -55,10 +55,10 @@ class ADAM2Fasta(val args: ADAM2FastaArgs) extends BDGSparkCommand[ADAM2FastaArg
   override def run(sc: SparkContext): Unit = {
     checkWriteablePath(args.outputPath, sc.hadoopConfiguration)
 
-    log.info("Loading ADAM nucleotide contig fragments from disk.")
+    info("Loading ADAM nucleotide contig fragments from disk.")
     val contigFragments = sc.loadContigFragments(args.inputPath)
 
-    log.info("Merging fragments and writing FASTA to disk.")
+    info("Merging fragments and writing FASTA to disk.")
     val contigs = contigFragments.mergeFragments()
 
     val cc = if (args.coalesce > 0) {

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala
@@ -80,7 +80,7 @@ class ADAM2Fastq(val args: ADAM2FastqArgs) extends BDGSparkCommand[ADAM2FastqArg
     var reads = sc.loadAlignments(args.inputPath, optProjection = projectionOpt)
 
     if (args.repartition != -1) {
-      log.info("Repartitioning reads to to '%d' partitions".format(args.repartition))
+      info("Repartitioning reads to to '%d' partitions".format(args.repartition))
       reads = reads.transform(_.repartition(args.repartition))
     }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala
@@ -21,7 +21,7 @@ import java.util.logging.Level._
 import javax.inject.Inject
 import com.google.inject.AbstractModule
 import net.codingwell.scalaguice.ScalaModule
-import org.bdgenomics.utils.misc.Logging
+import grizzled.slf4j.Logging
 import org.bdgenomics.adam.util.ParquetLogger
 import org.bdgenomics.utils.cli._
 
@@ -106,7 +106,7 @@ class ADAMMain @Inject() (commandGroups: List[CommandGroup]) extends Logging {
   }
 
   def apply(args: Array[String]) {
-    log.info("ADAM invoked with args: %s".format(argsToString(args)))
+    info("ADAM invoked with args: %s".format(argsToString(args)))
     if (args.length < 1) {
       printCommands()
     } else if (args.contains("--version") || args.contains("-version")) {

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountContigKmers.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountContigKmers.scala
@@ -17,11 +17,11 @@
  */
 package org.bdgenomics.adam.cli
 
+import grizzled.slf4j.Logging
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.cli.FileSystemUtils._
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object CountContigKmers extends BDGCommandCompanion {

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala
@@ -17,12 +17,12 @@
  */
 package org.bdgenomics.adam.cli
 
+import grizzled.slf4j.Logging
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.cli.FileSystemUtils._
 import org.bdgenomics.adam.projections.{ AlignmentRecordField, Projection }
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object CountReadKmers extends BDGCommandCompanion {
@@ -60,7 +60,7 @@ class CountReadKmers(protected val args: CountReadKmersArgs) extends BDGSparkCom
     )
 
     if (args.repartition != -1) {
-      log.info("Repartitioning reads to '%d' partitions".format(args.repartition))
+      info("Repartitioning reads to '%d' partitions".format(args.repartition))
       adamRecords = adamRecords.transform(_.repartition(args.repartition))
     }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fasta2ADAM.scala
@@ -17,11 +17,11 @@
  */
 package org.bdgenomics.adam.cli
 
+import grizzled.slf4j.Logging
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.cli.FileSystemUtils._
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object Fasta2ADAM extends BDGCommandCompanion {
@@ -54,14 +54,14 @@ class Fasta2ADAM(protected val args: Fasta2ADAMArgs) extends BDGSparkCommand[Fas
   def run(sc: SparkContext) {
     checkWriteablePath(args.outputPath, sc.hadoopConfiguration)
 
-    log.info("Loading FASTA data from disk.")
+    info("Loading FASTA data from disk.")
     val adamFasta = sc.loadFasta(args.fastaFile, maximumLength = args.maximumLength)
 
     if (args.verbose) {
-      log.info("FASTA contains: %s", adamFasta.sequences.toString)
+      info("FASTA contains: %s".format(adamFasta.sequences.toString))
     }
 
-    log.info("Writing records to disk.")
+    info("Writing records to disk.")
     val finalFasta = if (args.partitions > 0) {
       adamFasta.transform(_.repartition(args.partitions))
     } else {

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FileSystemUtils.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/FileSystemUtils.scala
@@ -20,12 +20,11 @@ package org.bdgenomics.adam.cli
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.Path
 import org.apache.hadoop.mapred.FileAlreadyExistsException
-import org.bdgenomics.utils.misc.Logging
 
 /**
  * Utility methods for file systems.
  */
-private[cli] object FileSystemUtils extends Logging {
+private[cli] object FileSystemUtils {
   private def exists(pathName: String, conf: Configuration): Boolean = {
     val p = new Path(pathName)
     val fs = p.getFileSystem(conf)

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala
@@ -20,6 +20,7 @@ package org.bdgenomics.adam.cli
 import java.time.Instant
 import java.lang.{ Boolean => JBoolean }
 
+import grizzled.slf4j.Logging
 import htsjdk.samtools.ValidationStringency
 import org.apache.parquet.filter2.predicate.FilterApi
 import org.apache.parquet.filter2.predicate.Operators.BooleanColumn
@@ -37,7 +38,6 @@ import org.bdgenomics.adam.rdd.read.{ AlignmentRecordDataset, QualityScoreBin }
 import org.bdgenomics.adam.rich.RichVariant
 import org.bdgenomics.formats.avro.ProcessingStep
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object TransformAlignments extends BDGCommandCompanion {
@@ -175,7 +175,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
    */
   private def maybeRepartition(rdd: AlignmentRecordDataset): AlignmentRecordDataset = {
     if (args.repartition != -1) {
-      log.info("Repartitioning reads to to '%d' partitions".format(args.repartition))
+      info("Repartitioning reads to to '%d' partitions".format(args.repartition))
       rdd.transform(_.repartition(args.repartition))
     } else {
       rdd
@@ -190,7 +190,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
    */
   private def maybeDedupe(rdd: AlignmentRecordDataset): AlignmentRecordDataset = {
     if (args.markDuplicates) {
-      log.info("Marking duplicates")
+      info("Marking duplicates")
       rdd.markDuplicates()
     } else {
       rdd
@@ -213,7 +213,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
                            sl: StorageLevel): AlignmentRecordDataset = {
     if (args.locallyRealign) {
 
-      log.info("Locally realigning indels.")
+      info("Locally realigning indels.")
 
       // has the user asked us to cache the rdd before multi-pass stages?
       if (args.cache) {
@@ -272,7 +272,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
                                sl: StorageLevel): AlignmentRecordDataset = {
     if (args.recalibrateBaseQualities) {
 
-      log.info("Recalibrating base qualities")
+      info("Recalibrating base qualities")
 
       // bqsr is a two pass algorithm, so cache the rdd if requested
       val optSl = if (args.cache) {
@@ -311,7 +311,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
    */
   private def maybeCoalesce(rdd: AlignmentRecordDataset): AlignmentRecordDataset = {
     if (args.coalesce != -1) {
-      log.info("Coalescing the number of partitions to '%d'".format(args.coalesce))
+      info("Coalescing the number of partitions to '%d'".format(args.coalesce))
       if (args.coalesce > rdd.rdd.partitions.length || args.forceShuffle) {
         rdd.transform(_.coalesce(args.coalesce, shuffle = true))
       } else {
@@ -341,7 +341,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
         rdd.rdd.persist(sl)
       }
 
-      log.info("Sorting reads")
+      info("Sorting reads")
 
       // are we sorting lexicographically or using legacy SAM sort order?
       val sortedRdd = if (args.sortLexicographically) {
@@ -373,7 +373,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
                          rdd: AlignmentRecordDataset,
                          stringencyOpt: Option[ValidationStringency]): AlignmentRecordDataset = {
     if (args.mdTagsReferenceFile != null) {
-      log.info(s"Adding MDTags to reads based on reference file ${args.mdTagsReferenceFile}")
+      info(s"Adding MDTags to reads based on reference file ${args.mdTagsReferenceFile}")
       val referenceFile = sc.loadReferenceFile(args.mdTagsReferenceFile,
         maximumLength = args.mdTagsFragmentSize)
       rdd.computeMismatchingPositions(
@@ -588,7 +588,7 @@ class TransformAlignments(protected val args: TransformAlignmentsArgs) extends B
 
     if (args.partitionByStartPos) {
       if (outputRdd.sequences.isEmpty) {
-        log.warn("This dataset is not aligned and therefore will not benefit from being saved as a partitioned dataset")
+        warn("This dataset is not aligned and therefore will not benefit from being saved as a partitioned dataset")
       }
       outputRdd.saveAsPartitionedParquet(args.outputPath, partitionSize = args.partitionedBinSize)
     } else {

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala
@@ -17,6 +17,7 @@
  */
 package org.bdgenomics.adam.cli
 
+import grizzled.slf4j.Logging
 import org.apache.spark.SparkContext
 import org.bdgenomics.adam.cli.FileSystemUtils._
 import org.bdgenomics.adam.io.FastqRecordReader
@@ -25,7 +26,6 @@ import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
 import org.bdgenomics.adam.rdd.read.QualityScoreBin
 import org.bdgenomics.adam.rdd.fragment.FragmentDataset
 import org.bdgenomics.utils.cli._
-import org.bdgenomics.utils.misc.Logging
 import org.kohsuke.args4j.{ Argument, Option => Args4jOption }
 
 object TransformFragments extends BDGCommandCompanion {
@@ -99,7 +99,7 @@ class TransformFragments(protected val args: TransformFragmentsArgs) extends BDG
     checkWriteablePath(args.outputPath, sc.hadoopConfiguration)
 
     if (args.loadAsReads && args.saveAsReads) {
-      log.warn("If loading and saving as reads, consider using TransformAlignments instead.")
+      warn("If loading and saving as reads, consider using TransformAlignments instead.")
     }
     if (args.sortReads) {
       require(args.saveAsReads,

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformGenotypes.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformGenotypes.scala
@@ -95,7 +95,7 @@ class TransformGenotypes(val args: TransformGenotypesArgs)
    */
   private def maybeCoalesce[U <: GenomicDataset[_, _, U]](rdd: U): U = {
     if (args.coalesce != -1) {
-      log.info("Coalescing the number of partitions to '%d'".format(args.coalesce))
+      info("Coalescing the number of partitions to '%d'".format(args.coalesce))
       if (args.coalesce > rdd.rdd.partitions.length || args.forceShuffle) {
         rdd.transform(_.coalesce(args.coalesce, shuffle = true))
       } else {
@@ -114,10 +114,10 @@ class TransformGenotypes(val args: TransformGenotypesArgs)
    */
   private def maybeSort[U <: GenomicDataset[_, _, U]](rdd: U): U = {
     if (args.sort) {
-      log.info("Sorting before saving")
+      info("Sorting before saving")
       rdd.sort()
     } else if (args.sortLexicographically) {
-      log.info("Sorting lexicographically before saving")
+      info("Sorting lexicographically before saving")
       rdd.sortLexicographically()
     } else {
       rdd
@@ -131,7 +131,7 @@ class TransformGenotypes(val args: TransformGenotypesArgs)
       "Cannot set both -sort_on_save and -sort_lexicographically_on_save.")
 
     if (args.nestedAnnotations) {
-      log.info("Populating the variant.annotation field in the Genotype records")
+      info("Populating the variant.annotation field in the Genotype records")
       sc.hadoopConfiguration.setBoolean(VariantContextConverter.nestAnnotationInGenotypesProperty, true)
     }
 

diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformVariants.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformVariants.scala
@@ -85,7 +85,7 @@ class TransformVariants(val args: TransformVariantsArgs)
    */
   private def maybeCoalesce[U <: GenomicDataset[_, _, U]](rdd: U): U = {
     if (args.coalesce != -1) {
-      log.info("Coalescing the number of partitions to '%d'".format(args.coalesce))
+      info("Coalescing the number of partitions to '%d'".format(args.coalesce))
       if (args.coalesce > rdd.rdd.partitions.length || args.forceShuffle) {
         rdd.transform(_.coalesce(args.coalesce, shuffle = true))
       } else {
@@ -104,10 +104,10 @@ class TransformVariants(val args: TransformVariantsArgs)
    */
   private def maybeSort[U <: GenomicDataset[_, _, U]](rdd: U): U = {
     if (args.sort) {
-      log.info("Sorting before saving")
+      info("Sorting before saving")
       rdd.sort()
     } else if (args.sortLexicographically) {
-      log.info("Sorting lexicographically before saving")
+      info("Sorting lexicographically before saving")
       rdd.sortLexicographically()
     } else {
       rdd

diff --git a/adam-cli/src/test/scala/org/bdgenomics/adam/cli/ParquetLister.scala b/adam-cli/src/test/scala/org/bdgenomics/adam/cli/ParquetLister.scala
@@ -19,11 +19,11 @@ package org.bdgenomics.adam.cli
 
 import java.io.File
 
+import grizzled.slf4j.Logging
 import org.apache.avro.Schema
 import org.apache.avro.generic.IndexedRecord
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.Path
-import org.bdgenomics.utils.misc.Logging
 import org.apache.parquet.avro.AvroReadSupport
 import org.apache.parquet.hadoop.ParquetReader
 
@@ -54,15 +54,15 @@ class ParquetLister[T <: IndexedRecord](projectionSchema: Option[Schema] = None)
             materialize(f)
           } catch {
             case e: IllegalArgumentException =>
-              logInfo("File %s doesn't appear to be a Parquet file; skipping".format(f))
+              info("File %s doesn't appear to be a Parquet file; skipping".format(f))
               Seq()
           }
       }.iterator
     }
   }
 
   private def materialize(file: File): Iterator[T] = {
-    logInfo("Materializing file %s".format(file))
+    info("Materializing file %s".format(file))
     val conf = new Configuration
     if (projectionSchema.isDefined) {
       AvroReadSupport.setRequestedProjection(conf, projectionSchema.get)

diff --git a/adam-core/pom.xml b/adam-core/pom.xml
@@ -232,6 +232,11 @@
       <artifactId>avro</artifactId>
       <scope>compile</scope>
     </dependency>
+    <dependency>
+      <groupId>org.clapper</groupId>
+      <artifactId>grizzled-slf4j_${scala.version.prefix}</artifactId>
+      <scope>compile</scope>
+    </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>
       <artifactId>slf4j-log4j12</artifactId>

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/FastqRecordConverter.scala
@@ -17,13 +17,13 @@
  */
 package org.bdgenomics.adam.converters
 
+import grizzled.slf4j.Logging
 import htsjdk.samtools.ValidationStringency
 import org.apache.hadoop.io.Text
 import org.bdgenomics.formats.avro.{
   AlignmentRecord,
   Fragment
 }
-import org.bdgenomics.utils.misc.Logging
 import scala.collection.JavaConversions._
 
 /**
@@ -91,7 +91,7 @@ private[adam] class FastqRecordConverter extends Serializable with Logging {
           if (stringency == ValidationStringency.STRICT) {
             throw e
           } else if (stringency == ValidationStringency.LENIENT) {
-            log.warn("Read had improper pair suffix: %s".format(e.getMessage))
+            warn("Read had improper pair suffix: %s".format(e.getMessage))
           }
         }
       }

diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
@@ -17,12 +17,12 @@
  */
 package org.bdgenomics.adam.converters
 
+import grizzled.slf4j.Logging
 import htsjdk.samtools.{
   SAMReadGroupRecord,
   SAMRecord,
   SAMUtils
 }
-import org.bdgenomics.utils.misc.Logging
 import org.bdgenomics.adam.models.Attribute
 import org.bdgenomics.adam.util.AttributeUtils
 import org.bdgenomics.formats.avro.AlignmentRecord
@@ -212,7 +212,7 @@ private[adam] class SAMRecordConverter extends Serializable with Logging {
       builder.build
     } catch {
       case t: Throwable => {
-        log.error("Conversion of read: " + samRecord + " failed.")
+        error("Conversion of read: " + samRecord + " failed.")
         throw t
       }
     }